dpet

• idpet package
  • Subpackages
    • idpet.data package
      • Submodules
      • idpet.data.api_client module
      • idpet.data.io_utils module
      • idpet.data.topology module
      • Module contents
    • idpet.featurization package
      • Submodules
      • idpet.featurization.angles module
      • idpet.featurization.distances module
      • idpet.featurization.ensemble_level module
      • idpet.featurization.glob module
      • idpet.featurization.utils module
      • Module contents
  • Submodules
  • idpet.comparison module
    • all_vs_all_comparison()
    • calc_freqs()
    • calc_jsd()
    • calc_kld_for_jsd()
    • check_feature_matrices()
    • confidence_interval()
    • get_adaJSD_matrix()
    • get_ataJSD_profile()
    • get_num_comparison_bins()
    • get_ramaJSD_profile()
    • percentile_func()
    • process_all_vs_all_output()
    • score_adaJSD()
    • score_ataJSD()
    • score_avg_2d_angle_jsd()
    • score_avg_jsd()
    • score_histogram_jsd()
    • score_ramaJSD()
    • sqrt_rule()
    • sturges_rule()
  • idpet.coord module
    • calc_chain_dihedrals()
    • contact_probability_map()
    • create_consecutive_indices_matrix()
    • dict_phi_psi_normal_cases()
    • get_contact_map()
    • get_distance_matrix()
    • site_specific_order_parameter()
    • split_dictionary_phipsiangles()
    • ss_measure_disorder()
  • idpet.dimensionality_reduction module
    • DimensionalityReduction
      • DimensionalityReduction.fit()
      • DimensionalityReduction.fit_transform()
      • DimensionalityReduction.transform()
    • DimensionalityReductionFactory
      • DimensionalityReductionFactory.get_reducer()
    • KPCAReduction
      • KPCAReduction.fit()
      • KPCAReduction.fit_transform()
      • KPCAReduction.transform()
    • PCAReduction
      • PCAReduction.fit()
      • PCAReduction.fit_transform()
      • PCAReduction.transform()
    • TSNEReduction
      • TSNEReduction.fit()
      • TSNEReduction.fit_transform()
      • TSNEReduction.transform()
    • UMAPReduction
      • UMAPReduction.cluster()
      • UMAPReduction.fit()
      • UMAPReduction.fit_transform()
      • UMAPReduction.transform()
    • unit_vector_distance()
    • unit_vector_kernel()
    • unit_vectorize()
  • idpet.ensemble module
    • Ensemble
      • Ensemble.extract_features()
      • Ensemble.get_chains_from_pdb()
      • Ensemble.get_features()
      • Ensemble.get_num_residues()
      • Ensemble.get_size()
      • Ensemble.load_trajectory()
      • Ensemble.normalize_features()
      • Ensemble.random_sample_trajectory()
  • idpet.ensemble_analysis module
    • EnsembleAnalysis
      • EnsembleAnalysis.comparison_scores()
      • EnsembleAnalysis.ens_codes
      • EnsembleAnalysis.execute_pipeline()
      • EnsembleAnalysis.exists_coarse_grained()
      • EnsembleAnalysis.extract_features()
      • EnsembleAnalysis.features
      • EnsembleAnalysis.get_features()
      • EnsembleAnalysis.get_features_summary_dataframe()
      • EnsembleAnalysis.load_trajectories()
      • EnsembleAnalysis.random_sample_trajectories()
      • EnsembleAnalysis.reduce_dim_data
      • EnsembleAnalysis.reduce_features()
      • EnsembleAnalysis.trajectories
  • idpet.utils module
    • set_verbosity()
  • idpet.visualization module
    • Visualization
      • Visualization.alpha_angles()
      • Visualization.asphericity()
      • Visualization.comparison_matrix()
      • Visualization.contact_prob_maps()
      • Visualization.dimensionality_reduction_scatter()
      • Visualization.distance_maps()
      • Visualization.end_to_end_distances()
      • Visualization.global_sasa()
      • Visualization.pca_1d_histograms()
      • Visualization.pca_2d_landscapes()
      • Visualization.pca_cumulative_explained_variance()
      • Visualization.pca_residue_correlation()
      • Visualization.pca_rg_correlation()
      • Visualization.per_residue_mean_sasa()
      • Visualization.plot_histogram_grid()
      • Visualization.plot_rama_grid()
      • Visualization.prolateness()
      • Visualization.radius_of_gyration()
      • Visualization.ramachandran_plots()
      • Visualization.relative_dssp_content()
      • Visualization.rg_vs_asphericity()
      • Visualization.rg_vs_prolateness()
      • Visualization.site_specific_flexibility()
      • Visualization.site_specific_order()
    • plot_comparison_matrix()
    • plot_histogram()
    • plot_violins()
  • Module contents