Index

A

accepts_distance_matrix (mdaencore.clustering.ClusteringMethod.KMeans attribute) AffinityPropagation (class in mdaencore.clustering.ClusteringMethod)

AffinityPropagation() (in module mdaencore.clustering.affinityprop) AffinityPropagationNative (class in mdaencore.clustering.ClusteringMethod) as_array() (mdaencore.utils.TriangularMatrix method)

B

bootstrapped_matrix() (in module mdaencore.bootstrap)

C

ces() (in module mdaencore.similarity) ces_convergence() (in module mdaencore.similarity) Cluster (class in mdaencore.clustering.ClusterCollection) cluster() (in module mdaencore.clustering.cluster) ClusterCollection (class in mdaencore.clustering.ClusterCollection)

clustering_ensemble_similarity() (in module mdaencore.similarity) ClusteringMethod (class in mdaencore.clustering.ClusteringMethod) conformational_distance_matrix() (in module mdaencore.confdistmatrix) covariance_matrix() (in module mdaencore.covariance) cumulative_clustering_ensemble_similarity() (in module mdaencore.similarity) cumulative_gen_kde_pdfs() (in module mdaencore.similarity)

D

DBSCAN (class in mdaencore.clustering.ClusteringMethod) DimensionalityReductionMethod (class in mdaencore.dimensionality_reduction.DimensionalityReductionMethod) dimred_ensemble_similarity() (in module mdaencore.similarity)

discrete_jensen_shannon_divergence() (in module mdaencore.similarity) discrete_kullback_leibler_divergence() (in module mdaencore.similarity) dres() (in module mdaencore.similarity) dres_convergence() (in module mdaencore.similarity)

E

encode_centroid_info() (in module mdaencore.clustering.ClusteringMethod)

G

gen_kde_pdfs() (in module mdaencore.similarity) get_centroids() (mdaencore.clustering.ClusterCollection.ClusterCollection method) get_distance_matrix() (in module mdaencore.confdistmatrix)

get_distance_matrix_bootstrap_samples() (in module mdaencore.bootstrap) get_ensemble_bootstrap_samples() (in module mdaencore.bootstrap) get_ids() (mdaencore.clustering.ClusterCollection.ClusterCollection method)

H

harmonic_ensemble_similarity() (in module mdaencore.similarity)

hes() (in module mdaencore.similarity)

K

KMeans (class in mdaencore.clustering.ClusteringMethod)

L

loadz() (mdaencore.utils.TriangularMatrix method)

M

mdaencore.bootstrap module mdaencore.clustering.affinityprop module mdaencore.clustering.cluster module mdaencore.clustering.ClusterCollection module mdaencore.clustering.ClusteringMethod module mdaencore.confdistmatrix module mdaencore.covariance module mdaencore.dimensionality_reduction.DimensionalityReductionMethod module mdaencore.dimensionality_reduction.reduce_dimensionality module mdaencore.dimensionality_reduction.stochasticproxembed module

mdaencore.similarity module mdaencore.utils module merge_universes() (in module mdaencore.utils) ml_covariance_estimator() (in module mdaencore.covariance) module mdaencore.bootstrap mdaencore.clustering.affinityprop mdaencore.clustering.cluster mdaencore.clustering.ClusterCollection mdaencore.clustering.ClusteringMethod mdaencore.confdistmatrix mdaencore.covariance mdaencore.dimensionality_reduction.DimensionalityReductionMethod mdaencore.dimensionality_reduction.reduce_dimensionality mdaencore.dimensionality_reduction.stochasticproxembed mdaencore.similarity mdaencore.utils

P

ParallelCalculation (class in mdaencore.utils) prepare_ensembles_for_convergence_increasing_window() (in module mdaencore.similarity)

PrincipalComponentAnalysis (class in mdaencore.dimensionality_reduction.DimensionalityReductionMethod) PureRMSD() (in module mdaencore.cutils)

R

reduce_dimensionality() (in module mdaencore.dimensionality_reduction.reduce_dimensionality)

run() (mdaencore.utils.ParallelCalculation method)

S

savez() (mdaencore.utils.TriangularMatrix method) set_rmsd_matrix_elements() (in module mdaencore.confdistmatrix)

shrinkage_covariance_estimator() (in module mdaencore.covariance) StochasticProximityEmbedding() (in module mdaencore.dimensionality_reduction.stochasticproxembed) StochasticProximityEmbeddingNative (class in mdaencore.dimensionality_reduction.DimensionalityReductionMethod)

T

TriangularMatrix (class in mdaencore.utils) trm_indices() (in module mdaencore.utils)

trm_indices_diag() (in module mdaencore.utils) trm_indices_nodiag() (in module mdaencore.utils)

W

worker() (mdaencore.utils.ParallelCalculation method)

write_output() (in module mdaencore.similarity)