Index

A

align_coordinates() (in module pensa.preprocessing.coordinates) atg_to_names() (in module pensa.features.hbond_features) average_jsd() (in module pensa.comparison.metrics)

average_kld() (in module pensa.comparison.metrics) average_ksp() (in module pensa.comparison.metrics) average_kss() (in module pensa.comparison.metrics) average_ssi() (in module pensa.comparison.metrics)

C

calculate_entropy() (in module pensa.statesinfo.discrete_states) calculate_entropy_multthread() (in module pensa.statesinfo.discrete_states) calculate_pca() (in module pensa.dimensionality.pca) calculate_tica() (in module pensa.dimensionality.tica) compare_mult_projections() (in module pensa.dimensionality.visualization)

compare_projections() (in module pensa.dimensionality.visualization) convert_to_occ() (in module pensa.preprocessing.density) correct_angle_periodicity() (in module pensa.features.processing) correct_spher_angle_periodicity() (in module pensa.features.processing) cossi_featens_analysis() (in module pensa.comparison.statespecific)

D

data_out() (in module pensa.preprocessing.density) dens_grid_pdb() (in module pensa.preprocessing.density)

determine_state_limits() (in module pensa.statesinfo.discrete_states) distances_visualization() (in module pensa.comparison.visualization) download_from_gpcrmd() (in module pensa.preprocessing.download)

E

extract_aligned_coordinates() (in module pensa.preprocessing.density) extract_combined_grid() (in module pensa.preprocessing.density)

extract_coordinates() (in module pensa.preprocessing.coordinates) extract_coordinates_combined() (in module pensa.preprocessing.coordinates)

F

feature_correlation() (in module pensa.comparison.statistics) find_atom_by_name() (in module pensa.features.mda_torsions)

find_atom_indices_per_residue() (in module pensa.features.mda_torsions) find_closest_frames() (in module pensa.clusters.clustering)

G

generate_grid() (in module pensa.preprocessing.density) get_common_features_data() (in module pensa.features.processing) get_components_pca() (in module pensa.dimensionality.pca) get_components_tica() (in module pensa.dimensionality.tica) get_discrete_states() (in module pensa.statesinfo.discrete_states) get_feature_data() (in module pensa.features.processing)

get_feature_subset() (in module pensa.features.processing) get_feature_timeseries() (in module pensa.features.processing) get_intersects() (in module pensa.statesinfo.discrete_states) get_multivar_res() (in module pensa.features.processing) get_multivar_res_timeseries() (in module pensa.features.processing) get_transmem_from_uniprot() (in module pensa.preprocessing.download)

K

kolmogorov_smirnov_analysis() (in module pensa.comparison.statistics)

L

list_depth() (in module pensa.features.mda_torsions)

load_selection() (in module pensa.preprocessing.selection) local_maxima_3D() (in module pensa.preprocessing.density)

M

match_sim_lengths() (in module pensa.features.processing) max_jsd() (in module pensa.comparison.metrics) max_kld() (in module pensa.comparison.metrics) max_ksp() (in module pensa.comparison.metrics) max_kss() (in module pensa.comparison.metrics) max_ssi() (in module pensa.comparison.metrics) mean_difference_analysis() (in module pensa.comparison.statistics) merge_and_sort_coordinates() (in module pensa.preprocessing.coordinates) merge_coordinates() (in module pensa.preprocessing.coordinates) min_ksp() (in module pensa.comparison.metrics) module pensa pensa.clusters pensa.clusters.clustering pensa.clusters.trajectory pensa.clusters.wss pensa.comparison pensa.comparison.metrics pensa.comparison.projections pensa.comparison.relative_entropy pensa.comparison.statespecific pensa.comparison.statistics pensa.comparison.uncertainty_analysis pensa.comparison.visualization pensa.dimensionality pensa.dimensionality.pca pensa.dimensionality.tica pensa.dimensionality.visualization pensa.features pensa.features.atom_features pensa.features.csv_features pensa.features.hbond_features pensa.features.mda_combined pensa.features.mda_distances pensa.features.mda_torsions pensa.features.processing pensa.features.water_features pensa.preprocessing pensa.preprocessing.coordinates pensa.preprocessing.density pensa.preprocessing.download pensa.preprocessing.selection pensa.statesinfo pensa.statesinfo.discrete_states

N

name_atom_features() (in module pensa.features.hbond_features)

name_pairs() (in module pensa.features.hbond_features)

O

obtain_clusters() (in module pensa.clusters.clustering)

obtain_combined_clusters() (in module pensa.clusters.clustering) obtain_mult_combined_clusters() (in module pensa.clusters.clustering)

P

pair_features_heatmap() (in module pensa.comparison.visualization) pca_eigenvalues_plot() (in module pensa.dimensionality.pca) pca_feature_correlation() (in module pensa.comparison.projections) pca_features() (in module pensa.dimensionality.pca) pca_sampling_efficiency() (in module pensa.comparison.metrics) pensa module pensa.clusters module pensa.clusters.clustering module pensa.clusters.trajectory module pensa.clusters.wss module pensa.comparison module pensa.comparison.metrics module pensa.comparison.projections module pensa.comparison.relative_entropy module pensa.comparison.statespecific module pensa.comparison.statistics module pensa.comparison.uncertainty_analysis module pensa.comparison.visualization module pensa.dimensionality module pensa.dimensionality.pca module pensa.dimensionality.tica module

pensa.dimensionality.visualization module pensa.features module pensa.features.atom_features module pensa.features.csv_features module pensa.features.hbond_features module pensa.features.mda_combined module pensa.features.mda_distances module pensa.features.mda_torsions module pensa.features.processing module pensa.features.water_features module pensa.preprocessing module pensa.preprocessing.coordinates module pensa.preprocessing.density module pensa.preprocessing.download module pensa.preprocessing.selection module pensa.statesinfo module pensa.statesinfo.discrete_states module project_on_eigenvector_pca() (in module pensa.dimensionality.visualization) project_on_eigenvector_tica() (in module pensa.dimensionality.visualization) project_on_pc() (in module pensa.dimensionality.pca) project_on_tic() (in module pensa.dimensionality.tica)

R

range_to_string() (in module pensa.preprocessing.selection) read_atom_features() (in module pensa.features.atom_features) read_atom_group_distances() (in module pensa.features.mda_distances) read_atom_self_distances() (in module pensa.features.mda_distances) read_calpha_distances() (in module pensa.features.mda_distances) read_csv_features() (in module pensa.features.csv_features) read_drormd_features() (in module pensa.features.csv_features) read_gpcr_calpha_distances() (in module pensa.features.mda_distances) read_h_bond_satisfaction() (in module pensa.features.hbond_features) read_h_bonds() (in module pensa.features.hbond_features) read_h_bonds_quickly() (in module pensa.features.hbond_features) read_nucleicacid_backbone_torsions() (in module pensa.features.mda_torsions)

read_nucleicacid_pseudotorsions() (in module pensa.features.mda_torsions) read_protein_backbone_torsions() (in module pensa.features.mda_torsions) read_protein_sidechain_torsions() (in module pensa.features.mda_torsions) read_structure_features() (in module pensa.features.mda_combined) read_torsions() (in module pensa.features.mda_torsions) read_water_features() (in module pensa.features.water_features) read_water_site_h_bonds() (in module pensa.features.hbond_features) read_water_site_h_bonds_quickly() (in module pensa.features.hbond_features) relative_entropy_analysis() (in module pensa.comparison.relative_entropy) relen_block_analysis() (in module pensa.comparison.uncertainty_analysis) relen_sem_analysis() (in module pensa.comparison.uncertainty_analysis) residue_visualization() (in module pensa.comparison.visualization) resnum_heatmap() (in module pensa.comparison.visualization)

S

select_common_features() (in module pensa.features.processing) select_gpcr_residues() (in module pensa.features.mda_distances) smart_gauss_fit() (in module pensa.statesinfo.discrete_states) sort_coordinates() (in module pensa.preprocessing.coordinates) sort_distances_by_resnum() (in module pensa.features.processing) sort_features() (in module pensa.features.processing) sort_features_alphabetically() (in module pensa.features.processing) sort_mult_trajs_along_common_pc() (in module pensa.dimensionality.pca) sort_mult_trajs_along_common_tic() (in module pensa.dimensionality.tica) sort_sincos_torsions_by_resnum() (in module pensa.features.processing) sort_torsions_by_resnum() (in module pensa.features.processing)

sort_traj_along_combined_feature() (in module pensa.features.mda_combined) sort_traj_along_feature() (in module pensa.features.processing) sort_traj_along_pc() (in module pensa.dimensionality.pca) sort_traj_along_projection() (in module pensa.dimensionality.visualization) sort_traj_along_tic() (in module pensa.dimensionality.tica) sort_trajs_along_common_pc() (in module pensa.dimensionality.pca) sort_trajs_along_common_tic() (in module pensa.dimensionality.tica) ssi_block_analysis() (in module pensa.comparison.uncertainty_analysis) ssi_ensemble_analysis() (in module pensa.comparison.statespecific) ssi_feature_analysis() (in module pensa.comparison.statespecific) ssi_sem_analysis() (in module pensa.comparison.uncertainty_analysis)

T

tica_eigenvalues_plot() (in module pensa.dimensionality.tica)

tica_feature_correlation() (in module pensa.comparison.projections) tica_features() (in module pensa.dimensionality.tica)

W

write_atom_to_pdb() (in module pensa.preprocessing.density) write_cluster_traj() (in module pensa.clusters.trajectory)

write_csv_features() (in module pensa.features.csv_features) wss_over_number_of_clusters() (in module pensa.clusters.wss) wss_over_number_of_combined_clusters() (in module pensa.clusters.wss)