pensa

Subpackages

• pensa.clusters
  • pensa.clusters.clustering
    • find_closest_frames()
    • obtain_clusters()
    • obtain_combined_clusters()
    • obtain_mult_combined_clusters()
  • pensa.clusters.trajectory
    • write_cluster_traj()
  • pensa.clusters.wss
    • wss_over_number_of_clusters()
    • wss_over_number_of_combined_clusters()
• pensa.comparison
  • pensa.comparison.metrics
    • average_jsd()
    • average_kld()
    • average_ksp()
    • average_kss()
    • average_ssi()
    • max_jsd()
    • max_kld()
    • max_ksp()
    • max_kss()
    • max_ssi()
    • min_ksp()
    • pca_sampling_efficiency()
  • pensa.comparison.projections
    • pca_feature_correlation()
    • tica_feature_correlation()
  • pensa.comparison.relative_entropy
    • relative_entropy_analysis()
  • pensa.comparison.statespecific
    • cossi_featens_analysis()
    • ssi_ensemble_analysis()
    • ssi_feature_analysis()
  • pensa.comparison.statistics
    • feature_correlation()
    • kolmogorov_smirnov_analysis()
    • mean_difference_analysis()
  • pensa.comparison.uncertainty_analysis
    • relen_block_analysis()
    • relen_sem_analysis()
    • ssi_block_analysis()
    • ssi_sem_analysis()
  • pensa.comparison.visualization
    • distances_visualization()
    • pair_features_heatmap()
    • residue_visualization()
    • resnum_heatmap()
• pensa.dimensionality
  • pensa.dimensionality.pca
    • calculate_pca()
    • get_components_pca()
    • pca_eigenvalues_plot()
    • pca_features()
    • project_on_pc()
    • sort_mult_trajs_along_common_pc()
    • sort_traj_along_pc()
    • sort_trajs_along_common_pc()
  • pensa.dimensionality.tica
    • calculate_tica()
    • get_components_tica()
    • project_on_tic()
    • sort_mult_trajs_along_common_tic()
    • sort_traj_along_tic()
    • sort_trajs_along_common_tic()
    • tica_eigenvalues_plot()
    • tica_features()
  • pensa.dimensionality.visualization
    • compare_mult_projections()
    • compare_projections()
    • project_on_eigenvector_pca()
    • project_on_eigenvector_tica()
    • sort_traj_along_projection()
• pensa.features
  • pensa.features.atom_features
    • read_atom_features()
  • pensa.features.csv_features
    • read_csv_features()
    • read_drormd_features()
    • write_csv_features()
  • pensa.features.hbond_features
    • atg_to_names()
    • name_atom_features()
    • name_pairs()
    • read_h_bond_satisfaction()
    • read_h_bonds()
    • read_h_bonds_quickly()
    • read_water_site_h_bonds()
    • read_water_site_h_bonds_quickly()
  • pensa.features.mda_combined
    • read_structure_features()
    • sort_traj_along_combined_feature()
  • pensa.features.mda_distances
    • read_atom_group_distances()
    • read_atom_self_distances()
    • read_calpha_distances()
    • read_gpcr_calpha_distances()
    • select_gpcr_residues()
  • pensa.features.mda_torsions
    • find_atom_by_name()
    • find_atom_indices_per_residue()
    • list_depth()
    • read_nucleicacid_backbone_torsions()
    • read_nucleicacid_pseudotorsions()
    • read_protein_backbone_torsions()
    • read_protein_sidechain_torsions()
    • read_torsions()
  • pensa.features.processing
    • correct_angle_periodicity()
    • correct_spher_angle_periodicity()
    • get_common_features_data()
    • get_feature_data()
    • get_feature_subset()
    • get_feature_timeseries()
    • get_multivar_res()
    • get_multivar_res_timeseries()
    • match_sim_lengths()
    • select_common_features()
    • sort_distances_by_resnum()
    • sort_features()
    • sort_features_alphabetically()
    • sort_sincos_torsions_by_resnum()
    • sort_torsions_by_resnum()
    • sort_traj_along_feature()
  • pensa.features.water_features
    • read_water_features()
• pensa.preprocessing
  • pensa.preprocessing.coordinates
    • align_coordinates()
    • extract_coordinates()
    • extract_coordinates_combined()
    • merge_and_sort_coordinates()
    • merge_coordinates()
    • sort_coordinates()
  • pensa.preprocessing.density
    • convert_to_occ()
    • data_out()
    • dens_grid_pdb()
    • extract_aligned_coordinates()
    • extract_combined_grid()
    • generate_grid()
    • local_maxima_3D()
    • write_atom_to_pdb()
  • pensa.preprocessing.download
    • download_from_gpcrmd()
    • get_transmem_from_uniprot()
  • pensa.preprocessing.selection
    • load_selection()
    • range_to_string()
• pensa.statesinfo
  • pensa.statesinfo.discrete_states
    • calculate_entropy()
    • calculate_entropy_multthread()
    • determine_state_limits()
    • get_discrete_states()
    • get_intersects()
    • smart_gauss_fit()