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)
(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.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.data.ReaderInterface method)
(pyemma.coordinates.pipelines.Pipeline method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.PCCA method)
(pyemma.msm.ReactiveFlux method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.plots.NetworkPlot method)

A

A (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
active_count_fraction (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
active_set (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
active_state_fraction (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
active_state_indexes (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
add_all() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_angles() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_backbone_torsions() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_chi1_torsions() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_contacts() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_custom_feature() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_custom_func() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_dihedrals() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_distances() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_distances_ca() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_element() (pyemma.coordinates.pipelines.Discretizer method)
(pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3]
add_group_mindist() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_inverse_distances() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_minrmsd_to_ref() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_residue_mindist() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
add_selection() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
assign() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
assign_to_centers() (in module pyemma.coordinates)
AssignCenters (class in pyemma.coordinates.clustering)
(class in pyemma.coordinates.clustering.assign)

B

B (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
backward_committor (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
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)
bootstrap_counts() (in module msmtools.estimation)
bootstrap_trajectories() (in module msmtools.estimation)

C

chunksize (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.data.DataInMemory attribute)
(pyemma.coordinates.data.FeatureReader attribute)
(pyemma.coordinates.data.NumPyFileReader attribute)
(pyemma.coordinates.data.PyCSVReader attribute)
(pyemma.coordinates.data.ReaderInterface attribute)
(pyemma.coordinates.pipelines.Pipeline attribute), [1]
(pyemma.coordinates.transform.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.Transformer attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
cktest() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM 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)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
cmatrix() (in module msmtools.estimation)
coarse_grain() (msmtools.flux.reactive_flux.ReactiveFlux method)
(msmtools.flux.ReactiveFlux method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.ReactiveFlux method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
coarsegrain() (in module msmtools.flux)
committor (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
committor() (in module msmtools.analysis)
committor_backward() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
committor_forward() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
committor_sensitivity() (in module msmtools.analysis)
configParser (in module pyemma.util.config)
connected_cmatrix() (in module msmtools.estimation)
connected_sets (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
connected_sets() (in module msmtools.estimation)
connectivity (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
correlation() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
count_matrix() (in module msmtools.estimation)
count_matrix_active (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
count_matrix_full (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
count_states() (in module msmtools.dtraj)
covariance_matrix (pyemma.coordinates.transform.pca.PCA attribute)
cumvar (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
CustomFeature (class in pyemma.coordinates.data)

D

data_producer (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.data.DataInMemory attribute)
(pyemma.coordinates.data.FeatureReader attribute)
(pyemma.coordinates.data.NumPyFileReader attribute)
(pyemma.coordinates.data.PyCSVReader attribute)
(pyemma.coordinates.data.ReaderInterface attribute)
(pyemma.coordinates.transform.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.Transformer attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
DataInMemory (class in pyemma.coordinates.data)
describe() (pyemma.coordinates.clustering.assign.AssignCenters method)
(pyemma.coordinates.clustering.KmeansClustering method)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.RegularSpaceClustering method)
(pyemma.coordinates.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.MDFeaturizer method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
dimension() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.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.data.ReaderInterface method)
(pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
discrete_trajectories_active (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
discrete_trajectories_full (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
discrete_trajectories_lagged (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
discrete_trajectories_obs (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
Discretizer (class in pyemma.coordinates.pipelines)
discretizer() (in module pyemma.coordinates)
dmin (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.pipelines.Discretizer attribute)

E

effective_count_matrix (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
eigenvalue_sensitivity() (in module msmtools.analysis)
eigenvalues (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
eigenvalues() (in module msmtools.analysis)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
eigenvector_sensitivity() (in module msmtools.analysis)
eigenvectors (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
eigenvectors() (in module msmtools.analysis)
eigenvectors_left() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
eigenvectors_left_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
eigenvectors_right() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
eigenvectors_right_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
error_perturbation() (in module msmtools.estimation)
estimate() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
estimate_hidden_markov_model() (in module pyemma.msm)
estimate_markov_model() (in module pyemma.msm)
estimators (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
expectation() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
expectation_sensitivity() (in module msmtools.analysis)
expected_counts() (in module msmtools.analysis)
expected_counts_stationary() (in module msmtools.analysis)

F

feature_TIC_correlation (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
FeatureReader (class in pyemma.coordinates.data)
featurizer() (in module pyemma.coordinates)
fingerprint_correlation() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
fingerprint_relaxation() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
fit() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
fit_transform() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
flux (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.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.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
fraction_of_frames (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)

G

generate_traj() (in module msmtools.generation)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
get_model_params() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
get_output() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
get_params() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
get_sample_conf() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.ImpliedTimescales method)
get_sample_mean() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.ImpliedTimescales method)
get_sample_std() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.ImpliedTimescales method)
get_timescales() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.ImpliedTimescales method)
gross_flux (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)

H

hmm() (pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
HMSM (class in pyemma.msm)

I

I (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
ImpliedTimescales (class in pyemma.msm)
(class in pyemma.msm.estimators.implied_timescales), [1], [2]
in_memory (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.data.DataInMemory attribute)
(pyemma.coordinates.data.FeatureReader attribute)
(pyemma.coordinates.data.NumPyFileReader attribute)
(pyemma.coordinates.data.PyCSVReader attribute)
(pyemma.coordinates.data.ReaderInterface attribute)
(pyemma.coordinates.transform.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.Transformer attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
index_clusters (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
index_states() (in module msmtools.dtraj)
is_connected() (in module msmtools.analysis)
(in module msmtools.estimation)
is_rate_matrix() (in module msmtools.analysis)
is_reversible (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
is_reversible() (in module msmtools.analysis)
is_sparse (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
is_tmatrix() (in module msmtools.analysis)
is_transition_matrix() (in module msmtools.analysis)
iterator() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
its() (in module pyemma.msm)

K

KmeansClustering (class in pyemma.coordinates.clustering)
(class in pyemma.coordinates.clustering.kmeans)
kmeanspp_center_assigned() (pyemma.coordinates.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)

L

lag (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
lags (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
lagtime (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
lagtimes (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
largest_connected_set (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
largest_connected_set() (in module msmtools.estimation)
largest_connected_submatrix() (in module msmtools.estimation)
lifetimes (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM 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)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.data.DataInMemory attribute)
(pyemma.coordinates.data.FeatureReader attribute)
(pyemma.coordinates.data.MDFeaturizer attribute)
(pyemma.coordinates.data.NumPyFileReader attribute)
(pyemma.coordinates.data.PyCSVReader attribute)
(pyemma.coordinates.data.ReaderInterface attribute)
(pyemma.coordinates.data.featurizer.MDFeaturizer attribute)
(pyemma.coordinates.transform.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.Transformer attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
(pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.ImpliedTimescales attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)

M

major_flux() (msmtools.flux.reactive_flux.ReactiveFlux method)
(msmtools.flux.ReactiveFlux method)
(pyemma.msm.ReactiveFlux method)
map() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.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.data.ReaderInterface method)
(pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
markov_model() (in module pyemma.msm)
max_centers (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
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)
MDFeaturizer (class in pyemma.coordinates.data)
(class in pyemma.coordinates.data.featurizer)
mean (pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
metastable_assignment (pyemma.msm.PCCA attribute)
metastable_assignments (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
metastable_distributions (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
metastable_memberships (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
metastable_sets (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.PCCA attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
mfpt (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
mfpt() (in module msmtools.analysis)
(in module msmtools.flux)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
mfpt_sensitivity() (in module msmtools.analysis)
MiniBatchKmeansClustering (class in pyemma.coordinates.clustering)
(class in pyemma.coordinates.clustering.kmeans)
model (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.ImpliedTimescales attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
models (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
MSM (class in pyemma.msm)
(class in pyemma.msm.models.msm)
msmtools.analysis (module)
msmtools.dtraj (module)
msmtools.estimation (module)
msmtools.flux (module)
msmtools.generation (module)

N

n_frames_total() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
name (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.data.DataInMemory attribute)
(pyemma.coordinates.data.FeatureReader attribute)
(pyemma.coordinates.data.MDFeaturizer attribute)
(pyemma.coordinates.data.NumPyFileReader attribute)
(pyemma.coordinates.data.PyCSVReader attribute)
(pyemma.coordinates.data.ReaderInterface attribute)
(pyemma.coordinates.data.featurizer.MDFeaturizer attribute)
(pyemma.coordinates.transform.PCA attribute)
(pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.Transformer attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
(pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.ImpliedTimescales attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
net_flux (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
NetworkPlot (class in pyemma.plots)
nstates (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.ReactiveFlux attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
nstates_full (pyemma.msm.BayesianMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
nstates_obs (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
ntraj (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)
(pyemma.coordinates.transform.pca.PCA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
number_of_states() (in module msmtools.dtraj)
number_of_timescales (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
number_of_trajectories() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
NumPyFileReader (class in pyemma.coordinates.data)

O

observable_set (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
observable_state_indexes (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
observation_probabilities (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
output_type() (pyemma.coordinates.clustering.assign.AssignCenters method)
(pyemma.coordinates.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
overwrite_dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute)
(pyemma.coordinates.clustering.AssignCenters attribute)
(pyemma.coordinates.clustering.KmeansClustering attribute)
(pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.UniformTimeClustering attribute)
(pyemma.coordinates.clustering.kmeans.KmeansClustering attribute)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)

P

pairs() (pyemma.coordinates.data.featurizer.MDFeaturizer static method)
(pyemma.coordinates.data.MDFeaturizer static method)
parametrize() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.pipelines.Discretizer method)
(pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3]
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
pathways() (in module msmtools.flux)
(msmtools.flux.ReactiveFlux method)
(msmtools.flux.reactive_flux.ReactiveFlux method)
(pyemma.msm.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() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
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)
(pyemma.plots.NetworkPlot method)
prior_const() (in module msmtools.estimation)
prior_neighbor() (in module msmtools.estimation)
prior_rev() (in module msmtools.estimation)
propagate() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(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.util.config (module)

R

rate (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
rate() (in module msmtools.flux)
rdl_decomposition() (in module msmtools.analysis)
ReactiveFlux (class in msmtools.flux)
(class in msmtools.flux.reactive_flux)
(class in pyemma.msm)
read_discrete_trajectory() (in module msmtools.dtraj)
read_dtraj() (in module msmtools.dtraj)
ReaderInterface (class in pyemma.coordinates.data)
register_progress_callback() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
RegularSpaceClustering (class in pyemma.coordinates.clustering)
(class in pyemma.coordinates.clustering.regspace)
relaxation() (in module msmtools.analysis)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)

S

sample_by_distributions() (pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
sample_by_observation_probabilities() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
sample_by_state() (pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
sample_conf() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
sample_f() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
sample_indexes_by_cluster() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering 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]
(pyemma.msm.ImpliedTimescales attribute)
sample_mean() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
sample_std (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
sample_std() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
SampledHMSM (class in pyemma.msm)
SampledMSM (class in pyemma.msm)
samples_available (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
(pyemma.msm.ImpliedTimescales attribute)
save_discrete_trajectory() (in module msmtools.dtraj)
save_dtraj() (in module msmtools.dtraj)
save_dtrajs() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.pipelines.Discretizer method)
save_traj() (in module pyemma.coordinates)
save_trajs() (in module pyemma.coordinates)
scatter_contour() (in module pyemma.plots)
select() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
select_Backbone() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
select_Ca() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
select_Heavy() (pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.data.MDFeaturizer method)
set_element() (pyemma.coordinates.pipelines.Discretizer method)
(pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3]
set_model_params() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
set_params() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.ImpliedTimescales method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
source() (in module pyemma.coordinates)
statdist() (in module msmtools.analysis)
stationary_distribution (msmtools.flux.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.ReactiveFlux attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
stationary_distribution() (in module msmtools.analysis)
stationary_distribution_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
stationary_distribution_sensitivity() (in module msmtools.analysis)

T

TICA (class in pyemma.coordinates.transform)
(class in pyemma.coordinates.transform.tica)
tica() (in module pyemma.coordinates)
timescale_sensitivity() (in module msmtools.analysis)
timescales (pyemma.coordinates.transform.TICA attribute)
(pyemma.coordinates.transform.tica.TICA attribute)
(pyemma.msm.ImpliedTimescales attribute)
(pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]
timescales() (in module msmtools.analysis)
(pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
timescales_hmsm() (in module pyemma.msm)
timescales_msm() (in module pyemma.msm)
timestep_model (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM 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.reactive_flux.ReactiveFlux attribute)
(msmtools.flux.ReactiveFlux attribute)
(pyemma.msm.ReactiveFlux attribute)
total_flux() (in module msmtools.flux)
tpt() (in module msmtools.flux)
(in module pyemma.msm)
trajectory_length() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
trajectory_lengths() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.DataInMemory method)
(pyemma.coordinates.data.FeatureReader method)
(pyemma.coordinates.data.NumPyFileReader method)
(pyemma.coordinates.data.PyCSVReader method)
(pyemma.coordinates.data.ReaderInterface method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
trajectory_weights() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
transform() (pyemma.coordinates.clustering.assign.AssignCenters method)
(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.clustering.kmeans.KmeansClustering method)
(pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method)
(pyemma.coordinates.clustering.regspace.RegularSpaceClustering method)
(pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method)
(pyemma.coordinates.data.MDFeaturizer method)
(pyemma.coordinates.data.featurizer.MDFeaturizer method)
(pyemma.coordinates.transform.PCA method)
(pyemma.coordinates.transform.TICA method)
(pyemma.coordinates.transform.Transformer method)
(pyemma.coordinates.transform.pca.PCA method)
(pyemma.coordinates.transform.tica.TICA method)
Transformer (class in pyemma.coordinates.transform)
transition_matrix (pyemma.msm.BayesianHMSM attribute)
(pyemma.msm.BayesianMSM attribute)
(pyemma.msm.HMSM attribute)
(pyemma.msm.MSM attribute)
(pyemma.msm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.SampledHMSM attribute)
(pyemma.msm.SampledMSM attribute)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute)
(pyemma.msm.models.msm.MSM attribute)
transition_matrix() (in module msmtools.estimation)
transition_matrix_metropolis_1d() (in module msmtools.generation)
transition_matrix_obs() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)

U

UniformTimeClustering (class in pyemma.coordinates.clustering)
(class in pyemma.coordinates.clustering.uniform_time)
update_model_params() (pyemma.msm.BayesianHMSM method)
(pyemma.msm.BayesianMSM method)
(pyemma.msm.HMSM method)
(pyemma.msm.MSM method)
(pyemma.msm.MaximumLikelihoodHMSM method)
(pyemma.msm.MaximumLikelihoodMSM method)
(pyemma.msm.SampledHMSM method)
(pyemma.msm.SampledMSM method)
(pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method)
(pyemma.msm.estimators.bayesian_msm.BayesianMSM method)
(pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)
(pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)
(pyemma.msm.models.msm.MSM method)
used_filenames (in module pyemma.util.config)

V

visited_set() (in module msmtools.dtraj)

W

write_discrete_trajectory() (in module msmtools.dtraj)
write_dtraj() (in module msmtools.dtraj)