Index

A

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

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

C

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

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

D

dict_phi_psi_normal_cases() (in module idpet.coord) dimensionality_reduction_scatter() (idpet.visualization.Visualization method), [1] DimensionalityReduction (class in idpet.dimensionality_reduction)

DimensionalityReductionFactory (class in idpet.dimensionality_reduction) distance_maps() (idpet.visualization.Visualization method), [1] download_response_content() (idpet.data.api_client.APIClient method)

E

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

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

F

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

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

G

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

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

I

idpet module idpet.comparison module, [1] idpet.coord module idpet.data module idpet.data.api_client module idpet.data.io_utils module idpet.data.topology module idpet.dimensionality_reduction module idpet.ensemble module, [1]

idpet.ensemble_analysis module, [1] idpet.featurization module idpet.featurization.angles module idpet.featurization.distances module idpet.featurization.ensemble_level module idpet.featurization.glob module idpet.featurization.utils module idpet.utils module idpet.visualization module, [1]

K

KPCAReduction (class in idpet.dimensionality_reduction)

L

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

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

M

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

N

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

P

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

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

R

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

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

S

score_adaJSD() (in module idpet.comparison), [1] score_ataJSD() (in module idpet.comparison), [1] score_avg_2d_angle_jsd() (in module idpet.comparison), [1] score_avg_jsd() (in module idpet.comparison), [1] score_histogram_jsd() (in module idpet.comparison), [1] score_ramaJSD() (in module idpet.comparison), [1] set_verbosity() (in module idpet.utils) setup_data_dir() (in module idpet.data.io_utils)

site_specific_flexibility() (idpet.visualization.Visualization method), [1] site_specific_order() (idpet.visualization.Visualization method), [1] site_specific_order_parameter() (in module idpet.coord) slice_traj_to_com() (in module idpet.data.topology) split_dictionary_phipsiangles() (in module idpet.coord) sqrt_rule() (in module idpet.comparison), [1] ss_measure_disorder() (in module idpet.coord) sturges_rule() (in module idpet.comparison), [1]

T

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

TSNEReduction (class in idpet.dimensionality_reduction)

U

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

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

V

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