Index

A

aggregate_pivot_by_donor() (in module phenoms.comparison) aggregate_replicate_data() (in module phenoms.dimensionality_reduction) align_and_renumber_pdb() (in module phenoms.cleanup) aligned_mobile_sequence (phenoms.cleanup.RenumberReport attribute)

aligned_reference_sequence (phenoms.cleanup.RenumberReport attribute) apply_community_annotations() (in module phenoms.connectivity) assess_series_convergence() (in module phenoms.qc) assign_greedy_modularity_communities() (in module phenoms.connectivity)

B

bond_delta_from_pivot_tables() (in module phenoms.connectivity) bond_label_to_donor_acceptor_residue_numbers() (in module phenoms.connectivity) bond_label_to_donor_residue() (in module phenoms.comparison) bond_occupancy_from_pivot_tables() (in module phenoms.connectivity)

bond_statistics (phenoms.SimulationSet property) build_mobile_to_reference_map() (in module phenoms.cleanup) build_residue_graph_from_bond_deltas() (in module phenoms.connectivity) build_residue_graph_with_communities() (in module phenoms.connectivity)

C

calculate_bond_statistics() (in module phenoms.analysis) chain (phenoms.cleanup.ResidueKey attribute) check_mdp_key_consistency() (in module phenoms.qc) community_by_node (phenoms.connectivity.CommunityGraphResult attribute) community_tables() (in module phenoms.connectivity)

CommunityGraphResult (class in phenoms.connectivity) compare() (phenoms.ComparisonSet method) compare_two_sets() (in module phenoms.comparison) comparison_sets_from_dirs() (in module phenoms) ComparisonSet (class in phenoms) create_pivot_table() (in module phenoms.analysis)

D

default_n_jobs() (in module phenoms) default_output_root() (in module phenoms) detect_hbonds() (in module phenoms)

detect_hbonds_with_occupancy() (in module phenoms) detect_replicate_input() (in module phenoms.preprocess) differentially_protected() (in module phenoms.comparison) discover_replicate_dirs() (in module phenoms.preprocess)

E

edges (phenoms.connectivity.ResidueGraph attribute) engine (phenoms.preprocess.ReplicateInput attribute) export_comparison_artifacts() (phenoms.ComparisonSet method) export_connectivity_community_graph_html() (phenoms.ComparisonSet method)

export_connectivity_graph_html() (phenoms.ComparisonSet method) export_hbond_occupancy_csv() (in module phenoms.hbond) export_residue_graph_html() (in module phenoms.connectivity) export_run_artifacts() (phenoms.SimulationSet method) extract_residue_numbers() (in module phenoms.analysis)

F

fluctuating_bonds() (in module phenoms.analysis)

from_trajectories() (phenoms.SimulationSet class method)

G

get_bond_labels_sorted() (phenoms.SimulationSet method) get_comparison_df() (phenoms.ComparisonSet method) get_fluctuating_bonds() (phenoms.SimulationSet method) get_hbond_dfs() (phenoms.SimulationSet method) get_occupancy_tables() (phenoms.SimulationSet method)

get_pivot_tables() (phenoms.SimulationSet method) get_plot_bond_labels_sorted() (phenoms.SimulationSet method) get_plot_pivot_tables() (phenoms.SimulationSet method) get_qc_report() (phenoms.SimulationSet method) get_unified_bond_labels() (phenoms.ComparisonSet method) graph (phenoms.connectivity.CommunityGraphResult attribute)

H

hbond_occupancy_table() (in module phenoms.hbond)

I

icode (phenoms.cleanup.ResidueKey attribute)

iter_pdb_models() (in module phenoms.cleanup)

L

label_hbond() (in module phenoms.hbond) label_hbond_all() (in module phenoms.hbond)

load_and_select_residues() (in module phenoms.io) load_trajectory() (in module phenoms.io)

M

modularity (phenoms.connectivity.CommunityGraphResult attribute) module phenoms.analysis phenoms.cleanup phenoms.comparison phenoms.connectivity phenoms.dimensionality_reduction phenoms.hbond phenoms.io phenoms.plotting phenoms.preprocess phenoms.qc phenoms.structure

N

n_filled_unmapped_mobile (phenoms.cleanup.RenumberReport attribute) n_mapped (phenoms.cleanup.RenumberReport attribute) n_mismatch_at_aligned_positions (phenoms.cleanup.RenumberReport attribute) n_mobile_only_gaps_in_reference (phenoms.cleanup.RenumberReport attribute) n_mobile_residues (phenoms.cleanup.RenumberReport attribute)

n_reference_residues (phenoms.cleanup.RenumberReport attribute) needleman_wunsch() (in module phenoms.cleanup) nodes (phenoms.connectivity.ResidueGraph attribute) normalize_replicate_to_pdb() (in module phenoms.preprocess) normalize_topology_list() (in module phenoms.io)

O

ordered_residue_run() (in module phenoms.cleanup)

P

parse_mdp() (in module phenoms.qc) per_donor_metric_from_pivots() (in module phenoms.comparison) phenoms.analysis module phenoms.cleanup module phenoms.comparison module phenoms.connectivity module phenoms.dimensionality_reduction module phenoms.hbond module phenoms.io module phenoms.plotting module phenoms.preprocess module phenoms.qc module

phenoms.structure module plot_aggregated_heatmap() (in module phenoms.plotting) (phenoms.SimulationSet method) plot_bond_lifetimes_with_error_bars() (in module phenoms.plotting) plot_bond_statistics() (phenoms.SimulationSet method) plot_break_frequencies_with_error_bars() (in module phenoms.plotting) plot_difference() (in module phenoms.plotting) (phenoms.ComparisonSet method) plot_heatmap() (in module phenoms.plotting) plot_heatmap_with_legend() (in module phenoms.plotting) plot_heatmaps() (phenoms.SimulationSet method) plot_heatmaps_both() (phenoms.ComparisonSet method) plot_manifold() (in module phenoms.dimensionality_reduction) plot_top_hbonds() (in module phenoms.plotting) (phenoms.SimulationSet method) prefer_difference_clipped_column() (in module phenoms.comparison) prepare_set_from_dir() (in module phenoms.preprocess) process_frame() (in module phenoms.hbond) process_frame_all() (in module phenoms.hbond) process_frames() (in module phenoms.hbond) process_frames_all() (in module phenoms.hbond)

R

renumber_many_to_reference() (in module phenoms.cleanup) renumber_pdb_atom_lines() (in module phenoms.cleanup) renumber_pdb_file() (in module phenoms.cleanup) RenumberReport (class in phenoms.cleanup) replicate_dir (phenoms.preprocess.ReplicateInput attribute) ReplicateInput (class in phenoms.preprocess) residue_value_map_from_comparison() (in module phenoms.structure) ResidueGraph (class in phenoms.connectivity) ResidueKey (class in phenoms.cleanup) resseq (phenoms.cleanup.ResidueKey attribute) rmsd_convergence_report() (in module phenoms.qc) run() (phenoms.SimulationSet method)

run_backbone_hbond_analysis() (in module phenoms) run_isomap() (in module phenoms.dimensionality_reduction) (phenoms.ComparisonSet method) (phenoms.SimulationSet method) run_manifold_suite() (in module phenoms.dimensionality_reduction) (phenoms.ComparisonSet method) (phenoms.SimulationSet method) run_pca() (in module phenoms.dimensionality_reduction) (phenoms.ComparisonSet method) (phenoms.SimulationSet method) run_tsne() (in module phenoms.dimensionality_reduction) (phenoms.ComparisonSet method) (phenoms.SimulationSet method)

S

save_comparison_csv() (phenoms.ComparisonSet method) simulation_set_from_dir() (in module phenoms)

SimulationSet (class in phenoms) suggest_difference_threshold_autocorr() (in module phenoms.plotting)

T

topology_path (phenoms.preprocess.ReplicateInput attribute)

tpr_to_mdtraj_topology() (in module phenoms.io) trajectory_path (phenoms.preprocess.ReplicateInput attribute)

W

write_pdb_bfactors() (in module phenoms.structure) (phenoms.ComparisonSet method)

write_structure_bfactors() (phenoms.SimulationSet method)