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

- c -

• c4ps_begin() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• c4ps_end() : T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• calc_arcs_out() : dp_mat_apurva< graph, lambda_matrix >
• call_to_clustalo() : Residue_mapping
• calphas_begin() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• calphas_end() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• cancel_pair() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• Canonical_edge() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_edge
• Canonical_facet() : T_Triangulation_extension_3_base< Triangulation3 >::Canonical_facet
• chain_identifier() : Molecular_chain< System >, T_Alignment_residue< ResidueBase >
• Chain_selection() : Chain_selection
• chains_begin() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• chains_end() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• charge() : Molecular_atom< System_, Point >
• check_cst_col_node() : problem< graph, dp_mat, lambda_mat, parameter >
• check_cst_row_node() : problem< graph, dp_mat, lambda_mat, parameter >
• check_filesystem_directory_exists() : Module_base
• check_options() : 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_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_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 >
• check_specification() : BM_Batch
• check_validity() : T_Molecular_system_loader< Molecular_system_ >
• children_begin() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• children_end() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• clear() : T_Union_find_base< T, VertexDS, InternalVertexTag >, T_Union_find_contains_with_map< T >
• clear_children() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• clear_lambda() : lambda_matrix< graph >
• clear_parents() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• clear_vertex() : T_Directed_acyclic_graph< VertexProperty, EdgeProperty >, T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• clone() : Module_base, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >
• clusters_in_meta_cluster_begin() : T_Spanning_tree_solver< IntersectionGraph, StopCondition, SpanningTreeGenerator, Algorithm >
• cofaces_begin() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• cofaces_end() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• compare_against_solution_set() : MCI_solutions
• compute_and_get_contacts_stats() : MCI_analysis
• compute_and_store_false_positive_counts() : MCI_solutions
• compute_and_store_solution_scores() : MCI_solutions
• compute_area() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• compute_consensus_interface() : Interface_pool
• compute_current_score() : T_Sub_graph< Graph >
• compute_curvature() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• compute_curvatures() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• compute_interface() : Interface_oneside
• compute_mapping() : Residue_mapping
• compute_mapping_MSA() : MISA
• compute_mapping_no_MSA() : MISA
• compute_mean_signed_curvature() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• compute_mean_unsigned_curvature() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• compute_MSA() : Residue_mapping
• compute_perimeter() : T_Molecular_interfaces_module_statistics< MolecularStructureClassifier >
• connect_critical_vertices() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• connected() : Union_find_DS
• connected_components_begin() : T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• connected_components_end() : T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• const_find_set() : T_Union_find_base< T, VertexDS, InternalVertexTag >
• construct_bbox_3_object() : T_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >
• construct_cartesian_const_iterator_3_object() : T_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >
• construct_point_3_object() : T_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >
• contacts_begin() : T_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >, T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• contacts_end() : T_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >, T_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >
• convert() : UiToJsonConverter
• convert_csvfile_to_xmlfile() : PALSE_DS_manipulator
• convert_listoflists_to_list() : PALSE_DS_manipulator
• convert_PDB_atom_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_chain_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_header_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_model_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_residue_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_structure_to_XML_ElementTree() : BioPDB_vs_XML_Etree
• convert_PDB_to_XML_Etree() : BioPDB_vs_XML_Etree
• convert_prefix_to_uri() : PALSE_xml_DB
• convert_python3_dictionary_to_XML_Etree() : Python_dico_vs_XML_Etree
• convert_XML_Etree_to_python3_dictionary() : Python_dico_vs_XML_Etree
• coplanar_side_of_bounded_circle_3_object() : T_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >
• count_landmarks() : T_Dijkstra_shortest_paths_with_landmarks< Graph, IsLandmark >, T_Geodesic_distances_generation< Graph, LandmarkFunctor, LandmarkInfo_functor >
• create() : THREEJSBuilder
• create_all_istring() : MISA
• create_chain() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >
• create_coarse_atoms() : Coarse_residue< Residue, Chain, Coarse_atom_ >
• create_FASTA() : Residue_mapping
• create_one_istring() : MISA
• create_residue_to_cc_mapping() : KpaxAlignmentGraph
• create_subproblem() : problem< graph, dp_mat, lambda_mat, parameter >
• critical_vertices_begin() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• critical_vertices_end() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• T_Cluster_engine_k_means_com_Sd() : T_Cluster_engine_k_means_com_Sd< VectorType, CenterOfMassInitializer >
• T_Conformation_loader() : T_Conformation_loader< Conformation_builder_ >
• T_Container_of_containers_const_iterator() : T_Container_of_containers_const_iterator< OuterContainerConstIterator >
• T_Container_of_containers_iterator() : T_Container_of_containers_iterator< OuterContainerIterator >
• T_Container_of_containers_iterator_base() : T_Container_of_containers_iterator_base< OuterContainerIterator, InnerContainerIterator >