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.np_vector.NPVec3D method), [1], [2], [3] __eq__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] (hbat.core.pdb_parser.Atom method) (hbat.core.pdb_parser.Bond method) (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Atom method), [1] (hbat.core.structure.Bond method), [1] (hbat.core.structure.Residue method), [1] __getitem__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] __init__() (hbat.ccd.ccd_analyzer.CCDDataManager method) (hbat.cli.main.ProgressBar method) (hbat.constants.parameters.AnalysisParameters method), [1] (hbat.core.analysis.AnalysisParameters method) (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.NPMolecularInteractionAnalyzer method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] (hbat.core.np_analyzer.NPMolecularInteractionAnalyzer method), [1], [2], [3] (hbat.core.np_vector.NPVec3D method), [1], [2], [3] (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] (hbat.core.pdb_parser.Atom method) (hbat.core.pdb_parser.Bond method) (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Atom method), [1] (hbat.core.structure.Bond method), [1] (hbat.core.structure.Residue 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)

__iter__() (hbat.core.pdb_parser.Atom method) (hbat.core.pdb_parser.Bond method) (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Atom method), [1] (hbat.core.structure.Bond method), [1] (hbat.core.structure.Residue method), [1] __mul__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] __repr__() (hbat.core.pdb_parser.Atom method) (hbat.core.pdb_parser.Bond method) (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Atom method), [1] (hbat.core.structure.Bond method), [1] (hbat.core.structure.Residue method), [1] __rmul__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] __sub__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] __truediv__() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] _safe_float_convert() (in module hbat.core.pdb_parser) _safe_int_convert() (in module hbat.core.pdb_parser)

A

acceptor (hbat.core.analysis.HalogenBond property) (hbat.core.analysis.HydrogenBond property) (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.HalogenBond property), [1], [2], [3] (hbat.core.interactions.HydrogenBond property), [1], [2], [3] (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] acceptor_residue (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] ADD_HEAVY_ATOMS (hbat.constants.parameters.PDBFixingModes attribute), [1] ADD_HYDROGENS (hbat.constants.parameters.PDBFixingModes attribute), [1] add_missing_heavy_atoms() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3], [4] (in module hbat.core.pdb_fixer), [1] add_missing_hydrogens() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3], [4] (in module hbat.core.pdb_fixer), [1] ALL_METHODS (hbat.constants.parameters.BondDetectionMethods attribute), [1] (hbat.constants.parameters.PDBFixingModes attribute), [1] ALL_MODES (hbat.constants.parameters.AnalysisModes attribute), [1] analysis_mode (hbat.constants.parameters.AnalysisParameters attribute), [1] ANALYSIS_MODE (hbat.constants.parameters.ParametersDefault attribute), [1] analysis_mode (hbat.core.analysis.AnalysisParameters attribute) AnalysisModes (class in hbat.constants.parameters), [1]

AnalysisParameters (class in hbat.constants.parameters), [1] (class in hbat.core.analysis) analyze_file() (hbat.core.analysis.NPMolecularInteractionAnalyzer method) (hbat.core.np_analyzer.NPMolecularInteractionAnalyzer method), [1], [2], [3] angle (hbat.core.analysis.HalogenBond property) (hbat.core.analysis.HydrogenBond property) (hbat.core.analysis.MolecularInteraction property) (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.HalogenBond property), [1], [2], [3] (hbat.core.interactions.HydrogenBond property), [1], [2], [3] (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] (hbat.core.interactions.PiInteraction property), [1], [2], [3] angle_to() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] APP_NAME (in module hbat.constants.app) APP_VERSION (in module hbat.constants.app) AROMATIC_CODES (in module hbat.constants.pdb_constants) Atom (class in hbat.core.pdb_parser) (class in hbat.core.structure), [1] atom_file (hbat.ccd.ccd_analyzer.CCDDataManager attribute) atom_url (hbat.ccd.ccd_analyzer.CCDDataManager attribute) ATOMIC_MASSES (hbat.constants.atomic_data.AtomicData attribute), [1] AtomicData (class in hbat.constants.atomic_data), [1]

B

BACKBONE_ATOMS (in module hbat.constants.pdb_constants), [1] BACKBONE_SIDECHAIN_CODES (in module hbat.constants.pdb_constants) batch_angle_between() (in module hbat.core.np_vector), [1], [2], [3] batch_dihedral_angle() (in module hbat.core.np_vector), [1], [2]

Bond (class in hbat.core.pdb_parser) (class in hbat.core.structure), [1] bond_file (hbat.ccd.ccd_analyzer.CCDDataManager attribute) bond_url (hbat.ccd.ccd_analyzer.CCDDataManager attribute) BondDetectionMethods (class in hbat.constants.parameters), [1]

C

ccd_folder (hbat.ccd.ccd_analyzer.CCDDataManager attribute) CCDDataManager (class in hbat.ccd.ccd_analyzer) center_of_mass() (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Residue method), [1] ChainVisualizationWindow (class in hbat.gui.chain_visualization) CHARGED_RESIDUES (in module hbat.constants.pdb_constants) 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.parameters.AnalysisModes attribute), [1] compute_distance_matrix() (in module hbat.core.np_vector), [1], [2], [3] CONECT_RECORDS (hbat.constants.parameters.BondDetectionMethods attribute), [1] convert_nonstandard_residues() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3], [4] (in module hbat.core.pdb_fixer), [1] CooperativityChain (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] covalent_cutoff_factor (hbat.constants.parameters.AnalysisParameters attribute), [1] COVALENT_CUTOFF_FACTOR (hbat.constants.parameters.ParametersDefault attribute), [1] covalent_cutoff_factor (hbat.core.analysis.AnalysisParameters attribute) COVALENT_RADII (hbat.constants.atomic_data.AtomicData attribute), [1] create_parser() (in module hbat.cli.main) cross() (hbat.core.np_vector.NPVec3D method), [1], [2], [3]

D

DEFAULT_ATOMIC_MASS (hbat.constants.atomic_data.AtomicData attribute), [1] DEFAULT_X (hbat.constants.misc.VectorDefaults attribute), [1] DEFAULT_Y (hbat.constants.misc.VectorDefaults attribute), [1] DEFAULT_Z (hbat.constants.misc.VectorDefaults attribute), [1] distance (hbat.core.analysis.HalogenBond property) (hbat.core.analysis.HydrogenBond property) (hbat.core.analysis.MolecularInteraction property) (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.HalogenBond property), [1], [2], [3] (hbat.core.interactions.HydrogenBond property), [1], [2], [3] (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] (hbat.core.interactions.PiInteraction property), [1], [2], [3] DISTANCE_BASED (hbat.constants.parameters.BondDetectionMethods attribute), [1] distance_to() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] DNA_RESIDUES (in module hbat.constants.pdb_constants), [1] DNA_RNA_BACKBONE_ATOMS (in module hbat.constants.pdb_constants), [1] DNA_RNA_BASE_ATOMS (in module hbat.constants.pdb_constants), [1] donor (hbat.core.analysis.HalogenBond property) (hbat.core.analysis.HydrogenBond property) (hbat.core.analysis.MolecularInteraction property) (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.HalogenBond property), [1], [2], [3] (hbat.core.interactions.HydrogenBond property), [1], [2], [3] (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] (hbat.core.interactions.PiInteraction property), [1], [2], [3]

donor_acceptor_distance (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] donor_acceptor_properties (hbat.core.analysis.HydrogenBond property) (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.HydrogenBond property), [1], [2], [3] (hbat.core.interactions.PiInteraction property), [1], [2], [3] donor_interaction_acceptor_angle (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] donor_interaction_distance (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] donor_residue (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] dot() (hbat.core.np_vector.NPVec3D method), [1], [2], [3]

E

ELECTRONEGATIVITY (hbat.constants.atomic_data.AtomicData attribute), [1] ensure_files_exist() (hbat.ccd.ccd_analyzer.CCDDataManager method)

export_to_csv() (in module hbat.cli.main) export_to_json() (in module hbat.cli.main) extract_residue_bonds_data() (hbat.ccd.ccd_analyzer.CCDDataManager method)

F

fields() (hbat.core.pdb_parser.Atom class method) (hbat.core.pdb_parser.Bond class method) (hbat.core.pdb_parser.Residue class method) (hbat.core.structure.Atom class method), [1] (hbat.core.structure.Bond class method), [1] (hbat.core.structure.Residue class method), [1] FileFormats (class in hbat.constants.misc), [1] finish() (hbat.cli.main.ProgressBar method) fix_pdb_add_heavy_atoms (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_ADD_HEAVY_ATOMS (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_add_heavy_atoms (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_add_hydrogens (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_ADD_HYDROGENS (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_add_hydrogens (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_enabled (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_ENABLED (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_enabled (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_file() (in module hbat.core.pdb_fixer), [1]

fix_pdb_file_to_file() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] fix_pdb_keep_water (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_KEEP_WATER (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_keep_water (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_method (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_METHOD (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_method (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_remove_heterogens (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_REMOVE_HETEROGENS (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_remove_heterogens (hbat.core.analysis.AnalysisParameters attribute) fix_pdb_replace_nonstandard (hbat.constants.parameters.AnalysisParameters attribute), [1] FIX_PDB_REPLACE_NONSTANDARD (hbat.constants.parameters.ParametersDefault attribute), [1] fix_pdb_replace_nonstandard (hbat.core.analysis.AnalysisParameters attribute) fix_structure_file() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3], [4] format_results_text() (in module hbat.cli.main) from_atoms() (hbat.core.np_vector.NPVec3D class method), [1], [2], [3] from_list() (hbat.core.np_vector.NPVec3D class method), [1], [2], [3] from_tuple() (hbat.core.np_vector.NPVec3D class method), [1], [2], [3]

G

get_acceptor() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_acceptor_atom() (hbat.core.analysis.MolecularInteraction method) (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] get_acceptor_residue() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_aromatic_center() (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Residue method), [1] get_atom() (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Residue method), [1] get_atom_by_id() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_atoms_by_element() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Residue method), [1] get_atoms_by_residue() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_available_components() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_backbone_sidechain_interaction() (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_bond_detection_statistics() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_bonded_atoms() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_bonds() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_bonds_for_atom() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_bonds_involving_atom() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_chain_ids() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_component_atoms() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_component_bonds() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_component_summary() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_donor() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_donor_acceptor_distance() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3]

get_donor_atom() (hbat.core.analysis.MolecularInteraction method) (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] get_donor_interaction_acceptor_angle() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_donor_interaction_distance() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_donor_residue() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_element_from_pdb_atom() (in module hbat.utilities.atom_utils), [1], [2] get_example_presets_directory() (in module hbat.cli.main) get_hydrogen_atoms() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_interaction() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_interaction_type() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_interaction_type_display() (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.PiInteraction method), [1], [2], [3] get_missing_hydrogen_info() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] get_parameters() (hbat.gui.parameter_panel.ParameterPanel method) get_partner() (hbat.core.pdb_parser.Bond method) (hbat.core.structure.Bond method), [1] get_residue_list() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3] get_statistics() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3], [4] get_summary() (hbat.core.analysis.NPMolecularInteractionAnalyzer method) (hbat.core.np_analyzer.NPMolecularInteractionAnalyzer method), [1], [2], [3] GUIDefaults (class in hbat.constants.misc), [1]

H

HALOGEN_BOND_ACCEPTOR_ELEMENTS (in module hbat.constants.pdb_constants), [1] HALOGEN_ELEMENTS (in module hbat.constants.pdb_constants), [1] halogen_residue (hbat.core.analysis.HalogenBond property) (hbat.core.interactions.HalogenBond property), [1], [2], [3] HalogenBond (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] has_hydrogens() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3], [4] hb_angle_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] HB_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1] hb_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute) HB_DA_DISTANCE (hbat.constants.parameters.ParametersDefault attribute), [1] hb_distance_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] HB_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1] hb_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute) hb_donor_acceptor_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] (hbat.core.analysis.AnalysisParameters attribute) hbat.cli.main module hbat.constants.app module hbat.constants.atomic_data module hbat.constants.misc module hbat.constants.parameters module hbat.constants.pdb_constants module hbat.core.analysis module

hbat.core.interactions module, [1] hbat.core.np_analyzer module, [1] hbat.core.np_vector module, [1] hbat.core.pdb_fixer module, [1] hbat.core.pdb_parser module, [1] hbat.core.structure module hbat.gui.chain_visualization module hbat.gui.main_window module hbat.gui.parameter_panel module hbat.gui.results_panel module hbat.utilities.atom_utils module HBondAnalyzer (in module hbat.core.analysis) HYDROGEN_BOND_ACCEPTOR_ELEMENTS (in module hbat.constants.pdb_constants), [1] HYDROGEN_BOND_DONOR_ELEMENTS (in module hbat.constants.pdb_constants), [1] HYDROGEN_ELEMENTS (in module hbat.constants.pdb_constants), [1] HydrogenBond (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] HYDROPHOBIC_RESIDUES (in module hbat.constants.pdb_constants)

I

input command line option interaction (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] interaction_type (hbat.core.analysis.MolecularInteraction property) (hbat.core.interactions.MolecularInteraction property), [1], [2], [3] involves_atom() (hbat.core.pdb_parser.Bond method) (hbat.core.structure.Bond method), [1] is_batch (hbat.core.np_vector.NPVec3D property), [1], [2], [3] is_donor_interaction_bonded() (hbat.core.analysis.CooperativityChain method) (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.MolecularInteraction method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.CooperativityChain method), [1], [2], [3] (hbat.core.interactions.HalogenBond method), [1], [2], [3] (hbat.core.interactions.HydrogenBond method), [1], [2], [3] (hbat.core.interactions.MolecularInteraction method), [1], [2], [3] (hbat.core.interactions.PiInteraction method), [1], [2], [3]

is_hydrogen() (hbat.core.pdb_parser.Atom method) (hbat.core.structure.Atom method), [1] is_metal() (hbat.core.pdb_parser.Atom method) (hbat.core.structure.Atom method), [1]

J

JSON_VERSION (hbat.constants.misc.FileFormats attribute), [1]

L

LEFT_PANEL_WIDTH (hbat.constants.misc.GUIDefaults attribute), [1] length() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] list_available_presets() (in module hbat.cli.main) load_atoms_data() (hbat.ccd.ccd_analyzer.CCDDataManager method)

load_bonds_data() (hbat.ccd.ccd_analyzer.CCDDataManager method) load_parameters_from_args() (in module hbat.cli.main) load_preset_file() (in module hbat.cli.main) LOCAL (hbat.constants.parameters.AnalysisModes attribute), [1]

M

magnitude() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] main() (in module hbat.cli.main), [1] MainWindow (class in hbat.gui.main_window) MAX_ANGLE (hbat.constants.parameters.ParameterRanges attribute), [1] MAX_BOND_DISTANCE (hbat.constants.parameters.ParametersDefault attribute), [1] MAX_COVALENT_FACTOR (hbat.constants.parameters.ParameterRanges attribute), [1] MAX_DISTANCE (hbat.constants.parameters.ParameterRanges attribute), [1] METAL_ELEMENTS (hbat.constants.atomic_data.AtomicData attribute), [1] MIN_ANGLE (hbat.constants.parameters.ParameterRanges attribute), [1] MIN_BOND_DISTANCE (hbat.constants.parameters.ParametersDefault attribute), [1] MIN_COVALENT_FACTOR (hbat.constants.parameters.ParameterRanges attribute), [1] MIN_DISTANCE (hbat.constants.parameters.ParameterRanges attribute), [1] MIN_HYDROGEN_RATIO (hbat.constants.atomic_data.AtomicData attribute), [1] MIN_WINDOW_HEIGHT (hbat.constants.misc.GUIDefaults attribute), [1] MIN_WINDOW_WIDTH (hbat.constants.misc.GUIDefaults attribute), [1] module hbat.cli.main hbat.constants.app hbat.constants.atomic_data hbat.constants.misc hbat.constants.parameters hbat.constants.pdb_constants hbat.core.analysis hbat.core.interactions, [1] hbat.core.np_analyzer, [1] hbat.core.np_vector, [1] hbat.core.pdb_fixer, [1] hbat.core.pdb_parser, [1] hbat.core.structure hbat.gui.chain_visualization hbat.gui.main_window hbat.gui.parameter_panel hbat.gui.results_panel hbat.utilities.atom_utils

MolecularInteraction (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] MolecularInteractionAnalyzer (in module hbat.core.analysis)

N

normalize() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] NPMolecularInteractionAnalyzer (class in hbat.core.analysis) (class in hbat.core.np_analyzer), [1], [2], [3]

NPVec3D (class in hbat.core.np_vector), [1], [2], [3]

O

OPENBABEL (hbat.constants.parameters.PDBFixingModes attribute), [1]

OPENBABEL_OPERATIONS (hbat.constants.parameters.PDBFixingModes attribute), [1] OUTPUT_EXTENSIONS (hbat.constants.misc.FileFormats attribute), [1]

P

ParameterPanel (class in hbat.gui.parameter_panel) ParameterRanges (class in hbat.constants.parameters), [1] ParametersDefault (class in hbat.constants.parameters), [1] parse_file() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3], [4] parse_lines() (hbat.core.pdb_parser.PDBParser method), [1], [2], [3], [4] PDB_ATOM_TO_ELEMENT (in module hbat.constants.pdb_constants), [1] pdb_atom_to_element() (in module hbat.utilities.atom_utils), [1], [2] PDB_EXTENSIONS (hbat.constants.misc.FileFormats attribute), [1] PDBFixer (class in hbat.core.pdb_fixer), [1], [2], [3] PDBFIXER (hbat.constants.parameters.PDBFixingModes attribute), [1] PDBFIXER_OPERATIONS (hbat.constants.parameters.PDBFixingModes attribute), [1] PDBFixerError, [1] (class in hbat.core.pdb_fixer), [1] PDBFixingModes (class in hbat.constants.parameters), [1] PDBParser (class in hbat.core.pdb_parser), [1], [2], [3] pi_angle_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] PI_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1]

pi_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute) pi_distance_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] PI_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1] pi_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute) PI_INTERACTION_ATOMS (in module hbat.constants.pdb_constants) PI_INTERACTION_DONOR (in module hbat.constants.pdb_constants) pi_residue (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.PiInteraction property), [1], [2], [3] PiInteraction (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] print_error() (in module hbat.cli.main) print_progress() (in module hbat.cli.main) PROGRESS_BAR_INTERVAL (hbat.constants.misc.GUIDefaults attribute), [1] ProgressBar (class in hbat.cli.main) PROTEIN_BACKBONE_ATOMS (in module hbat.constants.pdb_constants), [1] PROTEIN_RESIDUES (in module hbat.constants.pdb_constants), [1] PROTEIN_SIDECHAIN_ATOMS (in module hbat.constants.pdb_constants), [1] PROTEIN_SUBSTITUTIONS (in module hbat.constants.pdb_constants), [1]

R

REMOVE_HETEROGENS (hbat.constants.parameters.PDBFixingModes attribute), [1] remove_heterogens() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3], [4] (in module hbat.core.pdb_fixer), [1] REPLACE_NONSTANDARD (hbat.constants.parameters.PDBFixingModes attribute), [1] reset_to_defaults() (hbat.gui.parameter_panel.ParameterPanel method) Residue (class in hbat.core.pdb_parser) (class in hbat.core.structure), [1] RESIDUE_LOOKUP (hbat.constants.parameters.BondDetectionMethods attribute), [1] RESIDUE_TYPE_CODES (in module hbat.constants.pdb_constants)

RESIDUE_TYPES (in module hbat.constants.pdb_constants) RESIDUES (in module hbat.constants.pdb_constants), [1] RESIDUES_WITH_AROMATIC_RINGS (in module hbat.constants.pdb_constants), [1] resolve_preset_path() (in module hbat.cli.main) ResultsPanel (class in hbat.gui.results_panel) RING_ATOMS_FOR_RESIDUES_WITH_AROMATIC_RINGS (in module hbat.constants.pdb_constants), [1] RNA_RESIDUES (in module hbat.constants.pdb_constants), [1] run() (hbat.gui.main_window.MainWindow method) run_analysis() (in module hbat.cli.main)

S

set_parameters() (hbat.gui.parameter_panel.ParameterPanel method)

shape (hbat.core.np_vector.NPVec3D property), [1], [2], [3] SIDECHAIN_ATOMS (in module hbat.constants.pdb_constants), [1]

T

to_array() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] to_dict() (hbat.core.pdb_parser.Atom method) (hbat.core.pdb_parser.Bond method) (hbat.core.pdb_parser.Residue method) (hbat.core.structure.Atom method), [1] (hbat.core.structure.Bond method), [1] (hbat.core.structure.Residue method), [1]

to_list() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] to_tuple() (hbat.core.np_vector.NPVec3D method), [1], [2], [3]

U

unit_vector() (hbat.core.np_vector.NPVec3D method), [1], [2], [3]

update() (hbat.cli.main.ProgressBar method) update_results() (hbat.gui.results_panel.ResultsPanel method)

V

validate() (hbat.constants.parameters.AnalysisParameters method), [1] (hbat.core.analysis.AnalysisParameters method)

validate_input_file() (in module hbat.cli.main) VDW_RADII (hbat.constants.atomic_data.AtomicData attribute), [1] VectorDefaults (class in hbat.constants.misc), [1]

W

WATER_MOLECULES (in module hbat.constants.pdb_constants), [1]

WINDOW_HEIGHT (hbat.constants.misc.GUIDefaults attribute), [1] WINDOW_WIDTH (hbat.constants.misc.GUIDefaults attribute), [1]

X

x (hbat.core.np_vector.NPVec3D property), [1], [2], [3] xb_angle_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] XB_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1]

xb_angle_cutoff (hbat.core.analysis.AnalysisParameters attribute) xb_distance_cutoff (hbat.constants.parameters.AnalysisParameters attribute), [1] XB_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute), [1] xb_distance_cutoff (hbat.core.analysis.AnalysisParameters attribute)

Y

y (hbat.core.np_vector.NPVec3D property), [1], [2], [3]

Z

z (hbat.core.np_vector.NPVec3D property), [1], [2], [3]