Index

A

all_vs_all_comparison() (in module dpet.comparison), [1] alpha_angles() (dpet.visualization.Visualization method), [1]

APIClient (class in dpet.data.api_client) asphericity() (dpet.visualization.Visualization method), [1] average_distance_maps() (dpet.visualization.Visualization method), [1]

C

ca_com_distances() (dpet.visualization.Visualization method), [1] calc_ca_dmap() (in module dpet.featurization.distances) calc_chain_dihedrals() (in module dpet.data.coord) calc_com_dmap() (in module dpet.featurization.distances) calc_flory_scaling_exponent() (in module dpet.featurization.ensemble_level) calc_flory_scaling_exponent_cg() (in module dpet.featurization.ensemble_level) calc_freqs() (in module dpet.comparison), [1] calc_jsd() (in module dpet.comparison), [1] calc_kld_for_jsd() (in module dpet.comparison), [1] check_feature_matrices() (in module dpet.comparison), [1] close_session() (dpet.data.api_client.APIClient method)

cluster() (dpet.dimensionality_reduction.UMAPReduction method) comparison_matrix() (dpet.visualization.Visualization method), [1] comparison_scores() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] compute_asphericity() (in module dpet.featurization.glob) compute_end_to_end_distances() (in module dpet.featurization.glob) compute_ensemble_sasa() (in module dpet.featurization.glob) compute_prolateness() (in module dpet.featurization.glob) confidence_interval() (in module dpet.comparison), [1] contact_prob_maps() (dpet.visualization.Visualization method), [1] contact_probability_map() (in module dpet.data.coord) create_consecutive_indices_matrix() (in module dpet.data.coord)

D

dict_phi_psi_normal_cases() (in module dpet.data.coord) dimensionality_reduction_scatter() (dpet.visualization.Visualization method), [1] DimensionalityReduction (class in dpet.dimensionality_reduction) DimensionalityReductionFactory (class in dpet.dimensionality_reduction) download_response_content() (dpet.data.api_client.APIClient method) dpet module, [1] dpet.comparison module, [1] dpet.data module dpet.data.api_client module dpet.data.coord module dpet.data.extract_tar_gz module dpet.data.topology module

dpet.dimensionality_reduction module dpet.ensemble module, [1] dpet.ensemble_analysis module, [1] dpet.featurization module dpet.featurization.angles module dpet.featurization.distances module dpet.featurization.ensemble_level module dpet.featurization.glob module dpet.featurization.utils module dpet.visualization module, [1]

E

end_to_end_distances() (dpet.visualization.Visualization method), [1] ens_codes (dpet.ensemble_analysis.EnsembleAnalysis property), [1] Ensemble (class in dpet.ensemble), [1] EnsembleAnalysis (class in dpet.ensemble_analysis), [1]

execute_pipeline() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] exists_coarse_grained() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] extract_features() (dpet.ensemble.Ensemble method), [1] (dpet.ensemble_analysis.EnsembleAnalysis method), [1] extract_tar_gz() (in module dpet.data.extract_tar_gz)

F

features (dpet.ensemble_analysis.EnsembleAnalysis property), [1] featurize_a_angle() (in module dpet.featurization.angles) featurize_ca_dist() (in module dpet.featurization.distances) featurize_com_dist() (in module dpet.featurization.distances) featurize_phi_psi() (in module dpet.featurization.angles) featurize_tr_angle() (in module dpet.featurization.angles) featurize_tr_omega() (in module dpet.featurization.angles) featurize_tr_phi() (in module dpet.featurization.angles) fit() (dpet.dimensionality_reduction.DimensionalityReduction method) (dpet.dimensionality_reduction.KPCAReduction method) (dpet.dimensionality_reduction.PCAReduction method) (dpet.dimensionality_reduction.TSNEReduction method) (dpet.dimensionality_reduction.UMAPReduction method)

fit_transform() (dpet.dimensionality_reduction.DimensionalityReduction method) (dpet.dimensionality_reduction.KPCAReduction method) (dpet.dimensionality_reduction.PCAReduction method) (dpet.dimensionality_reduction.TSNEReduction method) (dpet.dimensionality_reduction.UMAPReduction method)

G

get_adaJSD_matrix() (in module dpet.comparison), [1] get_angles() (in module dpet.featurization.angles) get_ataJSD_profile() (in module dpet.comparison), [1] get_ca_topology() (in module dpet.data.topology) get_chains_from_pdb() (dpet.ensemble.Ensemble method), [1] get_contact_map() (in module dpet.data.coord) get_dihedrals() (in module dpet.featurization.angles) get_distance_matrix() (in module dpet.data.coord) get_features() (dpet.ensemble.Ensemble method), [1] (dpet.ensemble_analysis.EnsembleAnalysis method), [1]

get_features_summary_dataframe() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] get_max_sep() (in module dpet.featurization.utils) get_num_comparison_bins() (in module dpet.comparison), [1] get_num_residues() (dpet.ensemble.Ensemble method), [1] get_ramaJSD_profile() (in module dpet.comparison), [1] get_reducer() (dpet.dimensionality_reduction.DimensionalityReductionFactory method) (dpet.dimensionality_reduction.DimensionalityReductionFactory static method) get_triu_indices() (in module dpet.featurization.utils) global_sasa() (dpet.visualization.Visualization method), [1]

K

KPCAReduction (class in dpet.dimensionality_reduction)

L

load_trajectories() (dpet.ensemble_analysis.EnsembleAnalysis method), [1]

load_trajectory() (dpet.ensemble.Ensemble method), [1]

M

module dpet, [1] dpet.comparison, [1] dpet.data dpet.data.api_client dpet.data.coord dpet.data.extract_tar_gz dpet.data.topology dpet.dimensionality_reduction dpet.ensemble, [1] dpet.ensemble_analysis, [1] dpet.featurization dpet.featurization.angles dpet.featurization.distances dpet.featurization.ensemble_level dpet.featurization.glob dpet.featurization.utils dpet.visualization, [1]

N

normalize_features() (dpet.ensemble.Ensemble method), [1]

P

pca_1d_histograms() (dpet.visualization.Visualization method), [1] pca_2d_landscapes() (dpet.visualization.Visualization method), [1] pca_cumulative_explained_variance() (dpet.visualization.Visualization method), [1] pca_residue_correlation() (dpet.visualization.Visualization method), [1] pca_rg_correlation() (dpet.visualization.Visualization method), [1] PCAReduction (class in dpet.dimensionality_reduction) per_residue_mean_sasa() (dpet.visualization.Visualization method), [1] percentile_func() (in module dpet.comparison), [1]

perform_get_request() (dpet.data.api_client.APIClient method) plot_comparison_matrix() (in module dpet.visualization), [1] plot_histogram() (in module dpet.visualization), [1] plot_histogram_grid() (dpet.visualization.Visualization method), [1] plot_rama_grid() (dpet.visualization.Visualization method), [1] plot_violins() (in module dpet.visualization), [1] process_all_vs_all_output() (in module dpet.comparison), [1] prolateness() (dpet.visualization.Visualization method), [1]

R

radius_of_gyration() (dpet.visualization.Visualization method), [1] ramachandran_plots() (dpet.visualization.Visualization method), [1] random_sample_trajectories() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] random_sample_trajectory() (dpet.ensemble.Ensemble method), [1] reduce_dim_data (dpet.ensemble_analysis.EnsembleAnalysis property), [1]

reduce_features() (dpet.ensemble_analysis.EnsembleAnalysis method), [1] relative_dssp_content() (dpet.visualization.Visualization method), [1] rg_vs_asphericity() (dpet.visualization.Visualization method), [1] rg_vs_prolateness() (dpet.visualization.Visualization method), [1] rmsd() (in module dpet.featurization.distances)

S

score_adaJSD() (in module dpet.comparison), [1] score_ataJSD() (in module dpet.comparison), [1] score_avg_2d_angle_jsd() (in module dpet.comparison), [1] score_avg_jsd() (in module dpet.comparison), [1] score_histogram_jsd() (in module dpet.comparison), [1] score_ramaJSD() (in module dpet.comparison), [1] site_specific_order_parameter() (in module dpet.data.coord)

slice_traj_to_com() (in module dpet.data.topology) split_dictionary_phipsiangles() (in module dpet.data.coord) sqrt_rule() (in module dpet.comparison), [1] ss_flexibility() (dpet.visualization.Visualization method), [1] ss_measure_disorder() (in module dpet.data.coord) ss_order() (dpet.visualization.Visualization method), [1] sturges_rule() (in module dpet.comparison), [1]

T

trajectories (dpet.ensemble_analysis.EnsembleAnalysis property), [1] transform() (dpet.dimensionality_reduction.DimensionalityReduction method) (dpet.dimensionality_reduction.KPCAReduction method) (dpet.dimensionality_reduction.PCAReduction method) (dpet.dimensionality_reduction.TSNEReduction method) (dpet.dimensionality_reduction.UMAPReduction method)

TSNEReduction (class in dpet.dimensionality_reduction)

U

UMAPReduction (class in dpet.dimensionality_reduction) unit_vector_distance() (in module dpet.dimensionality_reduction)

unit_vector_kernel() (in module dpet.dimensionality_reduction) unit_vectorize() (in module dpet.dimensionality_reduction)

V

Visualization (class in dpet.visualization), [1]