A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X

A: AB_label_traits (SBL::Models); Accept_all_occupancy_policy (ESBTL); Accept_none_occupancy_policy (ESBTL); T_AD_buffer (SBL::CSB); T_AD_stack (SBL::CSB); T_Aligner_sequence_seqan_wrapper (SBL::CSB); T_Aligner_structure_apurva_wrapper (SBL::CSB); T_Alignment_engine (SBL::CSB); T_Alignment_engine_sequences_seqan (SBL::CSB); T_Alignment_engine_structures (SBL::CSB); T_Alignment_engine_structures_apurva (SBL::CSB); T_Alignment_engine_structures_identity (SBL::CSB); T_Alignment_engine_structures_iterative_identity (SBL::CSB); T_Alignment_engine_structures_kpax (SBL::CSB); T_Alignment_residue (SBL::CSB); T_Alignment_sequence (SBL::CSB); T_Alignment_sequences_module (SBL::Modules); T_Alignment_structures_module (SBL::Modules); All_atom_system_builder (ESBTL); T_Alpha_complex_base_3 (SBL::CSB); T_Alpha_complex_cell_base_3 (SBL::CSB); T_Alpha_complex_of_molecular_model (SBL::CSB); T_Alpha_complex_of_molecular_model_module (SBL::Modules); T_Alpha_complex_of_molecular_model_traits (SBL::CSB); T_Alpha_complex_vertex_base_3 (SBL::CSB); And_functors (ESBTL); T_Angular_internal_distance (SBL::CSB); T_ANN_FLANN_wrapper (SBL::GT); T_ANN_meta (SBL::GT); T_ANN_metric_space_LAESA (SBL::GT); T_ANN_metric_space_proximity_tree (SBL::GT); Annotated_sequence (SBL.Sequence_annotators); T_Dynamic_annotator_for_atoms::T_Annotations_with_dynamic (SBL::Models); T_Dynamic_annotator_for_atoms::T_Annotations_with_dynamic< void, DynamicAnnotation > (SBL::Models); T_Archive_file_loader (SBL::IO); Atom_data (SBL.Protein_complex_analysis_molecular_data_structures); Atom_list_occupancy_policy (ESBTL); T_Atom_with_flat_info (SBL::Models); T_Atom_with_flat_info_and_annotations_traits (SBL::Models); T_Atom_with_flat_info_traits (SBL::Models); T_Atom_with_flat_info_traits::Atom_with_flat_infos_builder (SBL::Models); T_Atom_with_hierarchical_info_and_annotations_traits (SBL::Models); T_Atom_with_hierarchical_info_traits (SBL::Models); Atomic_contact_data (SBL.Protein_complex_analysis_molecular_data_structures)

B: B_factor_color_engine (SBL.Multiple_interface_string_alignment); B_factor_coloring_parser (SBL.Multiple_interface_string_alignment); T_Polypeptide_chain_representation::Backbone_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Backbone_iterator (SBL::CSB); T_Delaunay_triangulation_spherical_traits_3_base::Base (SBL::GT); T_Betti_numbers_1 (SBL::GT); T_Betti_numbers_2 (SBL::GT); T_Bicolor_interface_data_structure_base (SBL::CSB); T_Bicolor_interface_oserialization (SBL::Modules); T_Bicolor_interface_oserialization (SBL::CSB); T_Bin_properties (SBL::GT); Bin_properties_Internal (SBL::GT); T_Binet_Cauchy_kernel_score (SBL::CSB); BioPDB_vs_XML_Etree (SBL.PALSE); BM_Batch (SBL.Batch_manager); BM_Database (SBL.Batch_manager); BM_Dataset (SBL.Batch_manager); BM_Run_specification_ensemble (SBL.Batch_manager); BM_Run_specification_tuple (SBL.Batch_manager); T_Polypeptide_chain_representation::Bond (SBL::CSB); T_Polypeptide_chain_representation::Bond_angle (SBL::CSB); T_Polypeptide_chain_representation::Bond_angle_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Bond_angle_iterator (SBL::CSB); T_Bond_angles_visitor (SBL::CSB); T_Polypeptide_chain_representation::Bond_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Bond_iterator (SBL::CSB); T_Bonded_particles_visitor (SBL::CSB); branch_and_bound; BSA_color_engine (SBL.Multiple_interface_string_alignment); BSA_coloring_parser (SBL.Multiple_interface_string_alignment); T_Buried_surface_area_with_labels (SBL::CSB); T_Buried_surface_area_with_labels_module (SBL::Modules); T_Buried_surface_area_without_label (SBL::CSB); T_Buried_surface_area_without_label_module (SBL::Modules)

C: T_Triangulation_extension_3_base::Canonical_edge (SBL::GT); T_Triangulation_extension_3_base::Canonical_facet (SBL::GT); T_Canonize_conformation (SBL::CSB); T_Cell_complex_shelling_diagram (SBL::CADS); T_Union_of_balls_boundary_patch_shelling_3::Face_complex_traits::Cell_handle (SBL::GT); Chain_data (SBL.Protein_complex_analysis_molecular_data_structures); Chain_instances (SBL.Multiple_interface_string_alignment); T_Chain_label_traits (SBL::Models); Chain_label_traits (SBL::Models); T_Chains_residues_contiguous_indexer (SBL::CSB); Class_II_filter (SBL.Sequence_filters); T_Cluster_engine_k_means (SBL::GT); T_Cluster_engine_k_means_center_of_mass (SBL::GT); T_Cluster_engine_k_means_com_euclidean (SBL::GT); T_Cluster_engine_k_means_com_Sd (SBL::GT); T_Cluster_engine_k_means_point_selector_minimax (SBL::GT); T_Cluster_engine_k_means_point_selector_plus_plus (SBL::GT); T_Cluster_engine_k_means_point_selector_random (SBL::GT); T_Cluster_engine_module (SBL::Modules); T_Cluster_engine_Morse_theory_based (SBL::GT); cMISA_constructor (SBL.Multiple_interface_string_alignment); cMISA_recorder (SBL.Multiple_interface_string_alignment); Coarse_atom (SBL::CSB); Coarse_atom (ESBTL); Coarse_atoms_iterators (ESBTL); Coarse_atoms_iterators (SBL::CSB); Coarse_creator_closest_to_barycenter (SBL::CSB); Coarse_creator_closest_to_barycenter (ESBTL); Coarse_creator_two_barycenters (SBL::CSB); Coarse_creator_two_barycenters (ESBTL); Coarse_residue (SBL::CSB); Coarse_residue (ESBTL); Color_of_atom (ESBTL); Color_of_residues (ESBTL); ColorbarTools (SBL.Multiple_interface_string_alignment); Colored_MISA (SBL.Multiple_interface_string_alignment); Combinations_of_variables_model_evaluation (SBL.Combinations_of_variables_model_evaluation); T_Combined_Move_Params (SBL::GT); T_Combined_Move_Set (SBL::GT); T_Combined_Move_Set_Controller (SBL::GT); T_Combined_Move_Stats (SBL::GT); Combined_WL_Move_Set_Data_Interface (SBL::GT); Complex_data_collector (SBL.Protein_complex_analysis_molecular_data_structures); Compute_interface_lRMSD (SBL.Multiple_interface_string_alignment); T_Conformation_builder_cartesian_default (SBL::CSB); T_Conformation_builder_cartesian_default (SBL::Models); T_Conformation_loader (SBL::IO); T_Conformation_traits (SBL::CSB); T_Conformation_traits< CGAL::Point_d< Kernel > > (SBL::CSB); T_Conformation_traits< std::vector< NT > > (SBL::CSB); T_Conformation_traits< T_Conformation_as_vector< NT > > (SBL::CSB); T_Conformation_traits< T_Conformation_with_covalent_structure< ConformationBase, CovalentStructure > > (SBL::CSB); T_Conformation_traits< T_Conformation_with_height< ConformationBase, HeightType > > (SBL::CSB); T_Conformation_traits< T_Conformation_with_implicit_height< ConformationBase, HeightFunctor > > (SBL::CSB); T_Conformation_with_covalent_structure (SBL::CSB); T_Conformation_with_height (SBL::CSB); T_Conformation_with_implicit_height (SBL::CSB); T_Conformations_file_loader (SBL::Models); Contact_map_for_one_ctype (SBL::CSB); T_Container_of_containers_const_iterator (SBL::CADS); T_Container_of_containers_iterator (SBL::CADS); T_Container_of_containers_iterator_base (SBL::CADS); Contants_for_embedding (SBL::CSB); Cradle_step1 (SBL.Molecular_cradle_step1); Cradle_step2 (SBL.Molecular_cradle_step2); Cradle_step2_selected (SBL.Molecular_cradle_step2_selected); Cradle_step3 (SBL.Molecular_cradle_step3); Create_And_Compute_iRMSD (SBL.Multiple_interface_string_alignment)

D: D_Solution (SBL::CADS); Darting_Move_Params (SBL::GT); T_Darting_Move_Set (SBL::GT); T_Darting_Move_Set_Controller (SBL::GT); Darting_Move_Set_Traits (SBL::GT); Darting_Move_Stats (SBL::GT); T_Default_amino_acid_seqan_sequence_converter (SBL::CSB); Default_color_engine (SBL.Multiple_interface_string_alignment); Default_radii_for_particles_with_annotated_name (SBL::Models); Default_system_items (ESBTL); Default_system_items (SBL::CSB); T_Delaunay_triangulation_extension_3 (SBL::GT); T_Delaunay_triangulation_spherical_traits_3 (SBL::GT); T_Delaunay_triangulation_spherical_traits_3_base (SBL::GT); Delta_ASA_color_engine (SBL.Multiple_interface_string_alignment); Delta_ASA_coloring_parser (SBL.Multiple_interface_string_alignment); Dendogram_processor (SBL.Molecular_cradle_utils_dendogram); T_Union_find_base::Descendants_iterator (SBL::CADS); T_Polypeptide_chain_representation::Dihedral_angle (SBL::CSB); T_Polypeptide_chain_representation::Dihedral_angle_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Dihedral_angle_iterator (SBL::CSB); T_Dihedral_angles_visitor (SBL::CSB); T_Dijkstra_shortest_paths_with_landmarks (SBL::CADS); T_Directed_acyclic_graph (SBL::CADS); Directed_acyclic_graph_default_property (SBL::CADS); T_Directed_acyclic_graph_with_layers (SBL::CADS); Distance_calculator (SBL.Molecular_cradle_utils_distance); T_Distance_default_for_graph (SBL::GT); T_Domain_annotator_for_particles (SBL::Models); Domain_label_traits (SBL::Models); T_Domain_label_traits (SBL::Models); dp_mat_apurva; T_DS_conformation (SBL::GT); T_DS_snapshot_default (SBL::GT); T_Dynamic_annotator_for_atoms (SBL::Models); T_Dynamic_annotator_for_residues (SBL::Models)

E: T_Earth_mover_distance (SBL::CADS); T_Earth_mover_distance_connectivity_constraints_checker (SBL::CADS); T_Earth_mover_distance_module (SBL::Modules); T_Earth_mover_distance_transportation_plan (SBL::CADS); T_Earth_mover_distance_vertices_accessor_graph (SBL::CADS); T_Earth_mover_distance_vertices_accessor_vector (SBL::CADS); T_Earth_mover_distance_with_connectivity_constraints (SBL::CADS); T_Tertiary_quaternary_structure_annotator::Edge_label_writer (SBL::CSB); T_Edge_product_graph_builder (SBL::CADS); T_Edge_product_graph_traits (SBL::CADS); T_Module_based_workflow::Edge_property_label_writer (SBL::Modules); T_EMD_CC_stat_triple (SBL::CADS); T_EMD_distance_default (SBL::CADS); T_EMD_LP_LP_format_writer (SBL::CADS); T_EMD_LP_MPS_format_writer (SBL::CADS); Exec_runner (SBL.Binding_affinity_utils); T_External_distance (SBL::CSB); Extra_label_traits (SBL::Models); Extract_shared_PDB_interface (SBL.Multiple_interface_string_alignment)

F: Feature (SBL.Sequence_annotators); File_data (SBL.Protein_complex_analysis_molecular_data_structures); T_Frechet_mean_S1 (SBL::GT)

G: Gaussian_Move_Params (SBL::GT); T_Gaussian_Move_Set (SBL::GT); T_Gaussian_Move_Set_Controller (SBL::GT); Gaussian_Move_Set_Traits (SBL::GT); Gaussian_Move_Stats (SBL::GT); T_Generic_annotator (SBL::Models); T_Generic_annotator_without_file (SBL::Models); Generic_classifier (ESBTL); Generic_line_selector (ESBTL); Genetrank_gene_radar (SBL.SBL_Genetrank_gene_radar_scatter_plot); Genetrank_GeneProteinTranslator (SBL.SBL_Genetrank_gene_to_protein); Genetrank_network_statistical_analysis (SBL.SBL_Genetrank_network_statistical_analysis); SBL_PPIN_simulation.Genetrank_simulation_input (SBL); Genetrank_Translations (SBL.SBL_Genetrank_gene_to_protein); T_Geodesic_distances_generation (SBL::CADS); T_Geometric_particle_traits (SBL::Models); Get_annotator_option_display_name_default (SBL::Models); Get_annotator_option_help_default (SBL::Models); Get_annotator_option_name_default (SBL::Models); T_Delaunay_triangulation_extension_3::Get_area_of_dual_of_edge (SBL::GT); T_Union_of_balls_boundary_patch_shelling_3::Face_complex_traits::Get_cell_boundary_from_halfedge (SBL::GT); T_Union_of_balls_boundary_patch_shelling_3::Face_complex_traits::Get_cell_from_face (SBL::GT); T_Triangulation_extension_3_base::Get_common_facet (SBL::GT); T_Delaunay_triangulation_extension_3::Get_dual_of_edge (SBL::GT); T_Delaunay_triangulation_extension_3::Get_dual_of_facet (SBL::GT); T_Atom_with_flat_info_traits::Get_geometric_representation (SBL::Models); T_Atom_with_hierarchical_info_and_annotations_traits::Get_geometric_representation (SBL::Models); T_Atom_with_hierarchical_info_traits::Get_geometric_representation (SBL::Models); T_Atom_with_flat_info_and_annotations_traits::Get_geometric_representation (SBL::Models); T_Geometric_particle_traits::Get_geometric_representation (SBL::Models); T_Pseudo_atom_per_residue_spec_with_flat_info_and_annotations_traits::Get_geometric_representation (SBL::Models); T_Pseudo_atom_per_residue_spec_with_flat_info_traits::Get_geometric_representation (SBL::Models); Get_not_annotator_option_name; T_Triangulation_extension_3_base::Get_other_two_edges (SBL::GT); T_Get_particle_default (SBL::CSB); T_Delaunay_triangulation_extension_3::Get_squared_length_of_dual_of_facet (SBL::GT); T_Module_based_workflow::Graph_property_label_writer (SBL::Modules); T_Greedy_selection (SBL::CADS); T_Greedy_selection_incremental (SBL::CADS); Grid_of_cubes (ESBTL)

H: T_Molecular_interface_connected_component_data_structure::Have_labels (SBL::CSB); T_Hierarchical_labels_forest (SBL::CSB); Hit_info (SBL.DB_hit_manager); Hits_manager (SBL.DB_hit_manager); Hits_manager_no_annotations (SBL.DB_hit_manager); HMM (SBL.HMMER_Wrapper)

I: T_IG_label_traits (SBL::Models); IG_label_traits (SBL::Models); IGAg_label_traits (SBL::Models); T_Improper_angles_visitor (SBL::CSB); T_Polypeptide_chain_representation::Incident_atoms_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Incident_atoms_iterator (SBL::CSB); T_Index_wrapper (SBL::IO); Interface_oneside (SBL.Multiple_interface_string_alignment); Interface_pool (SBL.Multiple_interface_string_alignment); Interface_strings (SBL.Multiple_interface_string_alignment); T_Triangulation_extension_3_base::Is_coface (SBL::GT); T_Triangulation_extension_3_base::Is_counter_clockwise_oriented (SBL::GT); T_Spherical_kernel_extension_3::Is_counter_clockwise_oriented (SBL::GT); T_Union_of_balls_boundary_patch_shelling_3::Face_complex_traits::Is_in_cell_complex (SBL::GT); T_Spherical_kernel_extension_3::Is_largest_circular_arc_3 (SBL::GT); T_Alignment_engine::Is_lower_name_pair (SBL::CSB); Is_product_edge_default (SBL::CADS); Is_product_vertex_default (SBL::CADS); T_Iterative_aligner (SBL::CSB); T_Iterative_aligner_identity (SBL::CSB)

K: K_means_scores (SBL::GT); T_Kpax (SBL::CSB)

L: Label_selector (SBL.Molecular_cradle_utils_label_selection); lambda_matrix; T_Least_RMSD_cartesian (SBL::CSB); T_Least_RMSD_cartesian_3 (SBL::GT); T_Least_RMSD_cartesian_with_chirality (SBL::CSB); Line_format (ESBTL::PDB); Line_reader (ESBTL); Line_reader_with_info (ESBTL); Loader_base (SBL::IO)

M: Make_no_annotation_key (SBL::Models); Mandatory_fields_default (ESBTL::PDB); T_Alignment_engine::Matrix_function (SBL::CSB); Matrix_processor (SBL.Molecular_cradle_utils_dendogram); Max_occupancy_policy (ESBTL); T_Maximum_clique_finder (SBL::CADS); T_Maximum_spanning_tree_generator (SBL::CADS); Maximum_spanning_tree_property (SBL::CADS); MCI_analysis (SBL.Connectivity_inference_analysis); MCI_bootstrap (SBL.mcibootstrap_iterative); MCI_Contact (SBL.Connectivity_inference_data_structures); MCI_MILP_engine (SBL.Connectivity_inference_engine); MCI_Oligomers (SBL.Connectivity_inference_data_structures); MCI_output_preprocessing (SBL.Connectivity_inference_analysis); MCI_regex (SBL.Connectivity_inference_data_structures); MCI_set_of_contacts (SBL.Connectivity_inference_data_structures); MCI_solutions (SBL.Connectivity_inference_data_structures); MCI_specification (SBL.Connectivity_inference_data_structures); MCI_string_tools (SBL.Connectivity_inference_data_structures); T_Mediated_interface_data_structure_base (SBL::CSB); T_Mediated_interface_oserialization (SBL::CSB); T_Mediated_interface_oserialization (SBL::Modules); Min_occupancy_policy (ESBTL); T_Minimal_oriented_spanning_forest_Boruvka (SBL::CADS); T_Minimal_oritend_spanning_forest_module; T_Minimizer_Ipopt_parameters_without_constraint (SBL::CSB); T_Minimizer_parameters_without_constraint (SBL::CSB); MISA (SBL.Multiple_interface_string_alignment); MISA_constructor (SBL.Multiple_interface_string_alignment); MISA_input_specification_parser (SBL.Multiple_interface_string_alignment); Module_base (SBL::Modules); Module_based_workflow (SBL::Modules); T_Module_based_workflow (SBL::Modules); T_Module_condition (SBL::Modules); T_Module_conjunction (SBL::Modules); T_Module_option_description (SBL::Modules); Modules_collection; Molecular_alignment_default (SBL::CSB); Molecular_atom (ESBTL); Molecular_atom (SBL::CSB); T_Molecular_cartesian_coordinates (SBL::CSB); Molecular_chain (ESBTL); Molecular_chain (SBL::CSB); Molecular_chain_with_SSE (ESBTL); Molecular_coordinates_utilities (SBL::CSB); T_Molecular_covalent_structure (SBL::CSB); T_Molecular_covalent_structure_bond_angle_gradient (SBL::CSB); T_Molecular_covalent_structure_bond_length_gradient (SBL::CSB); T_Molecular_covalent_structure_builder_for_protein_martini (SBL::CSB); T_Molecular_covalent_structure_builder_for_proteins (SBL::CSB); T_Molecular_covalent_structure_constraints_for_proteins (SBL::CSB); T_Molecular_covalent_structure_loader (SBL::IO); T_Molecular_covalent_structure_loader_from_MOL (SBL::IO); T_Molecular_covalent_structure_loader_from_PDB (SBL::IO); T_Molecular_covalent_structure_optimal (SBL::CSB); T_Molecular_covalent_structure_torsion_angle_gradient (SBL::CSB); T_Molecular_geometric_model_classifier_for_alpha_complex (SBL::CSB); T_Molecular_interface_connected_component_data_structure (SBL::CSB); T_Molecular_interface_connected_component_oserialization (SBL::CSB); T_Molecular_interface_data_structure_base (SBL::CSB); T_Molecular_interface_oserialization (SBL::CSB); T_Molecular_interfaces_builder (SBL::CSB); T_Molecular_interfaces_module (SBL::Modules); T_Molecular_interfaces_module_statistics (SBL::Modules); T_Molecular_interfaces_traits (SBL::CSB); Molecular_model (ESBTL); Molecular_model (SBL::CSB); T_Molecular_potential_energy (SBL::CSB); T_Molecular_potential_energy_bond_angle_gradient_harmonic (SBL::CSB); T_Molecular_potential_energy_bond_angle_gradient_Urey_Bradley (SBL::CSB); T_Molecular_potential_energy_bond_angle_term_harmonic (SBL::CSB); T_Molecular_potential_energy_bond_angle_term_Urey_Bradley (SBL::CSB); T_Molecular_potential_energy_bond_length_gradient_harmonic (SBL::CSB); T_Molecular_potential_energy_bond_length_term_harmonic (SBL::CSB); T_Molecular_potential_energy_bonded_contribution (SBL::CSB); T_Molecular_potential_energy_cmap_term (SBL::CSB); T_Molecular_potential_energy_contribution (SBL::CSB); T_Molecular_potential_energy_electrostatic_gradient (SBL::CSB); T_Molecular_potential_energy_electrostatic_term (SBL::CSB); T_Molecular_potential_energy_gradient (SBL::CSB); T_Molecular_potential_energy_gradient_contribution (SBL::CSB); T_Molecular_potential_energy_Lennard_Jones_gradient (SBL::CSB); T_Molecular_potential_energy_Lennard_Jones_term (SBL::CSB); T_Molecular_potential_energy_numerical_gradient (SBL::CSB); T_Molecular_potential_energy_torsion_angle_gradient_Fourier (SBL::CSB); T_Molecular_potential_energy_torsion_angle_gradient_harmonic (SBL::CSB); T_Molecular_potential_energy_torsion_angle_gradient_in_linear_structure (SBL::CSB); T_Molecular_potential_energy_torsion_angle_gradient_periodic (SBL::CSB); T_Molecular_potential_energy_torsion_angle_gradient_Ryckaert_Bellemans (SBL::CSB); T_Molecular_potential_energy_torsion_angle_in_linear_structure_term (SBL::CSB); T_Molecular_potential_energy_torsion_angle_term_Fourier (SBL::CSB); T_Molecular_potential_energy_torsion_angle_term_harmonic (SBL::CSB); T_Molecular_potential_energy_torsion_angle_term_periodic (SBL::CSB); T_Molecular_potential_energy_torsion_angle_term_Ryckaert_Bellemans (SBL::CSB); T_Molecular_primitive_internal_coordinates (SBL::CSB); Molecular_residue (ESBTL); Molecular_residue (SBL::CSB); Molecular_residue_with_SSE (ESBTL); Molecular_secondary_structure_element (SBL::CSB); Molecular_secondary_structure_element (ESBTL); Molecular_SS_bond (SBL::CSB); Molecular_SS_bond (ESBTL); T_Molecular_structure_classifier (SBL::CSB); T_Molecular_structure_classifier_module (SBL::Modules); T_Molecular_structure_traits (SBL::CSB); Molecular_system (SBL::CSB); Molecular_system (ESBTL); Molecular_system< System_items_with_SSE, Point > (ESBTL); T_Molecular_system_loader (SBL::IO); Molecular_view (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, CGAL::Point_3< K > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, CGAL::Sphere_3< K > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, CGAL::Triple< CGAL::Point_3< K >, CGAL::Point_3< K >, CGAL::Point_3< K > > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, CGAL::Triple< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, CGAL::Weighted_point< Point, Weight > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, std::pair< CGAL::Point_3< K >, CGAL::Point_3< K > > > (SBL::IO); Molecular_view< T_PyMOL_viewer< Dummy >, std::pair< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, CGAL::Point_3< K > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, CGAL::Sphere_3< K > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, CGAL::Triple< CGAL::Point_3< K >, CGAL::Point_3< K >, CGAL::Point_3< K > > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, CGAL::Triple< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, CGAL::Weighted_point< Point, Weight > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, std::pair< CGAL::Point_3< K >, CGAL::Point_3< K > > > (SBL::IO); Molecular_view< T_VMD_viewer< Dummy >, std::pair< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > > (SBL::IO); Molecular_view< Viewer, CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > * > (SBL::IO); Molecular_view< Viewer, CGAL::Alpha_shape_vertex_base_3< Gt, Vb, ExactAlphaComparisonTag, Weight_tag > > (SBL::IO); Molecular_view< Viewer, CGAL::Fixed_alpha_shape_3< Dt > * > (SBL::IO); Molecular_view< Viewer, CGAL::Fixed_alpha_shape_vertex_base_3< Gt, Vb > > (SBL::IO); Molecular_view< Viewer, CGAL::Regular_triangulation_3< Gt, Tds > * > (SBL::IO); Molecular_view< Viewer, CGAL::Regular_triangulation_vertex_base_3< Gt, Vb > > (SBL::IO); Molecular_view< Viewer, CGAL::Triangulation_3< Gt, Tds > * > (SBL::IO); Molecular_view< Viewer, CGAL::Triangulation_vertex_base_3< Gt, Vb > > (SBL::IO); Molecular_view< Viewer, CGAL::Triangulation_vertex_base_with_info_3< Info, Gt, Vb > > (SBL::IO); Molecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Alpha_shape_cell_base_3< Gt, Cb, ExactAlphaComparisonTag, Weight_tag >, Allocator >, Const >, int, int > > (SBL::IO); Molecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Fixed_alpha_shape_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > > (SBL::IO); Molecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Regular_triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > > (SBL::IO); Molecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > > (SBL::IO); Molecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Alpha_shape_cell_base_3< Gt, Cb, ExactAlphaComparisonTag, Weight_tag >, Allocator >, Const >, int > > (SBL::IO); Molecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Fixed_alpha_shape_cell_base_3< Gt, Cb >, Allocator >, Const >, int > > (SBL::IO); Molecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Regular_triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int > > (SBL::IO); Molecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > *, typename CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag >::Edge > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > *, typename CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag >::Facet > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Fixed_alpha_shape_3< Dt > *, typename CGAL::Fixed_alpha_shape_3< Dt >::Edge > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Fixed_alpha_shape_3< Dt > *, typename CGAL::Fixed_alpha_shape_3< Dt >::Facet > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Regular_triangulation_3< Gt, Tds > *, typename CGAL::Regular_triangulation_3< Gt, Tds >::Edge > > (SBL::IO); Molecular_view< Viewer, std::pair< const CGAL::Regular_triangulation_3< Gt, Tds > *, typename CGAL::Regular_triangulation_3< Gt, Tds >::Facet > > (SBL::IO); T_Morse_Smale_Witten_chain_complex (SBL::GT); T_Morse_Smale_Witten_chain_complex_from_NNG_builder (SBL::GT); T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder (SBL::GT); T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder (SBL::GT); T_Morse_theory_based_analyzer (SBL::GT); T_Morse_theory_based_analyzer_for_NNG_module (SBL::Modules); T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module (SBL::Modules); T_Morse_theory_based_analyzer_for_weighted_graph_module (SBL::Modules); T_Morse_theory_based_analyzer_module (SBL::Modules); T_Moveset_atomic (SBL::Models); T_Moveset_global (SBL::Models); T_Moveset_interpolation (SBL::Models); T_Multiple_archives_serialization_xml_iarchive (SBL::IO); T_Multiple_archives_serialization_xml_oarchive (SBL::IO); T_Multiple_archives_xml_archive_file_loader (SBL::IO); T_Multiple_sequence_alignment_DS (SBL::CSB); T_Multiple_sequence_alignment_DS_filtered (SBL::CSB)

N: T_Name_and_radius_annotations (SBL::Models); Name_and_radius_of_atom (ESBTL); T_Name_annotator_for_atoms (SBL::Models); Name_annotator_for_atoms_setter_default (SBL::Models); T_Name_annotator_for_pseudo_atoms (SBL::Models); Name_annotator_for_pseudo_atoms_setter_default (SBL::Models); Name_of_pair (ESBTL); NCBI_wrapper (SBL.DB_manipulators); Nearest_neighbors_graph_builder (SBL::GT); T_Nearest_neighbors_graph_builder_module (SBL::Modules); Nearest_neighbors_graph_builder_with_edge_weight (SBL::GT); T_Maximum_spanning_tree_generator::Negative_graph_vertex_property (SBL::CADS); T_NN_linear_scan (SBL::GT); T_NN_metric_tree (SBL::GT); No_label_traits (SBL::Models); No_occupancy_policy (ESBTL); No_Overstep_Cone_Move_Params (SBL::GT); T_No_Overstep_Cone_Move_Set (SBL::GT); T_No_Overstep_Cone_Move_Set_Controller (SBL::GT); No_Overstep_Cone_Move_Set_Traits (SBL::GT); No_Overstep_Cone_Move_Stats (SBL::GT); No_Overstep_Move_Params (SBL::GT); T_No_Overstep_Move_Set (SBL::GT); T_No_Overstep_Move_Set_Controller (SBL::GT); No_Overstep_Move_Set_Traits (SBL::GT); No_Overstep_Move_Stats (SBL::GT); No_particle_annotator (SBL::Models); Not_functor (ESBTL); T_Numbers_file_loader (SBL::IO)

O: One_label_traits (SBL::Models); Or_functors (ESBTL); T_Ordered_forest_edit_distance (SBL::CADS); T_Spherical_kernel_extension_3::Orientation_with_roots_3 (SBL::GT); Overall_default_anaysis (SBL.Combinations_of_variables_model_evaluation)

P: Pairwise_contacts_for_polypeptide_chain (SBL::CSB); PALSE_DS_manipulator (SBL.PALSE); PALSE_statistic_handle (SBL.PALSE); PALSE_xml_DB (SBL.PALSE); parameters; T_Particle_annotator_collector (SBL::Models); T_Particle_info_for_proteins (SBL::CSB); T_Particle_info_traits (SBL::CSB); T_Particle_vertex_base (SBL::CSB); T_Particle_with_annotations (SBL::Models); T_Particle_with_annotations_traits (SBL::Models); T_Particle_with_system_label (SBL::Models); T_Particle_with_system_label_traits (SBL::Models); PDB_complex_to_unbound_partners_matcher (SBL.PDB_complex_to_unbound_partners_matchings); T_PDB_file_loader (SBL::Models); PDB_line_selector (ESBTL); PDB_line_selector_chain (ESBTL); PDB_line_selector_two_systems (ESBTL); Per_model_binding_affinity_analysis (SBL.Combinations_of_variables_model_evaluation); Per_model_default_analysis (SBL.Combinations_of_variables_model_evaluation); T_Phi_psi_dihedral_angles_visitor (SBL::CSB); Phobius_annotator (SBL.Sequence_annotators); Plot_tools (SBL.Multiple_interface_string_alignment); Point_3 (ESBTL); T_Point_cloud_rigid_registration_3 (SBL::GT); T_Points_d_file_loader (SBL::Models); T_Polynomial_solver_interface (SBL::CSB); T_Polypeptide_chain_contacts_finder (SBL::CSB); T_Polypeptide_chain_representation (SBL::CSB); SBL_PPIN_application.PPIN_application (SBL); SBL_PPIN_gene_radar_scatter_plot.PPIN_gene_radar_scatter_plot (SBL); SBL_PPIN_simulation_statistics.PPIN_multiple_simulation_statistics (SBL); SBL_PPIN_simulation.PPIN_simulation (SBL); SBL_PPIN_simulation.PPIN_simulation_result (SBL); SBL_PPIN_simulation_statistics.PPIN_simulation_statistics (SBL); SBL_PPIN_simulation_statistics.PPIN_simulation_visualizations (SBL); Extra_label_traits::Primitive_label_classifier (SBL::Models); Water_label_traits::Primitive_label_classifier (SBL::Models); No_label_traits::Primitive_label_classifier (SBL::Models); One_label_traits::Primitive_label_classifier (SBL::Models); T_AB_label_traits::Primitive_label_classifier (SBL::Models); T_IGAg_label_traits::Primitive_label_classifier (SBL::Models); T_IG_label_traits::Primitive_label_classifier (SBL::Models); T_Domain_label_traits::Primitive_label_classifier (SBL::Models); T_Chain_label_traits::Primitive_label_classifier (SBL::Models); T_Primitive_labels_loader (SBL::IO); problem; T_Product_graph_builder (SBL::CADS); T_Protein_representation (SBL::CSB); T_Protein_representation_loader (SBL::IO); T_Pseudo_atom_per_residue_spec_with_flat_info (SBL::Models); T_Pseudo_atom_per_residue_spec_with_flat_info_and_annotations_traits (SBL::Models); T_Pseudo_atom_per_residue_spec_with_flat_info_traits (SBL::Models); PyMOL_viewer (SBL::IO); T_PyMOL_viewer (SBL::IO); Python_dico_vs_XML_Etree (SBL.PALSE)

R: T_Radius_annotator_for_particles_with_annotated_name (SBL::Models); Radius_annotator_for_particles_with_annotated_name_setter_default (SBL::Models); Radius_of_atom (ESBTL); Radius_of_coarse_atom (ESBTL); T_Random_spanning_tree_generator (SBL::CADS); T_Random_spanning_tree_property (SBL::CADS); T_Real_value_function_minimizer (SBL::CSB); T_Real_value_function_minimizer_Ipopt (SBL::CSB); T_Real_value_function_minimizer_LBFGS (SBL::CSB); T_Particle_vertex_base::Rebind_TDS (SBL::CSB); T_Polypeptide_chain_representation::Residue_atoms_const_iterator (SBL::CSB); T_Polypeptide_chain_representation::Residue_atoms_iterator (SBL::CSB); Residue_contact_data (SBL.Protein_complex_analysis_molecular_data_structures); Residue_data (SBL.Protein_complex_analysis_molecular_data_structures); Residue_mapping (SBL.Multiple_interface_string_alignment); ResSelector (SBL.Multiple_interface_string_alignment); T_RMSD_cartesian_3 (SBL::GT); T_RMSD_comb_edge_weighted (SBL::CSB); T_RMSD_comb_edge_weighted_module (SBL::Modules); T_Wang_Landau::Roll_Back_Restoration_Point (SBL::GT); T_Rotation_3 (SBL::GT)

S: SBL_init_tools (SBL); T_Score_computer_K (SBL::CSB); T_Seeder_basic (SBL::CSB); T_Seeder_DP_score (SBL::CSB); Select_by_atmname (ESBTL); Select_by_chainids (ESBTL); Select_by_element (ESBTL); Select_by_resname (ESBTL); Selected_atom_iterator (ESBTL); Set_dynamic_annotation_default (SBL::Models); T_Shelling_diagram_vertex_property (SBL::CADS); T_Spanning_tree_solver (SBL::CADS); T_Spatial_search_module (SBL::Modules); T_Spectral_clustering (SBL::GT); T_Spheres_3_file_loader (SBL::Models); T_Spherical_kernel_extension_3 (SBL::GT); T_Splitter_default (SBL::GT); T_Squared_angular_internal_distance (SBL::CSB); T_Squared_Least_RMSD_cartesian_3 (SBL::GT); T_Squared_RMSD_cartesian_3 (SBL::GT); T_Squared_RMSD_internal_distance (SBL::CSB); SSE_color_engine (SBL.Multiple_interface_string_alignment); SSE_coloring_parser (SBL.Multiple_interface_string_alignment); T_Stable_manifold_as_list_traits (SBL::GT); T_Sub_graph (SBL::CADS); T_Sub_graph::Sub_vertex_property (SBL::CADS); System_items_with_coarse_grain (SBL::CSB); System_items_with_coarse_grain (ESBTL); System_items_with_SSE (ESBTL); T_Particle_with_system_label::System_label (SBL::Models); System_updater_from_xdrfile (ESBTL)

T: T_Tertiary_quaternary_structure_annotator (SBL::CSB); T_Tertiary_quaternary_structure_annotator_module (SBL::Modules); T_TLC_polynomial_roots_to_embedings (SBL::CSB); Traits_for_grid (ESBTL); T_Transition_graph_loader (SBL::IO); T_Transition_graph_traits_compressed (SBL::CSB); T_Transition_graph_traits_standard (SBL::CSB); Transmembrane_filter (SBL.Sequence_filters); T_Tree (SBL::CADS); T_Tree_solver (SBL::CADS); T_Triangulation_extension_3 (SBL::GT); T_Triangulation_extension_3_base (SBL::GT); T_Triangulation_of_molecular_model (SBL::CSB); T_Tricolor_interface_data_structure_base (SBL::CSB); T_Tricolor_interface_oserialization (SBL::CSB); T_Tricolor_interface_oserialization (SBL::Modules); T_Tripeptide_anchors (SBL::CSB); T_Tripeptide_constraints (SBL::CSB); T_Tripeptide_constraints_to_polynomial (SBL::CSB); T_Tripeptide_loop_closure (SBL::CSB)

U: T_Unbonded_particles_visitor (SBL::CSB); T_Unbonded_particles_with_threshold_visitor (SBL::CSB); T_Union_find_base (SBL::CADS); T_Union_find_contains (SBL::CADS); T_Union_find_contains_with_map (SBL::CADS); Union_find_default (SBL::CADS); T_Union_find_specializes (SBL::CADS); Union_find_vertex_data_structure_base (SBL::CADS); T_Union_find_vertex_data_structure_contains (SBL::CADS); T_Union_find_vertex_data_structure_specializes (SBL::CADS); T_Union_of_balls_boundary_3_builder (SBL::GT); T_Union_of_balls_boundary_3_data_structure (SBL::GT); T_Union_of_balls_boundary_3_face (SBL::GT); T_Union_of_balls_boundary_3_half_edge (SBL::GT); T_Union_of_balls_boundary_3_item_info (SBL::GT); T_Union_of_balls_boundary_3_items (SBL::GT); T_Union_of_balls_boundary_3_module (SBL::Modules); T_Union_of_balls_boundary_3_side (SBL::GT); T_Union_of_balls_boundary_3_vertex (SBL::GT); T_Union_of_balls_boundary_patch_shelling_3 (SBL::GT); T_Union_of_balls_boundary_patch_shelling_3_module (SBL::Modules); T_Union_of_balls_epsilon_mesh_3 (SBL::GT); T_Union_of_balls_medial_axis_3_builder (SBL::GT); T_Union_of_balls_medial_axis_3_data_structure (SBL::GT); T_Union_of_balls_medial_axis_3_face (SBL::GT); T_Union_of_balls_medial_axis_3_halfedge (SBL::GT); T_Union_of_balls_medial_axis_3_items (SBL::GT); T_Union_of_balls_medial_axis_3_vertex (SBL::GT); T_Union_of_balls_mesh_3_module (SBL::Modules); T_Union_of_balls_surface_volume_3_module::Union_of_balls_surface_volume_3 (SBL::Modules); T_Union_of_balls_surface_volume_3 (SBL::GT); T_Union_of_balls_surface_volume_3_module (SBL::Modules); Uniprot_wrapper (SBL.DB_manipulators); T_Unit_system_traits_AKMA (SBL::Models); T_Unit_system_traits_for_potential_energy (SBL::Models); T_Unit_system_traits_none_AKMA (SBL::Models); T_Unit_system_traits_none_MD (SBL::Models)

V: T_Triangulation_extension_3_base::T_Vertex_handle_with_order (SBL::GT); T_Tertiary_quaternary_structure_annotator::Vertex_label_writer (SBL::CSB); T_Vertex_product_graph_builder (SBL::CADS); T_Vertex_product_graph_traits (SBL::CADS); T_RMSD_comb_edge_weighted::Vertex_property (SBL::CSB); T_Module_based_workflow::Vertex_property_label_writer (SBL::Modules); VMD_viewer (SBL::IO)

W: T_Wang_Landau (SBL::GT); Water_label_traits (SBL::Models); Weight_of_atoms (ESBTL); Weighted_atom_iterator (ESBTL); T_WL_Data_Structure_Internal (SBL::GT); T_WL_Data_Structure_MS (SBL::GT); T_Wang_Landau::WL_DS_Interface (SBL::GT); WL_histo_change_measure (SBL::GT); T_WL_Simulation (SBL::GT); T_WL_Simulation_Gaussian (SBL::GT); T_WL_Simulation_No_Overstep (SBL::GT); WL_stats_serializer (SBL::GT)

X: T_XTC_file_loader (SBL::Models)