Index

_

__init__() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.io.GenericParser method) (msmbuilder.io.HierarchyParser method) (msmbuilder.io.NumberedRunsParser method) (msmbuilder.io.TemplateProject method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

A

AffinityPropagation (class in msmbuilder.cluster) aic() (msmbuilder.cluster.GMM method) all_eigenvalues_ (msmbuilder.msm.BayesianMarkovStateModel attribute)

all_left_eigenvectors_ (msmbuilder.msm.BayesianMarkovStateModel attribute) all_right_eigenvectors_ (msmbuilder.msm.BayesianMarkovStateModel attribute) all_timescales_ (msmbuilder.msm.BayesianMarkovStateModel attribute) AtomPairsFeaturizer (class in msmbuilder.featurizer)

B

backup() (in module msmbuilder.io) BayesianMarkovStateModel (class in msmbuilder.msm)

bic() (msmbuilder.cluster.GMM method) Binarizer (class in msmbuilder.preprocessing) Butterworth (class in msmbuilder.preprocessing)

C

committors() (in module msmbuilder.tpt) conditional_committors() (in module msmbuilder.tpt)

ContactFeaturizer (class in msmbuilder.featurizer) ContinuousTimeMSM (class in msmbuilder.msm)

D

dataset() (in module msmbuilder.dataset) default_key_to_path() (in module msmbuilder.io.io) describe_features() (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method)

DihedralFeaturizer (class in msmbuilder.featurizer) do() (msmbuilder.io.TemplateProject method) DoubleEWMA (class in msmbuilder.preprocessing) draw_centroids() (msmbuilder.hmm.GaussianHMM method) draw_samples() (msmbuilder.hmm.GaussianHMM method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) DRIDFeaturizer (class in msmbuilder.featurizer) dump() (in module msmbuilder.utils)

E

eigenvalues_ (msmbuilder.msm.MarkovStateModel attribute)

eigtransform() (msmbuilder.msm.MarkovStateModel method) EWMA (class in msmbuilder.preprocessing)

F

FeatureSelector (class in msmbuilder.feature_selection) fit() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.hmm.GaussianHMM method) (msmbuilder.hmm.VonMisesHMM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method) fit_predict() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.hmm.GaussianHMM method) (msmbuilder.hmm.VonMisesHMM method)

fit_transform() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method) fluxes() (in module msmbuilder.tpt) fraction_visited() (in module msmbuilder.tpt)

G

gather_metadata() (in module msmbuilder.io) GaussianHMM (class in msmbuilder.hmm) GaussianSolventFeaturizer (class in msmbuilder.featurizer) GenericParser (class in msmbuilder.io) get_covariance() (msmbuilder.decomposition.PCA method) get_feature_names() (msmbuilder.preprocessing.PolynomialFeatures method) get_params() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

get_precision() (msmbuilder.decomposition.PCA method) get_support() (msmbuilder.feature_selection.VarianceThreshold method) GMM (class in msmbuilder.cluster)

H

HierarchyParser (class in msmbuilder.io)

hub_scores() (in module msmbuilder.tpt)

I

Imputer (class in msmbuilder.preprocessing) inverse_transform() (msmbuilder.decomposition.PCA method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

itertrajs() (in module msmbuilder.io)

K

KCenters (class in msmbuilder.cluster) KernelCenterer (class in msmbuilder.preprocessing)

KMeans (class in msmbuilder.cluster) KMedoids (class in msmbuilder.cluster)

L

LabelBinarizer (class in msmbuilder.preprocessing) LandmarkAgglomerative (class in msmbuilder.cluster) left_eigenvectors_ (msmbuilder.msm.MarkovStateModel attribute)

load() (in module msmbuilder.utils) load_generic() (in module msmbuilder.io) load_meta() (in module msmbuilder.io) load_trajs() (in module msmbuilder.io)

M

MarkovStateModel (class in msmbuilder.msm) MaxAbsScaler (class in msmbuilder.preprocessing) MeanShift (class in msmbuilder.cluster) mfpts() (in module msmbuilder.tpt)

MiniBatchKMeans (class in msmbuilder.cluster) MiniBatchKMedoids (class in msmbuilder.cluster) MinMaxScaler (class in msmbuilder.preprocessing) MultiLabelBinarizer (class in msmbuilder.preprocessing)

N

net_fluxes() (in module msmbuilder.tpt)

Normalizer (class in msmbuilder.preprocessing) NumberedRunsParser (class in msmbuilder.io)

O

overlap_ (msmbuilder.hmm.VonMisesHMM attribute)

P

partial_fit() (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method) partial_predict() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) partial_transform() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

paths() (in module msmbuilder.tpt) PCA (class in msmbuilder.decomposition) PolynomialFeatures (class in msmbuilder.preprocessing) predict() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.hmm.GaussianHMM method) (msmbuilder.hmm.VonMisesHMM method) predict_proba() (msmbuilder.cluster.GMM method) preload_top() (in module msmbuilder.io) preload_tops() (in module msmbuilder.io)

R

RawPositionsFeaturizer (class in msmbuilder.featurizer) RegularSpatial (class in msmbuilder.cluster) render_meta() (in module msmbuilder.io)

right_eigenvectors_ (msmbuilder.msm.MarkovStateModel attribute) RMSDFeaturizer (class in msmbuilder.featurizer) RobustScaler (class in msmbuilder.preprocessing)

S

sample() (msmbuilder.cluster.GMM method) sample_discrete() (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) save_generic() (in module msmbuilder.io) save_meta() (in module msmbuilder.io) save_trajs() (in module msmbuilder.io) score() (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method), [1] (msmbuilder.hmm.GaussianHMM method) (msmbuilder.hmm.VonMisesHMM method) (msmbuilder.msm.ContinuousTimeMSM method), [1] (msmbuilder.msm.MarkovStateModel method), [1] score_ (msmbuilder.decomposition.SparseTICA attribute) (msmbuilder.decomposition.tICA attribute) (msmbuilder.msm.ContinuousTimeMSM attribute) (msmbuilder.msm.MarkovStateModel attribute) score_ll() (msmbuilder.msm.MarkovStateModel method) score_samples() (msmbuilder.cluster.GMM method) (msmbuilder.decomposition.PCA method) set_params() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

SparseTICA (class in msmbuilder.decomposition) SpectralClustering (class in msmbuilder.cluster) StandardScaler (class in msmbuilder.preprocessing) summarize() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.hmm.GaussianHMM method) (msmbuilder.hmm.VonMisesHMM method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method) SuperposeFeaturizer (class in msmbuilder.featurizer)

T

TemplateProject (class in msmbuilder.io) tICA (class in msmbuilder.decomposition) timescales_ (msmbuilder.hmm.GaussianHMM attribute) (msmbuilder.hmm.VonMisesHMM attribute) (msmbuilder.msm.MarkovStateModel attribute) top_path() (in module msmbuilder.tpt) transform() (msmbuilder.cluster.AffinityPropagation method) (msmbuilder.cluster.GMM method) (msmbuilder.cluster.KCenters method) (msmbuilder.cluster.KMeans method) (msmbuilder.cluster.KMedoids method) (msmbuilder.cluster.LandmarkAgglomerative method) (msmbuilder.cluster.MeanShift method) (msmbuilder.cluster.MiniBatchKMeans method) (msmbuilder.cluster.MiniBatchKMedoids method) (msmbuilder.cluster.RegularSpatial method) (msmbuilder.cluster.SpectralClustering method) (msmbuilder.decomposition.PCA method) (msmbuilder.decomposition.SparseTICA method) (msmbuilder.decomposition.tICA method) (msmbuilder.feature_selection.FeatureSelector method) (msmbuilder.feature_selection.VarianceThreshold method) (msmbuilder.featurizer.AtomPairsFeaturizer method) (msmbuilder.featurizer.ContactFeaturizer method) (msmbuilder.featurizer.DRIDFeaturizer method) (msmbuilder.featurizer.DihedralFeaturizer method) (msmbuilder.featurizer.GaussianSolventFeaturizer method) (msmbuilder.featurizer.RMSDFeaturizer method) (msmbuilder.featurizer.RawPositionsFeaturizer method) (msmbuilder.featurizer.SuperposeFeaturizer method) (msmbuilder.msm.BayesianMarkovStateModel method) (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) (msmbuilder.preprocessing.Binarizer method) (msmbuilder.preprocessing.Butterworth method) (msmbuilder.preprocessing.DoubleEWMA method) (msmbuilder.preprocessing.EWMA method) (msmbuilder.preprocessing.Imputer method) (msmbuilder.preprocessing.KernelCenterer method) (msmbuilder.preprocessing.LabelBinarizer method) (msmbuilder.preprocessing.MaxAbsScaler method) (msmbuilder.preprocessing.MinMaxScaler method) (msmbuilder.preprocessing.MultiLabelBinarizer method) (msmbuilder.preprocessing.Normalizer method) (msmbuilder.preprocessing.PolynomialFeatures method) (msmbuilder.preprocessing.RobustScaler method) (msmbuilder.preprocessing.StandardScaler method)

U

uncertainty_eigenvalues() (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method) uncertainty_K() (msmbuilder.msm.ContinuousTimeMSM method)

uncertainty_pi() (msmbuilder.msm.ContinuousTimeMSM method) uncertainty_timescales() (msmbuilder.msm.ContinuousTimeMSM method) (msmbuilder.msm.MarkovStateModel method)

V

VarianceThreshold (class in msmbuilder.feature_selection)

VonMisesHMM (class in msmbuilder.hmm)