Here is a list of all documented functions with links to the class documentation for each member:

- g -

• gather_chains_by_MISA_id() : MISA_constructor
• generate() : GUIInputPanelJsonGenerator, GUIUpdatePanelJsonGenerator
• generate_codes() : CodeGenerator, GeneratorPanel, GeneratorPyQt6, GeneratorTkinter
• get_adjacent_vertices() : T_Sub_graph< Graph >
• get_all_data() : T_Archive_file_loader< InputArchive, SerializedData >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Numbers_file_loader< FT, Tag >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >
• get_all_data_values_from_database() : PALSE_xml_DB
• get_all_data_values_from_database_compare_to() : PALSE_xml_DB
• get_all_data_values_from_database_equal_to() : PALSE_xml_DB
• get_all_data_values_from_database_greater_than() : PALSE_xml_DB
• get_all_data_values_from_database_lower_than() : PALSE_xml_DB
• get_all_data_values_from_elements() : PALSE_xml_DB
• get_all_data_values_from_root() : PALSE_xml_DB
• get_all_data_values_from_tree() : PALSE_xml_DB
• get_all_elements_from_database() : PALSE_xml_DB
• get_all_elements_from_root() : PALSE_xml_DB
• get_all_elements_from_tree() : PALSE_xml_DB
• get_alpha_angle() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_alpha_complex() : T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• get_alpha_complex_edges() : T_Union_of_balls_medial_axis_3_builder< UnionOfBallsMedialAxis3 >
• get_angle_axis() : T_Rotation_3< Point_container_iterator, NT, Back_inserter >
• get_annotated_contacts() : MCI_specification
• get_annotations() : T_Particle_with_annotations< ParticleBase, AnnotationsType >
• get_annotator() : T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >
• get_arc_out() : dp_mat_apurva< graph, lambda_matrix >
• Get_area_of_dual_of_edge() : T_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_area_of_dual_of_edge
• get_atom_serial_number_particle() : T_Molecular_covalent_structure< Particle_info_ >
• get_attribute() : PALSE_xml_DB
• get_ball_shelling_forest() : T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >
• get_base_parser() : SBL_base_parser
• get_beta_angle() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_bicolor_interface() : T_Molecular_interfaces_builder< ParticleWithSystemLabelTraits, MolecularModelClassifier >, T_Molecular_interfaces_module< ModuleTraits >
• get_bin_index_from_energy() : T_WL_Data_Structure_Internal< Conformation, Bin_properties, DS_snapshot_ >
• get_bond() : T_Molecular_covalent_structure< Particle_info_ >
• get_bond_angle() : Molecular_coordinates_utilities
• get_bond_angle_ordered_vectors() : Molecular_coordinates_utilities
• get_bond_length() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond
• get_bond_rep() : T_Molecular_covalent_structure< Particle_info_ >
• get_boundary() : T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• get_bounds_info() : T_Minimizer_Ipopt_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >, T_Minimizer_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >
• get_buried_surface_area() : T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >
• get_by_particle_list() : T_Buried_surface_area_with_labels< ParticleWithSystemLabelTraits, ParticleBSARecord, FT >
• get_canonical_rep() : T_Molecular_covalent_structure< Particle_info_ >
• get_cells_location() : T_Union_of_balls_medial_axis_3_builder< UnionOfBallsMedialAxis3 >
• get_center_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle
• get_center_bond() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_chain() : T_Molecular_covalent_structure< Particle_info_ >, T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_chain_from_sheet_identifier() : Molecular_system< Items, Point >
• get_chain_id() : Chain_selection
• get_child() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_circle_resolution() : T_PyMOL_viewer< Dummy >
• get_classifier() : T_Molecular_structure_classifier_module< ModuleTraits >
• get_color_rgb() : T_PyMOL_viewer< Dummy >
• get_common_cofaces() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_common_hierarchy() : PALSE_xml_DB
• get_common_hierarchy_as_list() : PALSE_xml_DB
• get_common_hierarchy_as_xml() : PALSE_xml_DB
• get_conformations() : T_Conformation_loader< Conformation_builder_ >
• get_connected_component() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_connected_component_before_death() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_connected_components() : T_Sub_graph< Graph >
• get_consensus_contacts() : MCI_solutions
• get_consensus_solutions() : MCI_solutions
• get_consensus_solutions_obj() : MCI_output_preprocessing
• get_contact_score() : MCI_solutions
• get_contacts() : MCI_set_of_contacts
• get_contacts_at_interface() : T_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >
• get_contacts_from_file() : MCI_set_of_contacts
• get_contacts_to_counts_map() : MCI_solutions
• get_correct_value() : problem< graph, dp_mat, lambda_mat, parameter >
• get_cost_and_runtime_pair_for_a_solution() : MCI_solutions
• get_cost_components_average() : MCI_solutions
• get_count_for_the_contact_from_the_map() : MCI_solutions
• get_covalent_structure() : T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >
• get_coverage_score_tuple() : MCI_analysis
• get_critical_point() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_crossing_edges() : T_Union_of_balls_medial_axis_3_builder< UnionOfBallsMedialAxis3 >
• get_current_set_of_labels_index() : T_Domain_label_traits< Dummy >
• get_data() : BM_Dataset, T_Archive_file_loader< InputArchive, SerializedData >, T_Multiple_archives_serialization_xml_iarchive< DataType, InputArchive >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Numbers_file_loader< FT, Tag >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >
• get_data_source_file() : PALSE_xml_DB
• get_data_structure() : T_Wang_Landau< Physical_System, Move_Set_Traits, WL_DS_, NumCores >
• get_datasets() : BM_Database
• get_default_color() : T_PyMOL_viewer< Dummy >
• get_degree() : T_Sub_graph< Graph >
• get_density() : T_WL_Data_Structure_Internal< Conformation, Bin_properties, DS_snapshot_ >
• get_descendant_ancestor_subgraph() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_dic_sequence() : Residue_mapping
• get_dihedral_angle() : Molecular_coordinates_utilities, T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_directed_acyclic_graph() : T_Hierarchical_labels_forest< MolecularSystemLabelsTraits >, T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_directory() : BM_Dataset
• get_disconnectivity_forest() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_dp_mat_apurva() : problem< graph, dp_mat, lambda_mat, parameter >
• Get_dual_of_edge() : T_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_dual_of_edge
• Get_dual_of_facet() : T_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_dual_of_facet
• get_edge() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >, T_Triangulation_extension_3_base< Triangulation3 >::Canonical_edge
• get_edge_radius() : T_PyMOL_viewer< Dummy >
• get_edge_subgraph() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_edges() : T_Sub_graph< Graph >
• get_executable_path() : BM_Run_specification_ensemble, BM_Run_specification_tuple
• get_extra_classifier() : T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Molecular_structure_classifier_module< ModuleTraits >
• get_face_shelling_forest() : T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >
• get_facet() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_facet
• get_false_positive_count() : MCI_set_of_contacts
• get_file_names() : T_Numbers_file_loader< FT, Tag >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >
• get_filenames() : PALSE_xml_DB
• get_first_annotator() : T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >
• get_first_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond
• get_first_chain() : Molecular_SS_bond< System >
• get_first_partner() : T_Bicolor_interface_data_structure_base< MolecularInterfaceDataStructure >, T_Mediated_interface_data_structure_base< MolecularInterfaceDataStructure >, T_Tricolor_interface_data_structure_base< MolecularInterfaceDataStructure >
• get_first_residue() : Molecular_SS_bond< System >
• get_first_sos() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• get_first_vertex() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_edge
• get_forbidden_sets_of_length() : MCI_bootstrap
• get_geometric_model() : T_Spheres_3_file_loader< Sphere3, Point3 >
• get_geometric_model_ensemble() : T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >
• Get_global_minimum() : T_Frechet_mean_S1< Kernel >
• get_graph() : problem< graph, dp_mat, lambda_mat, parameter >, T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Graph_loader< GraphType, FT >
• get_height() : T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_incident_cell() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_facet
• get_induced_subgraph() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_infinite_factor() : T_PyMOL_viewer< Dummy >
• get_infinite_persistent_critical_vertices() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_input_file_name() : T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >
• get_interfaces_builder() : T_Molecular_interfaces_module< ModuleTraits >
• get_interfaces_graph() : T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >
• get_irreplaceable_contacts() : MCI_bootstrap
• get_is_in_partner() : T_Buried_surface_area_without_label_module< ModuleTraits >
• get_is_in_patch() : T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >
• get_iter() : problem< graph, dp_mat, lambda_mat, parameter >
• get_lambda_mat() : problem< graph, dp_mat, lambda_mat, parameter >
• get_landmarks() : T_Dijkstra_shortest_paths_with_landmarks< Graph, IsLandmark >
• get_lb() : branch_and_bound< problem >, problem< graph, dp_mat, lambda_mat, parameter >
• get_lb_father() : problem< graph, dp_mat, lambda_mat, parameter >
• get_left_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle, T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_left_bond() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle, T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_left_center_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_leftmost_data_value_from_tree() : PALSE_xml_DB
• get_leftmost_data_values_from_database() : PALSE_xml_DB
• get_length_of_contacts_to_counts_map() : MCI_solutions
• get_lists_of_run_options() : BM_Batch, BM_Run_specification_ensemble
• get_lnc() : lambda_matrix< graph >
• get_lo() : problem< graph, dp_mat, lambda_mat, parameter >
• Get_local_minimas() : T_Frechet_mean_S1< Kernel >
• get_lower_bound_of_stable_manifold() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_mapped_extreme_indexes() : Interface_oneside
• get_max_degree() : T_Sub_graph< Graph >
• get_mediated_interface() : T_Molecular_interfaces_builder< ParticleWithSystemLabelTraits, MolecularModelClassifier >, T_Molecular_interfaces_module< ModuleTraits >
• get_mediator() : T_Mediated_interface_data_structure_base< MolecularInterfaceDataStructure >, T_Tricolor_interface_data_structure_base< MolecularInterfaceDataStructure >
• get_mediator_classifier() : T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Molecular_structure_classifier_module< ModuleTraits >
• get_mediators_forest() : T_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >
• get_minimal_elements_from() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >
• get_model() : Molecular_system< Items, Point >
• get_model_number() : T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >
• get_module_instance_name() : Module_base
• get_molecular_covalent_structure_loader() : T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >
• get_molecular_covalent_structures() : T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >
• get_molecular_model() : T_Molecular_structure_classifier_module< ModuleTraits >
• get_molecular_system_loader() : T_Conformation_loader< Conformation_builder_ >
• get_molecular_systems() : T_Molecular_system_loader< Molecular_system_ >, T_Spheres_3_file_loader< Sphere3, Point3 >
• get_molecule() : T_Molecular_covalent_structure< Particle_info_ >
• get_molecules() : T_Molecular_covalent_structure< Particle_info_ >
• get_Morse_function() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_Morse_function_value() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >, T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_Morse_index() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_name() : T_Alignment_residue< ResidueBase >, T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >, Loader_base, T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Conformation_loader< Conformation_builder_ >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_system_loader< Molecular_system_ >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Numbers_file_loader< FT, Tag >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, No_particle_annotator, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, Module_base, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Module_based_workflow< Dummy >, T_Module_condition< Module, Predicate >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• get_nb_prb_in_list() : branch_and_bound< problem >
• get_neighborhood() : T_Molecular_geometric_model_classifier_for_alpha_complex< AlphaComplexOfMolecularModel >, T_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >
• get_nlp_info() : T_Minimizer_Ipopt_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >, T_Minimizer_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >
• get_node_col() : lambda_matrix< graph >
• get_node_degrees() : Genetrank_network_statistical_analysis
• get_node_row() : lambda_matrix< graph >
• get_nucleic_acid_representations() : T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >
• get_num_of_primitive_label() : T_Hierarchical_labels_forest< MolecularSystemLabelsTraits >
• get_number_of_bonds() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_number_of_buried_particles() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• get_number_of_chains() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_number_of_children() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_number_of_cofaces() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_number_of_connected_components() : T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• get_number_of_contacts() : T_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >, T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• get_number_of_contacts_at_interface() : T_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >
• get_number_of_critical_vertices() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_number_of_data() : T_Archive_file_loader< InputArchive, SerializedData >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Numbers_file_loader< FT, Tag >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >
• get_number_of_edges() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_number_of_embedded_bonds() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_number_of_embedded_particles() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_number_of_faces() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_number_of_independent_sets() : T_Union_find_base< T, VertexDS, InternalVertexTag >, T_Union_find_contains_with_map< T >
• get_number_of_labels() : Extra_label_traits, No_label_traits, One_label_traits, T_Domain_label_traits< Dummy >, T_IG_label_traits< Dummy >, Water_label_traits
• get_number_of_layers() : T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_number_of_loaded_covalent_structures() : T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >
• get_number_of_loaded_data() : T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >
• get_number_of_loaded_geometric_model_ensembles() : T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >
• get_number_of_loaded_geometric_models() : T_Spheres_3_file_loader< Sphere3, Point3 >
• get_number_of_modeled_particles() : T_Molecular_covalent_structure< Particle_info_ >
• get_number_of_parents() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_number_of_particles() : T_Molecular_covalent_structure< Particle_info_ >, T_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >, T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >, T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_number_of_primitive_labels() : Extra_label_traits, No_label_traits, One_label_traits, T_Domain_label_traits< Dummy >, T_IG_label_traits< Dummy >, Water_label_traits
• get_number_of_vertices() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >, T_Union_find_base< T, VertexDS, InternalVertexTag >, T_Union_find_contains_with_map< T >
• get_nz_sub_gr() : problem< graph, dp_mat, lambda_mat, parameter >
• get_oligomers() : MCI_specification
• get_omega_angle_Cter() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_omega_angle_Nter() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_opposite_vertex() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_facet
• get_options() : T_Module_option_description< Dummy >
• get_options_list() : BM_IFO_set
• get_or_create_model() : Molecular_system< Items, Point >
• get_orientation() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >
• get_output_directory() : BM_Batch
• get_output_prefix() : T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Conformation_loader< Conformation_builder_ >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_system_loader< Molecular_system_ >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Numbers_file_loader< FT, Tag >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, No_particle_annotator, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Module_based_workflow< Dummy >, T_Module_condition< Module, Predicate >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_option_description< Dummy >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• Get_p_mean() : T_Frechet_mean_S1< Kernel >
• get_parent() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_parent_of() : Extra_label_traits, No_label_traits, One_label_traits, T_Domain_label_traits< Dummy >, T_IG_label_traits< Dummy >, Water_label_traits
• get_particle() : T_Particle_vertex_base< ParticleTraits, GT, Vb >
• get_particle_rep() : T_Molecular_covalent_structure< Particle_info_ >
• get_particles() : T_Alpha_complex_of_molecular_model_module< ModuleTraits >
• get_particles_in_molecule() : T_Molecular_covalent_structure< Particle_info_ >
• get_partner_classifier() : T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Molecular_structure_classifier_module< ModuleTraits >
• get_partners_forest() : T_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >
• get_paths() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_persistence_diagram() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_persistence_intervals() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_phi_angle() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_point() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_points() : T_Stable_manifold_as_list_traits< Point >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >
• get_polypeptide_chain_representations() : T_Protein_representation< PolypeptideChain >
• get_pool_of_contacts_explored() : MCI_specification
• get_primitive_label_from_num() : T_Hierarchical_labels_forest< MolecularSystemLabelsTraits >
• get_protein_representations() : T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >
• get_protein_to_neighbors_in_union_of_solutions_map() : MCI_solutions
• get_protein_to_neighbors_map() : MCI_set_of_contacts
• get_psi_angle() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• get_quaternion() : T_Rotation_3< Point_container_iterator, NT, Back_inserter >
• get_raw_extreme_indexes() : Interface_oneside
• get_reachability_matrix() : Genetrank_network_statistical_analysis
• get_reference_centroid() : T_Point_cloud_rigid_registration_3< FT >
• get_report_mode() : Module_base
• get_right_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle, T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_right_bond() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle, T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_right_center_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle
• get_rightmost_data_value_from_tree() : PALSE_xml_DB
• get_rightmost_data_values_from_database() : PALSE_xml_DB
• Get_roots() : T_Frechet_mean_S1< Kernel >
• get_rotation() : T_Point_cloud_rigid_registration_3< FT >
• get_rotation_matrix() : T_Rotation_3< Point_container_iterator, NT, Back_inserter >
• get_run_commands() : BM_Batch
• get_run_options() : BM_Run_specification_tuple
• get_sampling() : T_Union_of_balls_mesh_3_module< ModuleTraits >
• get_second_annotator() : T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >
• get_second_atom() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond
• get_second_chain() : Molecular_SS_bond< System >
• get_second_partner() : T_Bicolor_interface_data_structure_base< MolecularInterfaceDataStructure >, T_Mediated_interface_data_structure_base< MolecularInterfaceDataStructure >, T_Tricolor_interface_data_structure_base< MolecularInterfaceDataStructure >
• get_second_residue() : Molecular_SS_bond< System >
• get_second_sos() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• get_second_vertex() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_edge
• get_secondary_data() : T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >
• get_set_of_solutions() : MCI_solutions
• get_size() : problem< graph, dp_mat, lambda_mat, parameter >
• get_size_of_frontier() : T_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >, T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• get_size_of_independent_set() : T_Union_find_base< T, VertexDS, InternalVertexTag >, T_Union_find_contains_with_map< T >
• get_solution() : branch_and_bound< problem >, problem< graph, dp_mat, lambda_mat, parameter >
• get_solution_score() : MCI_set_of_contacts, MCI_solutions
• get_solve_time() : branch_and_bound< problem >, problem< graph, dp_mat, lambda_mat, parameter >
• get_spatial_search_engine() : T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >
• get_spoke_angles() : Genetrank_gene_radar
• Get_squared_length_of_dual_of_facet() : T_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_squared_length_of_dual_of_facet
• get_ss_bonds() : Molecular_system< Items, Point >
• get_stable_manifold() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_stable_manifold_partition() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_starting_point() : T_Minimizer_Ipopt_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >, T_Minimizer_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >
• get_status() : problem< graph, dp_mat, lambda_mat, parameter >
• get_structure_classifier() : T_Molecular_interfaces_module< ModuleTraits >
• get_sub_structure() : T_Molecular_covalent_structure< Particle_info_ >
• get_subgraph() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• get_sublevelsets_connected_components() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• get_successful() : Genetrank_Translations
• get_surface_volume() : T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• get_the_list_with_signed_scores() : MCI_analysis
• get_the_unique_chain() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_top_scoring_consensus_contacts() : MCI_solutions
• get_top_scoring_contacts() : MCI_solutions
• get_torsion_angle() : Molecular_coordinates_utilities
• get_total_number_of_residues() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• get_translation() : T_Point_cloud_rigid_registration_3< FT >
• get_transportation_plans() : T_Earth_mover_distance_module< ModuleTraits >
• get_triangulation() : T_Alpha_complex_of_molecular_model_module< ModuleTraits >
• get_tricolor_interface() : T_Molecular_interfaces_builder< ParticleWithSystemLabelTraits, MolecularModelClassifier >, T_Molecular_interfaces_module< ModuleTraits >
• get_tuple_data() : BM_Dataset
• get_ub() : branch_and_bound< problem >, problem< graph, dp_mat, lambda_mat, parameter >
• get_ub_father() : problem< graph, dp_mat, lambda_mat, parameter >
• get_union_find_index() : Union_find_vertex_data_structure_base
• get_union_of_contacts() : MCI_solutions
• get_up() : problem< graph, dp_mat, lambda_mat, parameter >
• get_upper_bound_of_stable_manifold() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• get_valence_angle() : T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle
• get_vertex_radius() : T_PyMOL_viewer< Dummy >
• get_vertex_resolution() : T_PyMOL_viewer< Dummy >
• get_vertices() : MCI_specification, T_Sub_graph< Graph >
• T_Graph_loader() : T_Graph_loader< GraphType, FT >