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

- a -

• add() : Coarse_atom< Atom, Point >
• add_abstract_critical_vertex() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• add_bin() : T_WL_Data_Structure_Internal< Conformation, Bin_properties, DS_snapshot_ >
• add_bond() : T_Molecular_covalent_structure< Particle_info_ >
• add_chain() : MISA
• add_cif_atom_to_sbl_residue() : T_Molecular_system_loader< Molecular_system_ >
• add_coarse_atom() : Coarse_residue< Residue, Chain, Coarse_atom_ >
• add_connected_component() : T_Sub_graph< Graph >
• add_critical_vertex() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• add_dataset() : BM_Database
• add_datasets_from_directory() : BM_Database
• add_edge() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >, T_Sub_graph< Graph >
• add_file_option() : BM_Run_specification_tuple
• add_free_edges() : T_Sub_graph< Graph >
• add_helper() : T_Module_based_workflow< Dummy >
• add_induced_edges() : T_Sub_graph< Graph >
• add_input_file_name() : T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Spheres_3_file_loader< Sphere3, Point3 >
• add_input_gui_json() : GUIInputPanelJsonGenerator
• add_known_solutions() : MCI_solutions
• add_loader() : T_Module_based_workflow< Dummy >
• add_namespace() : PALSE_xml_DB
• add_new_representation() : T_PyMOL_viewer< Dummy >
• add_node_col() : lambda_matrix< graph >
• add_node_row() : lambda_matrix< graph >
• add_option() : BM_Run_specification_tuple
• add_option_from_nvp_list() : BM_IFO_set
• add_options() : Maximum_spanning_tree_property, T_Random_spanning_tree_property< Dummy >, T_Spanning_tree_solver< IntersectionGraph, StopCondition, SpanningTreeGenerator, Algorithm >, T_Tree_solver< Graph >, 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 >, 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_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_option_description< Dummy >, T_Molecular_interfaces_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, 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 >
• add_particle() : T_Molecular_covalent_structure< Particle_info_ >
• add_pdb_namespaces() : PALSE_xml_DB
• add_point() : T_Stable_manifold_as_list_traits< Point >
• add_point_to_stable_manifold() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• add_run_specification() : BM_Batch, BM_Run_specification_ensemble
• add_secondary_structure_element() : Molecular_system< Items, Point >
• add_ss_bond() : Molecular_system< Items, Point >
• add_update_panel_gui_json() : GUIUpdatePanelJsonGenerator
• add_vertex() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >, T_Sub_graph< Graph >
• add_vertex_with_induced_edges() : T_Sub_graph< Graph >
• add_water() : T_Molecular_covalent_structure_builder_for_protein_martini< Molecular_covalent_structure_ >, T_Molecular_covalent_structure_builder_for_proteins< Molecular_covalent_structure_ >
• add_XML_etree() : PALSE_xml_DB
• align() : T_Alignment_engine_sequences_seqan< SequenceType, SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >
• allow() : lambda_matrix< graph >
• alpha_angles_begin() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• alpha_angles_end() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• alternate_location() : Molecular_atom< System_, Point >, Molecular_system< Items, Point >
• analyze_pairs() : KpaxAlignmentGraph
• append() : PALSE_xml_DB
• append_solution_tuple() : MCI_solutions
• apply_mapping() : Chain_instances, Interface_oneside
• apply_windows() : MISA
• are_1_2() : T_Molecular_covalent_structure< Particle_info_ >
• are_1_3() : T_Molecular_covalent_structure< Particle_info_ >
• are_1_4() : T_Molecular_covalent_structure< Particle_info_ >
• are_files_valid() : T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_system_loader< Molecular_system_ >
• atom_name() : Molecular_atom< System_, Point >, T_Atom_with_flat_info< NT >
• atom_serial_number() : Molecular_atom< System_, Point >
• T_Alignment_engine() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• T_Alignment_engine_structures() : T_Alignment_engine_structures< StructureType, AlignerAlgorithm, FT, MolecularDistance >
• T_Alignment_engine_structures_apurva() : T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance >
• T_Alignment_engine_structures_identity() : T_Alignment_engine_structures_identity< StructureType, FT, MolecularDistance >
• T_Alignment_engine_structures_iterative_identity() : T_Alignment_engine_structures_iterative_identity< StructureType, FT, MolecularDistance >
• T_Alignment_engine_structures_kpax() : T_Alignment_engine_structures_kpax< StructureType, FT, MolecularDistance >
• T_Alignment_residue() : T_Alignment_residue< ResidueBase >
• T_Alignment_sequence() : T_Alignment_sequence< ResidueBase >
• T_Alpha_complex_base_3() : T_Alpha_complex_base_3< Dt, AlphaExactComparisonTag >
• T_Archive_file_loader() : T_Archive_file_loader< InputArchive, SerializedData >