Index

Symbols

--covalent-factor command line option --csv command line option --da-distance command line option --hb-angle command line option --hb-distance command line option --help command line option --json command line option --list-presets command line option --mode command line option --no-halogen-bonds command line option --no-hydrogen-bonds command line option --no-pi-interactions command line option --output command line option

--pi-angle command line option --pi-distance command line option --preset command line option --quiet command line option --summary-only command line option --verbose command line option --version command line option --xb-angle command line option --xb-distance command line option -h command line option -o command line option -q command line option -v command line option

_

__add__() (hbat.core.vector.Vec3D method), [1] __eq__() (hbat.core.vector.Vec3D method), [1] __getitem__() (hbat.core.vector.Vec3D method), [1] __init__() (hbat.core.analysis.AnalysisParameters method), [1] (hbat.core.analysis.CooperativityChain method), [1] (hbat.core.analysis.HalogenBond method), [1] (hbat.core.analysis.HBondAnalyzer method), [1] (hbat.core.analysis.HydrogenBond method), [1] (hbat.core.analysis.PiInteraction method), [1] (hbat.core.pdb_parser.Atom method), [1] (hbat.core.pdb_parser.PDBParser method), [1] (hbat.core.pdb_parser.Residue method), [1] (hbat.core.vector.Vec3D method), [1] (hbat.gui.chain_visualization.ChainVisualizationWindow method) (hbat.gui.main_window.MainWindow method) (hbat.gui.parameter_panel.ParameterPanel method) (hbat.gui.results_panel.ResultsPanel method)

__mul__() (hbat.core.vector.Vec3D method), [1] __rmul__() (hbat.core.vector.Vec3D method), [1] __setitem__() (hbat.core.vector.Vec3D method), [1] __sub__() (hbat.core.vector.Vec3D method), [1] __truediv__() (hbat.core.vector.Vec3D method), [1]

A

acceptor (hbat.core.analysis.HalogenBond attribute), [1] (hbat.core.analysis.HydrogenBond attribute), [1] acceptor_residue (hbat.core.analysis.HalogenBond attribute), [1] (hbat.core.analysis.HydrogenBond attribute), [1] ALL_MODES (hbat.constants.AnalysisModes attribute) alt_loc (hbat.core.pdb_parser.Atom attribute), [1] ANALYSIS_MODE (hbat.constants.AnalysisDefaults attribute) analysis_mode (hbat.core.analysis.AnalysisParameters attribute), [1] AnalysisDefaults (class in hbat.constants) AnalysisModes (class in hbat.constants) AnalysisParameters (class in hbat.core.analysis), [1]

analyze_file() (hbat.core.analysis.HBondAnalyzer method), [1] angle (hbat.core.analysis.HalogenBond attribute), [1] (hbat.core.analysis.HydrogenBond attribute), [1] (hbat.core.analysis.MolecularInteraction property), [1] (hbat.core.analysis.PiInteraction attribute), [1] angle_between_vectors() (in module hbat.core.vector), [1] angle_to() (hbat.core.vector.Vec3D method), [1] Atom (class in hbat.core.pdb_parser), [1] ATOMIC_MASSES (hbat.constants.AtomicData attribute) AtomicData (class in hbat.constants) atoms (hbat.core.pdb_parser.Residue attribute), [1]

B

bond_type (hbat.core.analysis.HalogenBond attribute), [1] (hbat.core.analysis.HydrogenBond attribute), [1]

C

center_of_mass() (hbat.core.pdb_parser.Residue method), [1] chain_id (hbat.core.pdb_parser.Atom attribute), [1] (hbat.core.pdb_parser.Residue attribute), [1] chain_length (hbat.core.analysis.CooperativityChain attribute), [1] chain_type (hbat.core.analysis.CooperativityChain attribute), [1] ChainVisualizationWindow (class in hbat.gui.chain_visualization) charge (hbat.core.pdb_parser.Atom attribute), [1] clear_results() (hbat.gui.results_panel.ResultsPanel method) command line option --covalent-factor --csv --da-distance --hb-angle --hb-distance --help --json --list-presets --mode --no-halogen-bonds --no-hydrogen-bonds --no-pi-interactions --output --pi-angle --pi-distance --preset --quiet --summary-only --verbose --version --xb-angle --xb-distance -h -o -q -v input

COMPLETE (hbat.constants.AnalysisModes attribute) CooperativityChain (class in hbat.core.analysis), [1] coords (hbat.core.pdb_parser.Atom attribute), [1] COVALENT_CUTOFF_FACTOR (hbat.constants.AnalysisDefaults attribute) covalent_cutoff_factor (hbat.core.analysis.AnalysisParameters attribute), [1] COVALENT_RADII (hbat.constants.AtomicData attribute) create_parser() (in module hbat.cli.main) cross() (hbat.core.vector.Vec3D method), [1]

D

DEFAULT_ATOMIC_MASS (hbat.constants.AtomicData attribute) DEFAULT_X (hbat.constants.VectorDefaults attribute) DEFAULT_Y (hbat.constants.VectorDefaults attribute) DEFAULT_Z (hbat.constants.VectorDefaults attribute) dihedral_angle() (in module hbat.core.vector), [1] distance (hbat.core.analysis.HalogenBond attribute), [1] (hbat.core.analysis.HydrogenBond attribute), [1] (hbat.core.analysis.MolecularInteraction property), [1] (hbat.core.analysis.PiInteraction attribute), [1]

distance_to() (hbat.core.vector.Vec3D method), [1] donor (hbat.core.analysis.HydrogenBond attribute), [1] (hbat.core.analysis.PiInteraction attribute), [1] donor_acceptor_distance (hbat.core.analysis.HydrogenBond attribute), [1] donor_residue (hbat.core.analysis.HydrogenBond attribute), [1] (hbat.core.analysis.PiInteraction attribute), [1] dot() (hbat.core.vector.Vec3D method), [1]

E

ELECTRONEGATIVITY (hbat.constants.AtomicData attribute) element (hbat.core.pdb_parser.Atom attribute), [1]

export_to_csv() (in module hbat.cli.main) export_to_json() (in module hbat.cli.main)

F

FileFormats (class in hbat.constants) format_results_text() (in module hbat.cli.main)

from_list() (hbat.core.vector.Vec3D class method), [1] from_tuple() (hbat.core.vector.Vec3D class method), [1]

G

get_acceptor_atom() (hbat.core.analysis.HalogenBond method), [1] (hbat.core.analysis.HydrogenBond method), [1] (hbat.core.analysis.MolecularInteraction method), [1] (hbat.core.analysis.PiInteraction method), [1] get_acceptor_residue() (hbat.core.analysis.HalogenBond method), [1] (hbat.core.analysis.HydrogenBond method), [1] (hbat.core.analysis.MolecularInteraction method), [1] (hbat.core.analysis.PiInteraction method), [1] get_atom() (hbat.core.pdb_parser.Residue method), [1] get_atoms_by_element() (hbat.core.pdb_parser.PDBParser method), [1] (hbat.core.pdb_parser.Residue method), [1] get_atoms_by_residue() (hbat.core.pdb_parser.PDBParser method), [1] get_chain_ids() (hbat.core.pdb_parser.PDBParser method), [1] get_donor_atom() (hbat.core.analysis.HalogenBond method), [1] (hbat.core.analysis.HydrogenBond method), [1] (hbat.core.analysis.MolecularInteraction method), [1] (hbat.core.analysis.PiInteraction method), [1]

get_donor_residue() (hbat.core.analysis.HalogenBond method), [1] (hbat.core.analysis.HydrogenBond method), [1] (hbat.core.analysis.MolecularInteraction method), [1] (hbat.core.analysis.PiInteraction method), [1] get_example_presets_directory() (in module hbat.cli.main) get_hydrogen_atoms() (hbat.core.pdb_parser.PDBParser method), [1] get_parameters() (hbat.gui.parameter_panel.ParameterPanel method) get_residue_list() (hbat.core.pdb_parser.PDBParser method), [1] get_results_summary() (hbat.core.analysis.HBondAnalyzer method), [1] get_statistics() (hbat.core.analysis.HBondAnalyzer method), [1] (hbat.core.pdb_parser.PDBParser method), [1] GUIDefaults (class in hbat.constants)

H

halogen (hbat.core.analysis.HalogenBond attribute), [1] halogen_residue (hbat.core.analysis.HalogenBond attribute), [1] HalogenBond (class in hbat.core.analysis), [1] has_hydrogens() (hbat.core.pdb_parser.PDBParser method), [1] HB_ANGLE_CUTOFF (hbat.constants.AnalysisDefaults attribute) hb_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1] HB_DA_DISTANCE (hbat.constants.AnalysisDefaults attribute) HB_DISTANCE_CUTOFF (hbat.constants.AnalysisDefaults attribute) hb_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1] hb_donor_acceptor_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1] hbat.cli.main module hbat.constants module hbat.core.analysis module

hbat.core.pdb_parser module hbat.core.vector module hbat.gui.chain_visualization module hbat.gui.main_window module hbat.gui.parameter_panel module hbat.gui.results_panel module HBondAnalyzer (class in hbat.core.analysis), [1] hydrogen (hbat.core.analysis.HydrogenBond attribute), [1] (hbat.core.analysis.PiInteraction attribute), [1] HydrogenBond (class in hbat.core.analysis), [1]

I

i_code (hbat.core.pdb_parser.Atom attribute), [1] (hbat.core.pdb_parser.Residue attribute), [1] input command line option interaction_type (hbat.core.analysis.HalogenBond property), [1] (hbat.core.analysis.HydrogenBond property), [1] (hbat.core.analysis.MolecularInteraction property), [1] (hbat.core.analysis.PiInteraction property), [1]

interactions (hbat.core.analysis.CooperativityChain attribute), [1] is_hydrogen() (hbat.core.pdb_parser.Atom method), [1] is_metal() (hbat.core.pdb_parser.Atom method), [1]

J

JSON_VERSION (hbat.constants.FileFormats attribute)

L

LEFT_PANEL_WIDTH (hbat.constants.GUIDefaults attribute) length() (hbat.core.vector.Vec3D method), [1] list_available_presets() (in module hbat.cli.main)

load_parameters_from_args() (in module hbat.cli.main) load_preset_file() (in module hbat.cli.main) LOCAL (hbat.constants.AnalysisModes attribute)

M

magnitude() (hbat.core.vector.Vec3D method), [1] main() (in module hbat.cli.main), [1] MainWindow (class in hbat.gui.main_window) MAX_ANGLE (hbat.constants.ParameterRanges attribute) MAX_COVALENT_FACTOR (hbat.constants.ParameterRanges attribute) MAX_DISTANCE (hbat.constants.ParameterRanges attribute) MIN_ANGLE (hbat.constants.ParameterRanges attribute) MIN_COVALENT_FACTOR (hbat.constants.ParameterRanges attribute) MIN_DISTANCE (hbat.constants.ParameterRanges attribute) MIN_HYDROGEN_RATIO (hbat.constants.AtomicData attribute) MIN_WINDOW_HEIGHT (hbat.constants.GUIDefaults attribute)

MIN_WINDOW_WIDTH (hbat.constants.GUIDefaults attribute) module hbat.cli.main hbat.constants hbat.core.analysis hbat.core.pdb_parser hbat.core.vector hbat.gui.chain_visualization hbat.gui.main_window hbat.gui.parameter_panel hbat.gui.results_panel MolecularInteraction (class in hbat.core.analysis), [1]

N

name (hbat.core.pdb_parser.Atom attribute), [1] (hbat.core.pdb_parser.Residue attribute), [1]

normalize() (hbat.core.vector.Vec3D method), [1]

O

occupancy (hbat.core.pdb_parser.Atom attribute), [1]

OUTPUT_EXTENSIONS (hbat.constants.FileFormats attribute)

P

ParameterPanel (class in hbat.gui.parameter_panel) ParameterRanges (class in hbat.constants) parse_file() (hbat.core.pdb_parser.PDBParser method), [1] parse_lines() (hbat.core.pdb_parser.PDBParser method), [1] PDB_EXTENSIONS (hbat.constants.FileFormats attribute) PDBParser (class in hbat.core.pdb_parser), [1] PI_ANGLE_CUTOFF (hbat.constants.AnalysisDefaults attribute) pi_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1]

pi_center (hbat.core.analysis.PiInteraction attribute), [1] PI_DISTANCE_CUTOFF (hbat.constants.AnalysisDefaults attribute) pi_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1] pi_residue (hbat.core.analysis.PiInteraction attribute), [1] PiInteraction (class in hbat.core.analysis), [1] print_error() (in module hbat.cli.main) print_progress() (in module hbat.cli.main) PROGRESS_BAR_INTERVAL (hbat.constants.GUIDefaults attribute)

R

record_type (hbat.core.pdb_parser.Atom attribute), [1] res_name (hbat.core.pdb_parser.Atom attribute), [1] res_seq (hbat.core.pdb_parser.Atom attribute), [1] reset_to_defaults() (hbat.gui.parameter_panel.ParameterPanel method)

Residue (class in hbat.core.pdb_parser), [1] resolve_preset_path() (in module hbat.cli.main) ResultsPanel (class in hbat.gui.results_panel) run() (hbat.gui.main_window.MainWindow method) run_analysis() (in module hbat.cli.main)

S

seq_num (hbat.core.pdb_parser.Residue attribute), [1]

serial (hbat.core.pdb_parser.Atom attribute), [1] set_parameters() (hbat.gui.parameter_panel.ParameterPanel method)

T

temp_factor (hbat.core.pdb_parser.Atom attribute), [1]

to_list() (hbat.core.vector.Vec3D method), [1] to_tuple() (hbat.core.vector.Vec3D method), [1]

U

unit_vector() (hbat.core.vector.Vec3D method), [1]

unit_vector_between() (in module hbat.core.vector), [1] update_results() (hbat.gui.results_panel.ResultsPanel method)

V

validate_input_file() (in module hbat.cli.main) VDW_RADII (hbat.constants.AtomicData attribute)

Vec3D (class in hbat.core.vector), [1] VectorDefaults (class in hbat.constants)

W

WINDOW_HEIGHT (hbat.constants.GUIDefaults attribute)

WINDOW_WIDTH (hbat.constants.GUIDefaults attribute)

X

XB_ANGLE_CUTOFF (hbat.constants.AnalysisDefaults attribute) xb_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1]

XB_DISTANCE_CUTOFF (hbat.constants.AnalysisDefaults attribute) xb_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute), [1]