Index Symbols | _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z Symbols --covalent-factor command line option --csv command line option --da-distance command line option --fix-method command line option --fix-pdb 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 --save-fixed 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] __del__() (hbat.gui.graphviz_renderer.GraphVizRenderer method) __eq__() (hbat.constants.parameters.AnalysisParameters method) (hbat.core.analysis.AnalysisParameters method) (hbat.core.np_vector.NPVec3D method), [1], [2], [3] (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] __hash__() (hbat.constants.parameters.AnalysisParameters method) (hbat.core.analysis.AnalysisParameters method) __init__() (hbat.ccd.ccd_analyzer.CCDDataManager method) (hbat.ccd.constants_generator.CCDConstantsGenerator method) (hbat.cli.main.ProgressBar method) (hbat.constants.parameters.AnalysisParameters method) (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.PDBParser method), [1], [2] (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.export_manager.ExportDialog method) (hbat.gui.export_manager.ExportManager method) (hbat.gui.geometry_cutoffs_dialog.GeometryCutoffsDialog method) (hbat.gui.graphviz_preferences_dialog.GraphVizPreferencesDialog method) (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.main_window.MainWindow method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.pdb_fixing_dialog.PDBFixingDialog method) (hbat.gui.preset_manager_dialog.PresetManagerDialog method) (hbat.gui.results_panel.ResultsPanel method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) __iter__() (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.constants.parameters.AnalysisParameters method) (hbat.core.analysis.AnalysisParameters 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] 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) ADD_HYDROGENS (hbat.constants.parameters.PDBFixingModes attribute) add_missing_heavy_atoms() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] (in module hbat.core.pdb_fixer), [1], [2] add_missing_hydrogens() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] (in module hbat.core.pdb_fixer), [1], [2] ALL_METHODS (hbat.constants.parameters.BondDetectionMethods attribute) (hbat.constants.parameters.PDBFixingModes attribute) ALL_MODES (hbat.constants.parameters.AnalysisModes attribute) ANALYSIS_MODE (hbat.constants.parameters.ParametersDefault attribute) AnalysisModes (class in hbat.constants.parameters) AnalysisParameters (class in hbat.constants.parameters) (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), [1] Atom (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) AtomicData (class in hbat.constants.atomic_data) B BACKBONE_ATOMS (in module hbat.constants.pdb_constants), [1] BACKBONE_SIDECHAIN_CODES (in module hbat.constants.pdb_constants), [1] BaseVisualizationRenderer (class in hbat.gui.visualization_renderer) 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.structure), [1] bond_file (hbat.ccd.ccd_analyzer.CCDDataManager attribute) bond_url (hbat.ccd.ccd_analyzer.CCDDataManager attribute) BondDetectionMethods (class in hbat.constants.parameters) C ccd_folder (hbat.ccd.ccd_analyzer.CCDDataManager attribute) ccd_manager (hbat.ccd.constants_generator.CCDConstantsGenerator attribute) CCDConstantsGenerator (class in hbat.ccd.constants_generator) CCDDataManager (class in hbat.ccd.ccd_analyzer) center_of_mass() (hbat.core.structure.Residue method), [1] ChainVisualizationWindow (class in hbat.gui.chain_visualization) CHARGED_RESIDUES (in module hbat.constants.pdb_constants) cleanup() (hbat.gui.graphviz_renderer.GraphVizRenderer method) clear() (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) clear_cache() (hbat.utilities.graphviz_utils.GraphVizDetector static method) clear_results() (hbat.gui.results_panel.ResultsPanel method) command line option --covalent-factor --csv --da-distance --fix-method --fix-pdb --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 --save-fixed --summary-only --verbose --version --xb-angle --xb-distance -h -o -q -v input COMPLETE (hbat.constants.parameters.AnalysisModes attribute) compute_distance_matrix() (in module hbat.core.np_vector), [1], [2], [3] CONECT_RECORDS (hbat.constants.parameters.BondDetectionMethods attribute) convert_nonstandard_residues() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] (in module hbat.core.pdb_fixer), [1], [2] CooperativityChain (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] COVALENT_CUTOFF_FACTOR (hbat.constants.parameters.ParametersDefault attribute) COVALENT_RADII (hbat.constants.atomic_data.AtomicData attribute) create_parser() (in module hbat.cli.main) create_renderer() (hbat.gui.visualization_renderer.RendererFactory static method) cross() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] D DEFAULT_ATOMIC_MASS (hbat.constants.atomic_data.AtomicData attribute) DEFAULT_X (hbat.constants.misc.VectorDefaults attribute) DEFAULT_Y (hbat.constants.misc.VectorDefaults attribute) DEFAULT_Z (hbat.constants.misc.VectorDefaults attribute) detect_output_format() (in module hbat.cli.main) 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) 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.HalogenBond property) (hbat.core.analysis.HydrogenBond 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.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) ensure_files_exist() (hbat.ccd.ccd_analyzer.CCDDataManager method) export() (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) export_to_csv() (in module hbat.cli.main) export_to_csv_files() (in module hbat.cli.main) export_to_json() (in module hbat.cli.main) export_to_json_files() (in module hbat.cli.main) export_visualization() (hbat.gui.export_manager.ExportManager method) ExportDialog (class in hbat.gui.export_manager) ExportManager (class in hbat.gui.export_manager) extract_residue_bonds_data() (hbat.ccd.ccd_analyzer.CCDDataManager method) F fields() (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) finish() (hbat.cli.main.ProgressBar method) FIX_PDB_ADD_HEAVY_ATOMS (hbat.constants.parameters.ParametersDefault attribute) FIX_PDB_ADD_HYDROGENS (hbat.constants.parameters.ParametersDefault attribute) FIX_PDB_ENABLED (hbat.constants.parameters.ParametersDefault attribute) fix_pdb_file() (in module hbat.core.pdb_fixer), [1], [2] fix_pdb_file_to_file() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] FIX_PDB_KEEP_WATER (hbat.constants.parameters.ParametersDefault attribute) FIX_PDB_METHOD (hbat.constants.parameters.ParametersDefault attribute) FIX_PDB_REMOVE_HETEROGENS (hbat.constants.parameters.ParametersDefault attribute) FIX_PDB_REPLACE_NONSTANDARD (hbat.constants.parameters.ParametersDefault attribute) fix_structure_file() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] format_results_text() (in module hbat.cli.main) from_atoms() (hbat.core.np_vector.NPVec3D class method), [1], [2], [3] from_dict() (hbat.constants.parameters.AnalysisParameters class method) (hbat.core.analysis.AnalysisParameters class method) 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 generate_analysis_report() (hbat.ccd.constants_generator.CCDConstantsGenerator method) generate_dot() (hbat.gui.graphviz_renderer.GraphVizRenderer method) GeometryCutoffsDialog (class in hbat.gui.geometry_cutoffs_dialog) 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.structure.Residue method), [1] get_atom() (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] (hbat.core.structure.Residue method), [1] get_atoms_by_residue() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_available_components() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_available_engines() (hbat.utilities.graphviz_utils.GraphVizDetector static method) get_available_renderers() (hbat.gui.visualization_renderer.RendererFactory static method) get_backbone_sidechain_interaction() (hbat.core.analysis.HalogenBond method) (hbat.core.analysis.HydrogenBond method) (hbat.core.analysis.PiInteraction method) (hbat.core.interactions.HalogenBond method), [1], [2], [3] (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] get_bonded_atoms() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_bonds() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_bonds_for_atom() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_bonds_involving_atom() (hbat.ccd.ccd_analyzer.CCDDataManager method) get_canvas() (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) get_chain_ids() (hbat.core.pdb_parser.PDBParser method), [1], [2] 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_engine_path() (hbat.utilities.graphviz_utils.GraphVizDetector static method) get_example_presets_directory() (in module hbat.cli.main) get_figure() (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) get_format_info() (hbat.gui.export_manager.ExportManager method) get_graphviz_info() (in module hbat.utilities.graphviz_utils) get_graphviz_version() (hbat.utilities.graphviz_utils.GraphVizDetector static method) get_hydrogen_atoms() (hbat.core.pdb_parser.PDBParser method), [1], [2] 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_last_export_path() (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) get_missing_hydrogen_info() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] get_parameters() (hbat.gui.geometry_cutoffs_dialog.GeometryCutoffsDialog method) (hbat.gui.pdb_fixing_dialog.PDBFixingDialog method) get_partner() (hbat.core.structure.Bond method), [1] get_renderer_name() (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) get_residue_list() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_result() (hbat.gui.geometry_cutoffs_dialog.GeometryCutoffsDialog method) (hbat.gui.preset_manager_dialog.PresetManagerDialog method) get_statistics() (hbat.core.pdb_parser.PDBParser method), [1], [2] get_summary() (hbat.core.analysis.NPMolecularInteractionAnalyzer method) (hbat.core.np_analyzer.NPMolecularInteractionAnalyzer method), [1], [2], [3] get_supported_formats() (hbat.gui.export_manager.ExportManager method) (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) get_supported_layouts() (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) GraphVizDetector (class in hbat.utilities.graphviz_utils) GraphVizPreferencesDialog (class in hbat.gui.graphviz_preferences_dialog) GraphVizRenderer (class in hbat.gui.graphviz_renderer) GUIDefaults (class in hbat.constants.misc) 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] HB_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) HB_DA_DISTANCE (hbat.constants.parameters.ParametersDefault attribute) HB_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault 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.export_manager module hbat.gui.geometry_cutoffs_dialog module hbat.gui.graphviz_preferences_dialog module hbat.gui.graphviz_renderer module hbat.gui.main_window module hbat.gui.matplotlib_renderer module hbat.gui.pdb_fixing_dialog module hbat.gui.preset_manager_dialog module hbat.gui.results_panel module hbat.gui.visualization_renderer module hbat.utilities.atom_utils module hbat.utilities.graphviz_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.structure.Bond method), [1] is_available() (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) 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_graphviz_available() (hbat.utilities.graphviz_utils.GraphVizDetector static method) is_hydrogen() (hbat.core.structure.Atom method), [1] is_metal() (hbat.core.structure.Atom method), [1] J JSON_VERSION (hbat.constants.misc.FileFormats attribute) L LEFT_PANEL_WIDTH (hbat.constants.misc.GUIDefaults attribute) 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) M magnitude() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] main() (in module hbat.cli.main) MainWindow (class in hbat.gui.main_window) MatplotlibRenderer (class in hbat.gui.matplotlib_renderer) MAX_ANGLE (hbat.constants.parameters.ParameterRanges attribute) MAX_BOND_DISTANCE (hbat.constants.parameters.ParametersDefault attribute) MAX_COVALENT_FACTOR (hbat.constants.parameters.ParameterRanges attribute) MAX_DISTANCE (hbat.constants.parameters.ParameterRanges attribute) METAL_ELEMENTS (hbat.constants.atomic_data.AtomicData attribute) MIN_ANGLE (hbat.constants.parameters.ParameterRanges attribute) MIN_BOND_DISTANCE (hbat.constants.parameters.ParametersDefault attribute) MIN_COVALENT_FACTOR (hbat.constants.parameters.ParameterRanges attribute) MIN_DISTANCE (hbat.constants.parameters.ParameterRanges attribute) MIN_HYDROGEN_RATIO (hbat.constants.atomic_data.AtomicData attribute) MIN_WINDOW_HEIGHT (hbat.constants.misc.GUIDefaults attribute) MIN_WINDOW_WIDTH (hbat.constants.misc.GUIDefaults attribute) 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.export_manager hbat.gui.geometry_cutoffs_dialog hbat.gui.graphviz_preferences_dialog hbat.gui.graphviz_renderer hbat.gui.main_window hbat.gui.matplotlib_renderer hbat.gui.pdb_fixing_dialog hbat.gui.preset_manager_dialog hbat.gui.results_panel hbat.gui.visualization_renderer hbat.utilities.atom_utils hbat.utilities.graphviz_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) OPENBABEL_OPERATIONS (hbat.constants.parameters.PDBFixingModes attribute) OUTPUT_EXTENSIONS (hbat.constants.misc.FileFormats attribute) P ParameterRanges (class in hbat.constants.parameters) ParametersDefault (class in hbat.constants.parameters) parse_file() (hbat.core.pdb_parser.PDBParser method), [1], [2] parse_lines() (hbat.core.pdb_parser.PDBParser method), [1], [2] 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) PDBFixer (class in hbat.core.pdb_fixer), [1], [2], [3] PDBFIXER (hbat.constants.parameters.PDBFixingModes attribute) PDBFIXER_OPERATIONS (hbat.constants.parameters.PDBFixingModes attribute) PDBFixerError, [1] (class in hbat.core.pdb_fixer), [1] PDBFixingDialog (class in hbat.gui.pdb_fixing_dialog) PDBFixingModes (class in hbat.constants.parameters) PDBParser (class in hbat.core.pdb_parser), [1], [2] PI_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CBR_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CBR_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CCL_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CCL_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CH_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CH_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CI_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_CI_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_INTERACTION_ATOMS (in module hbat.constants.pdb_constants) PI_INTERACTION_DONOR (in module hbat.constants.pdb_constants) PI_NH_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_NH_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_OH_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_OH_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) pi_residue (hbat.core.analysis.PiInteraction property) (hbat.core.interactions.PiInteraction property), [1], [2], [3] PI_SH_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PI_SH_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) PiInteraction (class in hbat.core.analysis) (class in hbat.core.interactions), [1], [2], [3] prepare_graph_data() (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) PresetManagerDialog (class in hbat.gui.preset_manager_dialog) print_analysis_report() (hbat.ccd.constants_generator.CCDConstantsGenerator method) print_error() (in module hbat.cli.main) print_progress() (in module hbat.cli.main) PROGRESS_BAR_INTERVAL (hbat.constants.misc.GUIDefaults attribute) 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) remove_heterogens() (hbat.core.pdb_fixer.PDBFixer method), [1], [2], [3] (in module hbat.core.pdb_fixer), [1], [2] render() (hbat.gui.graphviz_renderer.GraphVizRenderer method) (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) render_with_graphviz() (hbat.gui.graphviz_renderer.GraphVizRenderer method) RendererFactory (class in hbat.gui.visualization_renderer) REPLACE_NONSTANDARD (hbat.constants.parameters.PDBFixingModes attribute) reset_to_defaults() (hbat.gui.geometry_cutoffs_dialog.GeometryCutoffsDialog method) Residue (class in hbat.core.structure), [1] RESIDUE_LOOKUP (hbat.constants.parameters.BondDetectionMethods attribute) RESIDUE_TYPE_CODES (in module hbat.constants.pdb_constants), [1] 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_last_export_path() (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) set_parameters() (hbat.gui.geometry_cutoffs_dialog.GeometryCutoffsDialog method) (hbat.gui.pdb_fixing_dialog.PDBFixingDialog method) set_title() (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) shape (hbat.core.np_vector.NPVec3D property), [1], [2], [3] show() (hbat.gui.export_manager.ExportDialog method) (hbat.gui.graphviz_preferences_dialog.GraphVizPreferencesDialog method) show_export_dialog() (hbat.gui.export_manager.ExportManager method) show_graphviz_preferences() (in module hbat.gui.graphviz_preferences_dialog) show_quick_export_dialog() (in module hbat.gui.export_manager) SIDECHAIN_ATOMS (in module hbat.constants.pdb_constants), [1] T to_array() (hbat.core.np_vector.NPVec3D method), [1], [2], [3] to_dict() (hbat.constants.parameters.AnalysisParameters method) (hbat.core.analysis.AnalysisParameters 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_layout() (hbat.gui.matplotlib_renderer.MatplotlibRenderer method) (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) (hbat.gui.visualization_renderer.VisualizationRenderer method) update_results() (hbat.gui.results_panel.ResultsPanel method) V validate() (hbat.constants.parameters.AnalysisParameters method) (hbat.core.analysis.AnalysisParameters method) validate_engine() (hbat.utilities.graphviz_utils.GraphVizDetector static method) validate_input_file() (in module hbat.cli.main) validate_layout() (hbat.gui.visualization_renderer.BaseVisualizationRenderer method) VDW_RADII (hbat.constants.atomic_data.AtomicData attribute) VectorDefaults (class in hbat.constants.misc) VisualizationRenderer (class in hbat.gui.visualization_renderer) W WATER_MOLECULES (in module hbat.constants.pdb_constants), [1] WHB_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) WHB_DA_DISTANCE (hbat.constants.parameters.ParametersDefault attribute) WHB_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) WINDOW_HEIGHT (hbat.constants.misc.GUIDefaults attribute) WINDOW_WIDTH (hbat.constants.misc.GUIDefaults attribute) write_residue_bonds_constants() (hbat.ccd.constants_generator.CCDConstantsGenerator method) X x (hbat.core.np_vector.NPVec3D property), [1], [2], [3] XB_ANGLE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) XB_DISTANCE_CUTOFF (hbat.constants.parameters.ParametersDefault attribute) Y y (hbat.core.np_vector.NPVec3D property), [1], [2], [3] Z z (hbat.core.np_vector.NPVec3D property), [1], [2], [3]
