Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
 Cbranch_and_bound< problem >
 CclassReselect seeds in reverse order using D2 weighting
 Cdp_mat_apurva< graph, lambda_matrix >
 CGet_not_annotator_option_nameReturns empty option name
 Clambda_matrix< graph >
 CModules_collectionBase module from which any module should inherit
 COrdered_chain_cosnt_iteratorGeneric dihedral angle iterator for arbitrary ordred atom chain (const)
 COrdered_chain_iteratorIterative enumeration of torsion angles by finding consecutive four-tuples along the side chain
 Cparameters
 Cproblem< graph, dp_mat, lambda_mat, parameter >
 CAF_filtrations_result\sbl_add_package_main_class{sbl-package-name, SBL.AF_filtrations.AF_filtrations_result , Long: Class storing all results for the pLDDT/arity analysis using filtrations Short: Class storing all results for the pLDDT/arity analysis using filtrations } i################################################################################
 CAF_filtrations_directory\sbl_add_package_main_class{PDB_utilities, SBL::AF_filtrations::AF_filtrations_directory, Long: class implementing the arity based operations for all files in a directory Short: class implementing the arity based operations for all files in a directory } i################################################################################
 CAF_filtrations_directory_static\sbl_add_package_main_class{PDB_utilities, SBL::AF_filtrations::AF_filtrations_parallel, Long: class implementing the arity based operations for a directory in parallel mode Short: class implementing the arity based operations for a directory in parallel mode } i################################################################################
 CSummaryWriter
 CTHREEJSBuilder
 CStatsParser
 CTableWriter
 CBM_Batch
 CBM_Database
 CBM_Dataset
 CBM_IFO_setSet of input file options with multiple values
 CBM_Run_specification_ensemble
 CBM_Run_specification_tuple
 CSummaryWriter
 CExec_runner
 CD_SolutionThe solution space for the Maximum Spanning tree algorithm
 CDirected_acyclic_graph_default_propertyDefault data structure containing information associated to an edge or a vertex of a directed acyclic graph
 CIs_product_edge_defaultDefault functor for product edge always returning true
 CIs_product_vertex_defaultDefault functor for product vertex always returning true
 CMaximum_spanning_tree_propertyThe solution space for the maximum spanning tree algorithm
 CT_Container_of_containers_iterator_base< OuterContainerIterator, InnerContainerIterator >Base representation of an iterator over nested containers
 CT_Container_of_containers_iterator_base< OuterContainerConstIterator, OuterContainerConstIterator::value_type::const_iterator >
 CT_Container_of_containers_iterator_base< OuterContainerConstIterator, typename OuterContainerConstIterator::value_type::const_iterator >
 CT_Container_of_containers_iterator_base< OuterContainerIterator, OuterContainerIterator::value_type::iterator >
 CT_Container_of_containers_iterator_base< OuterContainerIterator, typename OuterContainerIterator::value_type::iterator >
 CT_Dijkstra_shortest_paths_with_landmarks< Graph, IsLandmark >Brief todo
 CT_Directed_acyclic_graph< VertexProperty, EdgeProperty >Generic representation of a directed acyclic graph
 CT_Directed_acyclic_graph< Directed_acyclic_graph_default_property, Directed_acyclic_graph_default_property >
 CT_Directed_acyclic_graph< T_Shelling_diagram_vertex_property< Cell, std::less< Cell > >, Directed_acyclic_graph_default_property >
 CT_Directed_acyclic_graph< VertexProperty, EdgeProperty >
 CT_Earth_mover_distance< VerticesAccessor, DistanceFunctor >Earth mover distance algorithm using lp_solve software for solving linear program problems
 CT_Earth_mover_distance_connectivity_constraints_checker< EarthMoverDistance >Functor measuring the violation of the connectivity constraints of any Earth Mover Distance algorithm
 CT_Earth_mover_distance_transportation_plan< VertexRep, FT >Transportation plan for the Earth Mover Distance algorithms
 CT_Earth_mover_distance_vertices_accessor_graph< VertexType, MassType >Accessors for weighted vertices stored in a boost graph
 CT_Earth_mover_distance_vertices_accessor_vector< VertexType, MassType >Accessors for weighted vertices stored in a simple vector with no connectivity
 CT_Earth_mover_distance_with_connectivity_constraints< VerticesAccessor, DistanceFunctor >Earth mover distance algorithm with connectivity constraints on the input data
 CT_Edge_product_graph_traits< Graph1, Graph2, EdgeProperty >Traits clas defining types for an edge product graph
 CT_EMD_CC_stat_triple< FT >Internal data structure used to store information for the transportation plan
 CT_EMD_distance_default< VerticesAccessor >Default distance used by the EMD algorithm returning always the null distance
 CT_EMD_LP_LP_format_writer< VerticesAccessor, DistanceFunctor >Writing a LP problem using the LP format
 CT_EMD_LP_MPS_format_writer< VerticesAccessor, DistanceFunctor >Writing a LP problem using the MPS format
 CT_Geodesic_distances_generation< Graph, LandmarkFunctor, LandmarkInfo_functor >Brief todo
 CT_Greedy_selection< Arrangement, GetWeightOfArrangement, GetOverlappingArrangements >Generic greedy selection algorithm of arrangements of cells
 CT_Greedy_selection_incremental< Arrangement, GetWeightOfArrangement, GetOverlappingArrangements >Generic Greedy selection algorithm of arrangements of cells
 CT_Maximum_clique_finder< GraphType >Functor returning the vertices of a maximum clique of an input graph
 CT_Maximum_spanning_tree_generator< Graph >Generates a Maximum spanning tree over a given graph (using boost::graph)
 CT_Maximum_spanning_tree_generator< Graph >::Negative_graph_vertex_propertyTo compute the Maximum spanning tree, we use a negative version of the original graph
 CT_Minimal_oriented_spanning_forest_Boruvka< GraphType >Minimal Spanning Forest algorithm
 CT_Ordered_forest_edit_distance< Forest, GetCost, IsLowerSiblingVertex >Generic Forest Edit Distance algorithm for ordered forests
 CT_Product_graph_builder< ProductGraphTraits, IsProductVertex, IsProductEdge >Builder class for product graphs
 CT_Product_graph_builder< ProductGraphTraits, Is_product_vertex_default, Is_product_edge_default >
 CT_Product_graph_builder< ProductGraphTraits, IsProductVertex, IsProductEdge >
 CT_Random_spanning_tree_generator< Graph >Generates a Random spanning tree over a given graph (using boost::graph)
 CT_Random_spanning_tree_property< Dummy >The solution space for the random spanning tree algorithm
 CT_Spanning_tree_solver< IntersectionGraph, StopCondition, SpanningTreeGenerator, Algorithm >A heuristic algorithm to solve the D-Family-matching problem by using spanning trees
 CT_Spanning_tree_solver< Graph, Maximum_spanning_tree_property, T_Maximum_spanning_tree_generator< Graph >, T_Tree_solver< Graph > >
 CT_Spanning_tree_solver< Graph, Random_spanning_tree_property, T_Random_spanning_tree_generator< Graph >, T_Tree_solver< Graph > >
 CT_Sub_graph< Graph >A superstructure over the Graph used to represent non-induced sub-graphs
 CT_Sub_graph< Graph >::Sub_vertex_propertySub graph vertex property (wee link it to the vertex it represents in the Graph)
 CT_Tree< Graph >A superstructure over the Graph used to represent trees
 CT_Tree_solver< Graph >A dynamic programming algorithm which solves the D family matching problem for trees
 CT_Union_find_base< T, VertexDS, InternalVertexTag >Base class implementing the Union-Find data structure
 CT_Union_find_base< T, VertexDS, InternalVertexTag >::Descendants_iteratorIterator over the descendants of a given vertex
 CT_Union_find_base< bool, Union_find_vertex_data_structure_base, true >
 CT_Union_find_base< T, T_Union_find_vertex_data_structure_contains< T >, true >
 CT_Union_find_base< T, T_Union_find_vertex_data_structure_specializes< T >, false >
 CT_Vertex_product_graph_traits< Graph1, Graph2, EdgeProperty >Traits clas defining types for a vertex product graph
 CUnion_find_vertex_data_structure_baseBase representation of a vertex in the Union-Find data structure
 CCombinations_of_variables_model_evaluation
 COverall_default_anaysisOverall analysis provided in our paper
 CPer_model_default_analysisAnalysis for each model provided in our paper
 CMCI_analysis
 CMCI_output_preprocessing
 CMCI_Contact
 CMCI_Oligomers
 CMCI_regexA set of static regular expression to parse specification files and results files
 CMCI_set_of_contacts
 CMCI_solutions
 CMCI_specification
 CMCI_string_toolsCleaning/Trimming the string before use Endline characters are removed, double spaces to single spaces, space at the beginning of the line are removed
 CMCI_MILP_engine
 CCoarse_atom< Atom, Point >
 CCoarse_atom< Atom, typename K_Base::Point_3 >
 CCoarse_atom< Atom_base, typename Geometric_kernel::Point_3 >
 CCoarse_atoms_iterators< Model >
 CCoarse_creator_closest_to_barycenter< Residue, FT_ >
 CCoarse_creator_two_barycenters< Residue >
 CCoarse_residue< Residue, Chain, Coarse_atom_ >
 CCoarse_residue< Residue, Chain, Coarse_atom< Atom, Point_3 > >
 CContact_map_for_one_ctypeRecords pairs of interacting residues for one contact type
 CContants_for_embedding< NT >Values obtained when converting constraints to polynomial coefficients and used once more to convert roots to cartesian embeddings of solution in tripeptide loop closure
 CDefault_system_items
 CMolecular_alignment_defaultMake an alignment between two molecules with the same numbers of atoms, with the same order
 CMolecular_atom< System_, Point >A class representing a molecular atom
 CMolecular_atom< System, Point >
 CMolecular_atom< System, Point_3 >
 CMolecular_chain< System >A class representing a molecular chain
 CMolecular_coordinates_utilitiesClass with static methods for internal coordinates computations
 CMolecular_model< System_ >A class representing a molecular model
 CMolecular_residue< System >A class representing a molecular residue
 CMolecular_secondary_structure_element< System >A class representing a secondary structure element
 CMolecular_SS_bond< System >A class representing a SS bond between two residues
 CMolecular_system< Items, Point >A class representing a molecular system
 CPairwise_contacts_for_polypeptide_chain
 CSystem_items_with_coarse_grain
 CT_AD_buffer< Dummy >Todo
 CT_AD_stack< Dummy >Todo
 CT_Aligner_sequence_seqan_wrapper< SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >Wrapper of the Seqan algorithm for aligning pairwise sequences
 CT_Aligner_structure_apurva_wrapper< StructureType >Wrapper of the Apurva algorithm for aligning pairwise structures
 CT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >Base engine for making alignments between structures and sequences. Base engine for making alignments between structures and sequences
 CT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >::Is_lower_name_pairPredicate for comparing two pairs whatever the order of Alignment_unit_rep in each pair
 CT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >::Matrix_functionFunctor for the substitution matrix. Is imposed the following properties: (i) symmetry, (ii) undefined values are 0. Thus, it is just enough to specify non null values on only one triangle of the matrix
 CT_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
 CT_Alignment_engine< StructureType, AlignerAlgorithm, double >
 CT_Alignment_engine< StructureType, AlignerAlgorithm, FT >
 CT_Alignment_engine< StructureType, SBL::CSB::T_Identity_alignment_iterative< StructureType >, double >
 CT_Alignment_engine< StructureType, SBL::CSB::T_Kpax< StructureType >, double >
 CT_Alignment_engine< StructureType, T_Aligner_structure_apurva_wrapper< StructureType >, double >
 CT_Alignment_engine< StructureType, T_Identity_alignment< StructureType >, double >
 CT_Alignment_residue< ResidueBase >Representation of a residue in the alignement engines Representation of a residue in the alignement engines
 CT_Alignment_sequence< ResidueBase >Representation of a sequence of residues in the alignement engines Representation of a sequence of residues in the alignement engines
 CT_Alignment_sequence< Alignment_residue >
 CT_Alignment_sequence< Particle_traits::Molecular_system::Residue >
 CT_Alpha_complex_base_3< Dt, AlphaExactComparisonTag >Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
 CT_Alpha_complex_base_3< T_Triangulation_of_molecular_model< ParticleTraits, T_Alpha_complex_vertex_base_3, T_Alpha_complex_cell_base_3 >, CGAL::Tag_false >
 CT_Alpha_complex_cell_base_3< Traits, Cb, ExactAlphaComparisonTag, WeightedTag >Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
 CT_Alpha_complex_of_molecular_model< Particle_traits, CGAL::Alpha_shape_vertex_base_3, CGAL::Alpha_shape_cell_base_3, CGAL::Alpha_shape_3 >
 CT_Alpha_complex_of_molecular_model< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase, TAlphaComplexBase >
 CT_Alpha_complex_of_molecular_model_traits< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase >Class defining all the types related to the $\alpha$-complex of a molecular model
 CT_Alpha_complex_vertex_base_3< Traits, Vb, ExactAlphaComparisonTag, WeightedTag >Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
 CT_Bicolor_interface_data_structure_base< MolecularInterfaceDataStructure >Container defining what is a bicolor interface between two partners
 CT_Bicolor_interface_data_structure_base< Bicolor_interface_base >
 CT_Bicolor_interface_data_structure_base< Molecular_interface_connected_component_data_structure >
 CT_Bicolor_interface_oserialization< BicolorInterface >Serialization of a bicolor interface
 CT_Binet_Cauchy_kernel_score< Conformation, GetParticle, MolecularAlignment >Model of Distances for defining distance between two conformations
 CT_Bond_angles_visitor< CovalentStructure >Defines iterator over the bond angles of a covalent structure
 CT_Bonded_particles_visitor< CovalentStructure >Defines iterator over the bonds of a covalent structure
 CT_Buried_surface_area_with_labels< ParticleWithSystemLabelTraits, ParticleBSARecord, FT >
Compute the buried surface area of two given partners
 CT_Buried_surface_area_without_label< ParticleTraits, FT >Compute the buried surface area of two given partners
 CT_Canonize_conformation< CovalentStructure, ConformationType >Given a structure , a conformation and a C-alpha, translate and rotate the structure so that this C-alpha is at the origin, its neighbor C is on the z-axis (negative), and its neighbor N is on the zx plane (x positive)
 CT_Chains_residues_contiguous_indexer< PCRep >Data structure to handle the contiguous indices of residues/un its in a chain even in the presence of missing residues/units
 CT_Conformation_builder_cartesian_default< Conformation_ >Default builder for conformations with cartesian coordinates,
 CT_Conformation_traits< Conformation >Traits class to be specialized
 CT_Conformation_with_covalent_structure< ConformationBase, CovalentStructure >Class enhancing a conformation with a covalent structure e.g. from the package Molecular_covalent_structure
 CT_Conformation_with_height< ConformationBase, HeightType >Struct SBL::CSB::T_Conformation_with_implicit_height which enhances a conformation with coordinates by adding a height
 CT_Conformation_with_implicit_height< ConformationBase, HeightFunctor >Provides the struct SBL::CSB::T_Conformation_with_implicit_height which enhances a conformation with coordinates by adding a height and also takes a functor to apply a function to the height
 CT_Default_amino_acid_seqan_sequence_converter< Dummy >Default converter that justs returns the input name as the seqan amino acid name, and recirpocally
 CT_Dihedral_angles_visitor< CovalentStructure >Defines iterator over the dihedral angles of a covalent structure
 CT_External_distance< Conformation, NumberType >Distance computed from an external executable (sbl-conf-distance.exe) Distance computed from an external executable (sbl-conf-distance.exe)
 CT_Get_particle_default< Conformation, ParticleRep >Model of Distance for defining distance between two conformations
 CT_Hierarchical_labels_forest< MolecularSystemLabelsTraits >Provides a forest structure associated to the labels defined in MolecularSystemLabelsTraits
 CT_Improper_angles_visitor< CovalentStructure >Defines iterator over the improper angles of a covalent structure
 CT_Iterative_aligner< StructureType, SeederType, ScoreComputer >
 CT_Iterative_aligner< StructureType, T_Seeder_DP_score< StructureType, T_Score_computer_K< StructureType::value_type > >, G_Score_computer >
 CT_Iterative_aligner_identity< StructureType, Seeder, ScoreComputer >
 CT_Iterative_aligner_identity< StructureType, T_Seeder_basic< StructureType >, G_Score_computer >
 CT_Least_RMSD_cartesian< Conformation, GetParticle, MolecularAlignment >Model of Distances for defining distance between two conformations
 CT_Least_RMSD_cartesian< Conformation, GetParticle, MolecularAlignment >
 CT_Least_RMSD_cartesian< Point_d >
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Backbone_const_iteratorIterator through the atoms of the chain backbone (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Backbone_iteratorIterator through the atoms of the chain backbone
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::BondRepresentation of a bond between two atoms
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angleRepresentation of a valence angle between three atoms
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_const_iteratorIterator through all the valence angles in the chain (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_iteratorIterator through all the valence angles in the chain
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_const_iteratorIterator through all the bonds in the chain (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_iteratorIterator through all the bonds in the chain
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angleRepresentation of a proper dihedral angle between four atoms
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_const_iteratorIterator through all the proper dihedral angles in the chain (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_iteratorIterator through all the proper dihedral angles in the chain
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_const_iteratorIterator through bonded atoms to an input atom (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_iteratorIterator through bonded atoms to an input atom
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Ordered_chain_iteratorGeneric dihedral angle iterator for arbitrary ordred atom chain
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_const_iteratorIterator through all the atoms of an input residue (const)
 CT_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_iteratorIterator through all the atoms of an input residue
 CT_Mediated_interface_data_structure_base< MolecularInterfaceDataStructure >Container defining what is a mediated interface between two partners and a mediator
 CT_Mediated_interface_data_structure_base< Mediated_interface_base >
 CT_Mediated_interface_data_structure_base< Molecular_interface_connected_component_data_structure >
 CT_Mediated_interface_oserialization< MediatedInterface >Serialization of a mediated interface
 CT_Minimizer_Ipopt_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >Constraints for minimizing without any constraint
 CT_Minimizer_parameters_without_constraint< PointType, RealValueFunction, GradientFunction >Constraints for minimizing without any constraint
 CT_Molecular_cartesian_coordinates< ConformationType, CovalentStructure >Computes the cartesian coordinates from the internal coordinates and the covalent structure of a molecular conformation
 CT_Molecular_covalent_structure< Particle_info_ >Representation of the covalent structure of a molecular conformation
 CT_Molecular_covalent_structure_bond_angle_gradient< ConformationType, CovalentStructure >Defines the gradient associated to the bond angle
 CT_Molecular_covalent_structure_bond_length_gradient< ConformationType, CovalentStructure >Defines the gradient associated to the bond length
 CT_Molecular_covalent_structure_builder_for_protein_martini< Molecular_covalent_structure_ >Builds a covalent structure from a given model
 CT_Molecular_covalent_structure_builder_for_proteins< Molecular_covalent_structure_ >Builds a covalent structure from a given model
 CT_Molecular_covalent_structure_constraints_for_proteins< CovalentStructure, Conformation >Returns true iff the input conformation respects the input constraints
 CT_Molecular_covalent_structure_optimal< ParticleInfo >Optimized representation of the covalent structure of a molecular conformation
 CT_Molecular_covalent_structure_torsion_angle_gradient< ConformationType, CovalentStructure >Defines the gradient associated to the torsion angle
 CT_Molecular_geometric_model_classifier_for_alpha_complex< AlphaComplexOfMolecularModel >Functor returning true or false if a tupel of particles is represented in the alpha-complex of an input molecular model
 CT_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >Container for interfaces edges of the alpha-complex that are connected and share the same interface
 CT_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >::Have_labelsPredicate initialized with one or two labels, that checks that a vertex has an ancestor of or equal given label, or an edge has ancestors of or equal given pair of labels
 CT_Molecular_interface_connected_component_data_structure< ParticleWithSystemLabelTraits, MolecularModel >
 CT_Molecular_interface_connected_component_oserialization< MolecularInterface >Serialization of a connected component of a molecular interface
 CT_Molecular_interface_data_structure_base< MolecularInterfaceConnectedComponent >Container for Molecular interface connected components that share the same interface
 CT_Molecular_interface_data_structure_base< Bicolor_interface_connected_component >
 CT_Molecular_interface_data_structure_base< Mediated_interface_connected_component >
 CT_Molecular_interface_data_structure_base< Tricolor_interface_connected_component >
 CT_Molecular_interface_oserialization< MolecularInterface >Serialization of a molecular interface
 CT_Molecular_interfaces_builder< ParticleWithSystemLabelTraits, MolecularModelClassifier >Construct all the primitive and hierarchical interfaces associated to a molecular model represented by an alpha-complex
 CT_Molecular_interfaces_traits< ParticleWithSystemLabelTraits, MolecularModel >Traits class defining the different kind of molecular interfaces
 CT_Molecular_potential_energy< Contribution, Contributions >Potential energy function adding up all the input contributions (C++11 only)
 CT_Molecular_potential_energy_bond_angle_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard gradient associated to the bond angle contribution
 CT_Molecular_potential_energy_bond_angle_gradient_Urey_Bradley< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Urey-Bradley gradient associated to a bond angle
 CT_Molecular_potential_energy_bond_angle_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard term associated to the bond angle contribution
 CT_Molecular_potential_energy_bond_angle_term_Urey_Bradley< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Urey-Bradley term associated to a bond angle
 CT_Molecular_potential_energy_bond_length_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard gradient associated to the bond length contribution
 CT_Molecular_potential_energy_bond_length_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard term associated to the bond length contribution
 CT_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >Contribution of all bonded energy terms to the potential energy function
 CT_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, T_Molecular_potential_energy_bond_length_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >, T_Molecular_potential_energy_bond_angle_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >, T_Molecular_potential_energy_torsion_angle_in_linear_structure_term< ConformationType, CovalentStructure, PotentialEnergyParameters > >
 CT_Molecular_potential_energy_cmap_term< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the CMap term associated to a pair of proper dihedral angles
 CT_Molecular_potential_energy_contribution< Visitor, Term, Terms >Contribution of an energy term to the potential energy function
 CT_Molecular_potential_energy_electrostatic_gradient< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines a standard gradient associated to the electrostatic contribution
 CT_Molecular_potential_energy_electrostatic_term< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines a standard term associated to the electrostatic contribution
 CT_Molecular_potential_energy_gradient< Contribution, Contributions >Sum of the contributions of an energy gradient term to the potential energy gradient function
 CT_Molecular_potential_energy_gradient_contribution< Visitor, Term, Terms >Contribution of an energy gradient term to the potential energy gradient function
 CT_Molecular_potential_energy_Lennard_Jones_gradient< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard gradient associated to the Lennard Jones contribution
 CT_Molecular_potential_energy_Lennard_Jones_term< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the standard term associated to the Lennard Jones contribution
 CT_Molecular_potential_energy_Lennard_Jones_term< Conformation, Covalent_structure, Potential_energy_parameters >
 CT_Molecular_potential_energy_numerical_gradient< MolecularPotentialEnergy, PotentialEnergyParameters >Computes numerically the gradient of a potential energy function
 CT_Molecular_potential_energy_torsion_angle_gradient_Fourier< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Fourier gradient associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the harmonic gradient associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_gradient_in_linear_structure< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the gradient associated to the torsion angle contribution in a linear structure
 CT_Molecular_potential_energy_torsion_angle_gradient_periodic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the periodic gradient associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_gradient_Ryckaert_Bellemans< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Ryckaert_Bellemans gradient associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_in_linear_structure_term< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the term associated to the torsion angle contribution in a linear structure
 CT_Molecular_potential_energy_torsion_angle_term_Fourier< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Fourier term associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the harmonic term associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_term_periodic< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the periodic term associated to the proper dihedral angle contribution
 CT_Molecular_potential_energy_torsion_angle_term_Ryckaert_Bellemans< ConformationType, CovalentStructure, PotentialEnergyParameters >Defines the Ryckaert_Bellemans term associated to the proper dihedral angle contribution
 CT_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >Computes the internal coordinates from the covalent structure of a molecular conformation
 CT_Molecular_structure_classifier< ParticleWithSystemLabelTraits, MolecularModelClassifier >Classify the particles of molecular systems that are at a given interface
 CT_Molecular_structure_traits< ParticleWithSystemLabelTraits, MolecularStructure >Traits clas defining types used for the Molecular Structure Classifier
 CT_Multiple_sequence_alignment_DS< SeqName, UnitRep, Score >
 CT_Nucleic_acid_representation< PolynucleotideChain >
 CT_Particle_info_biomolecules< ParticleTraits >Information on the particle to attach to the vertices of the covalent structure when using it with force fields
 CT_Particle_info_for_proteins< Particle_traits_ >Information on the particle to attach to the vertices of the covalent structure when using it with force fields
 CT_Particle_info_traits< ParticleTraits >Concept for manipulating particle info attached to a covalent structure
 CT_Particle_vertex_base< ParticleTraits, GT, Vb >Specialized vertex of a 3D triangulation with an attached particle
 CT_Particle_vertex_base< ParticleTraits, GT, Vb >::Rebind_TDS< TDS2 >Rebind data structure for inheriting from a vertex data structure as specified in the CGAL library
 CT_Particle_vertex_base< ParticleTraits, GT, Vb >
 CT_Particle_vertex_base< ParticleTraits, GT, Vb2 >
 CT_Particle_vertex_base< ParticleTraits, Triangulation_traits, CGAL::Triangulation_vertex_base_3< Triangulation_traits > >
 CT_Phi_psi_dihedral_angles_visitor< CovalentStructure >
Defines iterator over all successive pairs of dihedrals
 CT_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >Representation of a single polynucleotide chain within a Nucleic Acid representation
 CT_Polynucleotide_chain_representation< Particle_traits, Molecular_covalent_structure, Conformation_type >
 CT_Polypeptide_chain_contacts_finder< PCRep >Class to find pairwise atomic contacts withing a polypeptide chain
 CT_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >Representation of a single polypeptide chain within a Nucleic Acid representation
 CT_Polypeptide_chain_representation< Particle_traits, Covalent_structure, Conformation >
 CT_Polypeptide_chain_representation< Particle_traits, Molecular_covalent_structure, Conformation_type >
 CT_Protein_representation< PolypeptideChain >Representation of a protein with its polypeptide chains
 CT_Real_value_function_minimizer< PointType, RealValueFunction, GradientFunction, MinimizerConstraints >Minimizer of a real valued function
 CT_Real_value_function_minimizer_Ipopt< PointType, RealValueFunction, GradientFunction, MinimizerConstraints >Minimizer of a real valued function
 CT_Real_value_function_minimizer_LBFGS< PointType, RealValueFunction, GradientFunction >Minimizer of a real valued function using the header-only library LBFGS++
 CT_RMSD_comb_edge_weighted< Structure, MolecularDistance >Given a set of motifs instantiates the motif graph and computes the associated combined RMSD
 CT_RMSD_comb_edge_weighted< Structure, MolecularDistance >::Vertex_propertyVertex property for the motif graph
 CT_Score_computer_K< CanonizedResidue >
 CT_Seeder_basic< StructureType >Given two structures, align them using Kpax_seeder
 CT_Seeder_DP_score< StructureType, ScoreComputer >Given two structures, align them using Seeder_DP_score
 CT_Squared_angular_internal_distance< Conformation, NT, MolecularAlignment >Model of distance between angles of two conformations given with their internal coordinates
 CT_Squared_angular_internal_distance< Conformation, double, Molecular_alignment_default >
 CT_Squared_angular_internal_distance< Conformation, NT, MolecularAlignment >
 CT_Squared_RMSD_internal_distance< Conformation, InternalDistance, GetParticle, MolecularAlignment >Model of Distance for defining distance between two conformations
 CT_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >Builds a graph representing the biochemical interactions between units of a protein
 CT_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >::Edge_label_writerFunctor allowing to write two properties associated to a vertex or an edge into a dot file representing a graph
 CT_Tertiary_quaternary_structure_annotator< ParticleTraits, MolecularSystemLabelTraits >::Vertex_label_writerFunctor allowing to write two properties associated to a vertex into a dot file representing a graph
 CT_TLC_polynomial< Algebraic_Kernel >Converts the Tripeptide contraints given to a 16th degree polynomial
 CT_TLC_polynomial_roots_to_embedings< Algebraic_Kernel >Converts polynomial roots to embeddings using values defined in T_TLC_polynomial
 CT_TLC_polynomial_solver_interface< Algebraic_Kernel >Interface to the CGAL polynomial solver using Algebraic Number types
 CT_TLC_solver< Algebraic_Kernel >Computes the backbone coordinates of solutions to the Tripeptide loop closure with only phi and psi bond angles changing in internal coordinates
 CT_Transition_graph_traits_compressed< SampleRep, SampleWeight, VertexContainer, EdgeContainer >Note that all methods are static – no member data
 CT_Transition_graph_traits_standard< SampleRep, SampleWeight, VertexContainer, EdgeContainer >TG representation with explicit storage of the saddles as vertices of the TG
 CT_Triangulation_of_molecular_model< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase >Derived class from CGAL Regular triangulation for filling it with particles
 CT_Triangulation_of_molecular_model< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase >
 CT_Tricolor_interface_data_structure_base< MolecularInterfaceDataStructure >Container defining what is a tricolor interface between two partners
 CT_Tricolor_interface_data_structure_base< Molecular_interface_connected_component_data_structure >
 CT_Tricolor_interface_data_structure_base< Tricolor_interface_base >
 CT_Tricolor_interface_oserialization< TricolorInterface >Serialization of a tricolor interface
 CT_Tripeptide_anchors< NT >Anchor atoms around the moving atoms for the tripeptide loop closure
 CT_Tripeptide_constraints< NT >Constraints used to solve the tripeptide loop closure
 CT_Unbonded_particles_visitor< CovalentStructure >
Defines iterator over all distinct pairs of particles
 CT_Unbonded_particles_with_threshold_visitor< CovalentStructure, ConformationType >
Defines iterator over all distinct pairs of particles
 CHit_info
 CHits_manager
 CHits_manager_no_annotations
 CNCBI_wrapper
 CUniprot_wrapper
 CBin_properties_InternalThe Bin_properties struct defines which properties are stored per bin. by default, the density and the histogram, plus some custom user-defined stats
 CCombined_WL_Move_Set_Data_Interface< WL_DS_Interface, i >Class for the i-th move set to access its data stored in the WL DS To see how it works: index i: generates a new interface
for a MS: in each bin: data for each MS for a combined MS: in each bin: tuple for all MS class on top on the interface, to access the data of the i-th MS
 CDarting_Move_ParamsDarting Move set Params
 CDarting_Move_Set_TraitsDarting Move set traits (see paper for details of internal working)
 CDarting_Move_StatsDarting Move set Stats
 CGaussian_Move_ParamsGaussian Move params
 CGaussian_Move_Set_TraitsGaussian Move Set, simplest move set provided. Propose a move sampled from a normal distribution centered on the starting point
 CGaussian_Move_StatsGaussian Move Set stats
 CK_means_scoresVarious scores for K_means
 CNearest_neighbors_graph_builderBuilder for nearest neighbors graphs
 CNearest_neighbors_graph_builder_with_edge_weightBuilder for nearest neighbors graphs
 CNo_Overstep_Cone_Move_ParamsNo overstep cone move set params
 CNo_Overstep_Cone_Move_Set_TraitsNo overstep cone move set traits: a move set that aims to sample neighbourings energy strata, and uses the cone strategy for better mixing. See paper for details
 CNo_Overstep_Cone_Move_StatsNo overstep cone move set stats
 CNo_Overstep_Move_ParamsNo overstep move set params
 CNo_Overstep_Move_Set_TraitsNo overstep move set traits: a move set that aims to sample neighbourings energy strata. See paper for details
 CNo_Overstep_Move_StatsNo overstep move set stats
 CT_ANN_FLANN_wrapper< GetDistance, GetPoint, IndexParams, SearchParams >Nearest neighbor engine from FLANN library
 CT_ANN_meta< RandomizedANN, IsLowerPoint >Nearest neighbor engine designed for metric spaces
 CT_ANN_meta< SBL::GT::T_ANN_metric_space_proximity_tree< DistanceFunction > >
 CT_ANN_meta< SBL::GT::T_ANN_metric_space_proximity_tree< DistanceType > >
 CT_ANN_metric_space_LAESA< GetDistance, ExcludedPivots >Nearest neighbor engine designed for metric spaces
 CT_ANN_metric_space_proximity_tree< DistanceFunction, SplitterFunction >Nearest neighbor engine designed for metric spaces
 CT_Betti_numbers_1< GraphType >Compute the Betti numbers of a Graph
 CT_Betti_numbers_2< AlphaComplex3 >Compute the Betti numbers of a 3D Cell Complex from its alpha-complex
 CT_Cluster_engine_k_means< KMTraits >
 CT_Cluster_engine_k_means_com_euclidean< PointType, VectorType >Representation of a center of mass for k-means in Euclidean spaces
 CT_Cluster_engine_k_means_com_Sd< VectorType, CenterOfMassInitializer >Representation of a center of mass in k-means algorithm
 CT_Cluster_engine_Morse_theory_based< PointType, DistanceFunction, TNNQuery, TGetDensity >Morse theory based clustering algorithm
 CT_com_inertia_calculator< PointType, VectorType, Cost >
 CT_Combined_Move_Params< Conformation, Move_Set_Traits >Collect into a tuple the params of all move sets
 CT_Combined_Move_Set< Conformation, Move_Set_Selector, Move_Set_Traits >As above, but for move sets rather than controllers
 CT_Combined_Move_Set_Controller< Combined_Move_Set_Data_Interface, Conformation, Move_Set_Traits >Contoler : controls the MS WL calls the controller of the combined MS, which (recursively, thanks to templates) calls the defered controllers
 CT_Combined_Move_Stats< Conformation, Move_Set_Traits >Collect into a tuple the stats of all move sets
 CT_Darting_Move_Set< Conformation >Darting Move set. Physical conformation needs a function get_grad, compute_energy and get_energy and a member data
 CT_Darting_Move_Set_Controller< Conformation >Darting Move set Controller
 CT_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_area_of_dual_of_edgeGiven the dual of an edge, compute its area
 CT_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_dual_of_edgeGiven an edge, return its dual as a container of points
 CT_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_dual_of_facetGiven a facet, return its dual as a segment
 CT_Delaunay_triangulation_extension_3< DelaunayTriangulation3 >::Get_squared_length_of_dual_of_facetGiven a facet, return the squared length of its dual segment
 CT_Delaunay_triangulation_spherical_traits_3< FT, SphereRep >Kernel used for computations involving exact number types for coordinates of boundary points
 CT_Delaunay_triangulation_spherical_traits_3< NTBoundary, typename WeightedAlphaComplex3::Vertex_handle >
 CT_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >Model for the base of a geometric kernel for T_Delaunay_triangulation_spherical_traits_3
 CT_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >::Base< Kernel2 >Base for the kernel
 CT_Delaunay_triangulation_spherical_traits_3_base< Kernel2, BasicKernel, SphereRep >
 CT_Distance_default_for_graph< GraphType, NT >Base distance over vertices of a graph
 CT_DS_conformation< Conformation >This class contains a conformation from the physical system, to which we append information on the energy and the bin index
 CT_DS_snapshot_default< Bin_properties >A class storing the main pieces of information, at a given time stamp in the course of the algorithm
 CT_Frechet_mean_S1< Kernel >This class computes local and global minimums of the sum of p exponent distance function
 CT_Gaussian_Move_Set< Conformation >Gaussian Move Set
 CT_Gaussian_Move_Set_Controller< Conformation >Gaussian Move Set controller
 CT_Least_RMSD_cartesian_3< GeometricKernel >Perform a 3D rigid registration between two 3D point clouds, then computes the RMSD distance between the two aligned clouds
 CT_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >Representation of the complex of the same name
 CT_Morse_Smale_Witten_chain_complex_from_NNG_builder< GraphType, MorseFunction, DistanceFunction, StableManifoldTraits >Builds the Morse Smale Witten chain complex from a NNG
 CT_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< GraphType, GetVertexWeight >Builds the Morse Smale Witten chain complex from a vertex weighted graph
 CT_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >Builds the Morse Smale Witten chain complex from a weighted graph
 CT_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >Analysis of a Morse Smale Witten chain complex
 CT_NN_linear_scan< DistanceFunction >Naive algorithm looking for the nearest neighbors of a point in a database w.r.t a metric space Naive algorithm looking for the nearest neighbors of a point in a database w.r.t a metric space
 CT_NN_metric_tree< DistanceFunction, SplitterFunction >Nearest neighbor engine designed for metric spaces
 CT_No_Overstep_Cone_Move_Set< Conformation >No overstep cone move set
 CT_No_Overstep_Cone_Move_Set_Controller< Conformation >No overstep cone move set controller
 CT_No_Overstep_Move_Set< Conformation >No overstep move set
 CT_No_Overstep_Move_Set_Controller< Conformation >No overstep move set controller
 CT_Point_cloud_rigid_registration_3< FT >Model of Distances for defining distance between two point clouds
 CT_RMSD_cartesian_3< GeometricKernel >RMSD distance between two 3D point clouds
 CT_Rotation_3< Point_container_iterator, NT, Back_inserter >Static 3d rotation methods
 CT_SE3_representation< InputNT, InternalNT >SE3
 CT_SE3_representation< INT, ONT >
 CT_seed_inertia_calculator< PointType, VectorType, Cost >
 CT_Seed_reselector< PointType, VectorType, Cost, Candidate_metric_calculator >
 CT_Seed_selector_k_means_plus_plus< PointType, VectorType, Cost >Select seeds with D2 weighting
 CT_Seed_selector_minimax< PointType, VectorType, Cost >Select seeds by maximizing the min cost for seeds at each selection step
 CT_Seed_selector_random< PointType, VectorType >
 CT_Spectral_clustering< GraphType >Spectral clustering algorithm from Ng et al at NeurIPS 2001
 CT_Spherical_kernel_extension_3< SphericalKernel >Extension completing the 3D Spherical kernel of CGAL
 CT_Spherical_kernel_extension_3< SphericalKernel >::Is_counter_clockwise_orientedCheck that an oriented edge and a point on the circular arc represented by this edge defines a counter clockwise orientation
 CT_Spherical_kernel_extension_3< SphericalKernel >::Is_largest_circular_arc_3Returns a sign that is negative if the input circular arc is the largest one, positive if its opposite, and 0 if its angle is PI
 CT_Spherical_kernel_extension_3< SphericalKernel >::Orientation_with_roots_3Orientation predicate allowing input numbers as Root_of_2
 CT_Splitter_default< DistanceFunction, TNNEngine >Nearest neighbor engine designed for metric spaces
 CT_Squared_Least_RMSD_cartesian_3< GeometricKernel >Perform a 3D rigid registration between two 3D point clouds, then computes the squared RMSD distance between the two aligned clouds
 CT_Squared_RMSD_cartesian_3< GeometricKernel >Squared RMSD distance between two 3D point clouds
 CT_Stable_manifold_as_list_traits< Point >Simple representation of a stable manifold as a list of points
 CT_Trajectory< SE3 >Trajectory of a point undergoing a motion in 3D
 CT_Triangulation_extension_3_base< Triangulation3 >Defines simple predicates and constructions structure over a triangulation
 CT_Triangulation_extension_3_base< Triangulation3 >::Canonical_edgeCanonical representation of an edge in the 3D Triangulation
 CT_Triangulation_extension_3_base< Triangulation3 >::Canonical_facetCanonical representation of a facet in the 3D Triangulation
 CT_Triangulation_extension_3_base< Triangulation3 >::Get_common_facetGiven two cells, return the common facet of the two cells
 CT_Triangulation_extension_3_base< Triangulation3 >::Get_other_two_edgesGiven an edge and a facet bounding it, return the two other edges of the facet
 CT_Triangulation_extension_3_base< Triangulation3 >::Is_cofaceCheck that a simplex is the coface of a second simplex
 CT_Triangulation_extension_3_base< Triangulation3 >::Is_counter_clockwise_orientedPredicate checking that a facet of the 3D triangulation is counter-clockwise oriented
 CT_Triangulation_extension_3_base< Triangulation3 >::T_Vertex_handle_with_order< IsLessVertex >Check that a simplex is the coface of a second simplex
 CT_Triangulation_extension_3_base< SBL::CSB::T_Alpha_complex_of_molecular_model< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase, TAlphaComplexBase > >
 CT_Triangulation_extension_3_base< SBL::CSB::T_Triangulation_of_molecular_model< ParticleTraits, TAlphaComplexVertexBase, TAlphaComplexCellBase > >
 CT_Union_of_balls_boundary_3_builder< UnionOfBallsBoundaryDS, ExactNT >Functor filling a HDS of the Boundary of an union of balls
 CT_Union_of_balls_boundary_3_data_structure< WeightedAlphaComplex3, IS_CCW, HalfedgeDSBase >Representation of the boundary of the union of balls
 CT_Union_of_balls_boundary_3_data_structure< Alpha_complex >
 CT_Union_of_balls_boundary_3_data_structure< AlphaComplex3 >
 CT_Union_of_balls_boundary_3_data_structure< WeightedAlphaComplex3, IS_CCW, HalfedgeDSBase >
 CT_Union_of_balls_boundary_3_item_info< WeightedAlphaComplex3, Simplex >Attached a simplex of the $\alpha$-complex to an item of the half-edge data structure
 CT_Union_of_balls_boundary_3_item_info< WeightedAlphaComplex3, WeightedAlphaComplex3::Edge >
 CT_Union_of_balls_boundary_3_item_info< WeightedAlphaComplex3, WeightedAlphaComplex3::Facet >
 CT_Union_of_balls_boundary_3_item_info< WeightedAlphaComplex3, WeightedAlphaComplex3::Vertex_handle >
 CT_Union_of_balls_boundary_3_items< WeightedAlphaComplex3 >Instantiation of face, half-edge and vertex tpes of the half-edge data structure
 CT_Union_of_balls_boundary_3_side< AlphaComplex3, EXTERIOR_TAG >Construction of the mesh of the union of 3D balls such that any point at the surface of the union of balls has a point of the mesh in its epsilon-neighborhood
 CT_Union_of_balls_boundary_patch_shelling_3< UnionOfBallsBoundary3, IsInPatch >Shelling diagram of a patch on the boundary of the union of 3D balls
 CT_Union_of_balls_boundary_patch_shelling_3< UnionOfBallsBoundary3, IsInPatch >::Face_complex_traits::Cell_handleWrapper for the faces of the boundary in the cell complex shelling diagram
 CT_Union_of_balls_boundary_patch_shelling_3< UnionOfBallsBoundary3, IsInPatch >::Face_complex_traits::Get_cell_boundary_from_halfedgeFunctor casting a halfedge of the boundary to a cell's boundary of the cell complex
 CT_Union_of_balls_boundary_patch_shelling_3< UnionOfBallsBoundary3, IsInPatch >::Face_complex_traits::Get_cell_from_faceFunctor casting a face of the boundary to a cell of the cell complex
 CT_Union_of_balls_boundary_patch_shelling_3< UnionOfBallsBoundary3, IsInPatch >::Face_complex_traits::Is_in_cell_complexPredicate checking that a cell or the boundary of a cell is at an interface, i.e in a binding patch
 CT_Union_of_balls_epsilon_mesh_3< UnionOfBallsBoundary3, EXTERIOR_TAG >Construction of the mesh of the union of 3D balls such that any point at the surface of the union of balls has a point of the mesh in its epsilon-neighborhood
 CT_Union_of_balls_medial_axis_3_builder< UnionOfBallsMedialAxis3 >Algorithm constructing the medial axis of an union of balls
 CT_Union_of_balls_medial_axis_3_data_structure< WeightedAlphaComplex3, NTBoundary, HalfedgeDSBase >Representation of the medial-axis of the union of balls
 CT_Union_of_balls_medial_axis_3_data_structure< Alpha_complex >
 CT_Union_of_balls_medial_axis_3_data_structure< WeightedAlphaComplex3, NTBoundary, Base >
 CFace_iterator< WeightedAlphaComplex3, NTBoundary, HalfedgeDSBase >
 CHalfedge_handle< WeightedAlphaComplex3, NTBoundary, HalfedgeDSBase >
 CHalfedge_iterator< WeightedAlphaComplex3, NTBoundary, HalfedgeDSBase >
 CVertex_handle< WeightedAlphaComplex3, NTBoundary, HalfedgeDSBase >
 CT_Union_of_balls_medial_axis_3_face< Refs, WeightedAlphaComplex3, DelaunayTriangulation3 >Representation of a face in the half-edge data structure
 CT_Union_of_balls_medial_axis_3_halfedge< Refs, WeightedAlphaComplex3, DelaunayTriangulation3 >Representation of a half-edge in the half-edge data structure
 CT_Union_of_balls_medial_axis_3_items< WeightedAlphaComplex3, DelaunayTriangulation3 >Instantiation of face, half-edge and vertex tpes of the half-edge data structure
 CT_Union_of_balls_medial_axis_3_vertex< Refs, WeightedAlphaComplex3, DelaunayTriangulation3 >Representation of a vertex in the half-edge data structure
 CT_Union_of_balls_surface_volume_3< AlphaComplex3, SphericalKernel3, UnionOfBallsBoundary3 >Algorithm computing the surface area and the volume of the union of 3D balls
 CT_Wang_Landau< Physical_System, Move_Set_Traits, WL_DS_, NumCores >
This is the main class that runs a Wang-Landau simulation
 CT_Wang_Landau< Physical_System, Move_Set_Traits, WL_DS_, NumCores >::Roll_Back_Restoration_PointInformotion used to roll back, including the states for random number generators
 CT_Wang_Landau< Physical_System, Move_Set_Traits, WL_DS_, NumCores >::WL_DS_InterfaceClass used by the move set controllers (one for each move set), to access information stored in the DS Nb: for WL, there is a single move set, the combined one
 CT_WL_Data_Structure_Internal< Conformation, Bin_properties, DS_snapshot_ >Bin management: main data structure used by Wang_landau algorithm
 CT_WL_Data_Structure_Internal< Conformation, Bin_properties_custom< Move_Set_Traits::template Controller< Dual_Well_Physical_System::Conformation >::Move_Set_Controller_Data >, T_DS_snapshot_default >
 CT_WL_Data_Structure_Internal< Conformation, T_Bin_properties< Move_Set_Controller::Move_Set_Controller_Data >, T_DS_snapshot_default >
 CT_WL_Data_Structure_Internal< Conformation, T_Bin_properties< typename Move_Set_Traits::template Controller< typename Physical_System::Conformation >::Move_Set_Controller_Data >, T_DS_snapshot_default >
 CT_WL_Simulation< Physical_System, Move_Set_Traits >
 CT_WL_Simulation< Boltzman_Energy_Well_Physical_System, Combined_MS_Traits >
 CT_WL_Simulation< Isotrop_Energy_Well_Physical_System, Combined_MS_Traits >
 CT_WL_Simulation< Isotrop_Energy_Well_Physical_System, Move_Set_Traits >
 CT_WL_Simulation< Non_Isotrop_Energy_Well_Physical_System, Combined_MS_Traits >
 CT_WL_Simulation< Non_Isotrop_Energy_Well_Physical_System, Move_Set_Traits >
 CT_WL_Simulation< Physical_System, Combined_MS_Traits >
 CT_WL_Simulation< Physical_System, Gaussian_Move_Set_Traits >
 CT_WL_Simulation< Physical_System, No_Overstep_Cone_Move_Set_Traits >
 CT_WL_Simulation< Physical_System, No_Overstep_Move_Set_Traits >
 CT_WL_Simulation< Physical_System_Amber, Combined_MS_Traits >
 CWL_histo_change_measureChange from measure pi to measure mu, see paper
 CWL_stats_serializerHelper class which stores into files:
 CCodeGenerator
 CGeneratorPanel
 CGeneratorPyQt6
 CGeneratorTkinter
 CGUIGeneratorManager
 CGUI
 CMetadata
 CParseGUI
 CWidget
 CWindow
 CUItoJsonConverter
 CUiToJsonConverter
 CGUIInputPanelJsonGenerator
 CGUIUpdatePanelJsonGenerator
 CHMM
 CChain_selectionSelection object representing a chain selection for molecular viewers
 CMolecular_view< Viewer, ViewableObject >Base class for viewing an object in one of the available format (VMD, PyMOL)
 CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Point_3< K > >Views a 3D point in PyMOL format
 CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Sphere_3< K > >Views in PyMOL format a 3D sphere.
 CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Triple< CGAL::Point_3< K >, CGAL::Point_3< K >, CGAL::Point_3< K > > >Views a 3D triangle in PyMOL format
 CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Triple< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > >Views in PyMOL format a 3D triangle represented by the three input 3D weighted points
 CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Weighted_point< Point, Weight > >Views in PyMOL format a 3D sphere represented by the input 3D weighted point
 CMolecular_view< T_PyMOL_viewer< Dummy >, Chain_selection >PyMOL specialization for Chain_selection
 CMolecular_view< T_PyMOL_viewer< Dummy >, std::pair< CGAL::Point_3< K >, CGAL::Point_3< K > > >Views a 3D segment in PyMOL format
 CMolecular_view< T_PyMOL_viewer< Dummy >, std::pair< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > >Views in PyMOL format a 3D segment represented by the two input 3D weighted points
 CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Point_3< K > >Views a 3D point in VMD format
 CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Sphere_3< K > >Views in VMD format a 3D sphere.
 CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Triple< CGAL::Point_3< K >, CGAL::Point_3< K >, CGAL::Point_3< K > > >Views a 3D triangle in VMD format
 CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Triple< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > >Views in VMD format a 3D triangle represented by the three input 3D weighted points
 CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Weighted_point< Point, Weight > >Views in VMD format a 3D sphere represented by the input 3D weighted point
 CMolecular_view< T_VMD_viewer< Dummy >, Chain_selection >VMD specialization for Chain_selection
 CMolecular_view< T_VMD_viewer< Dummy >, std::pair< CGAL::Point_3< K >, CGAL::Point_3< K > > >Views a 3D segment in VMD format
 CMolecular_view< T_VMD_viewer< Dummy >, std::pair< CGAL::Weighted_point< Point, Weight >, CGAL::Weighted_point< Point, Weight > > >Views in VMD format a 3D segment represented by the two input 3D weighted points
 CMolecular_view< Viewer, CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > * >Views in Molecular format the edges and facets of the input 3D $\alpha$-complex for its $\alpha$ value
 CMolecular_view< Viewer, CGAL::Alpha_shape_vertex_base_3< Gt, Vb, ExactAlphaComparisonTag, Weight_tag > >Uses the Molecular viewer of the base vertex of the 3D $\alpha$-complex
 CMolecular_view< Viewer, CGAL::Fixed_alpha_shape_3< Dt > * >Views in Molecular format the edges and facets of the input fixed 3D $\alpha$-complex for its $\alpha$ value
 CMolecular_view< Viewer, CGAL::Fixed_alpha_shape_vertex_base_3< Gt, Vb > >Uses the Molecular viewer of the base vertex of the fixed 3D $\alpha$-complex
 CMolecular_view< Viewer, CGAL::Regular_triangulation_3< Gt, Tds > * >Views in Molecular format the edges and facets of the input 3D regular triangulation
 CMolecular_view< Viewer, CGAL::Regular_triangulation_vertex_base_3< Gt, Vb > >Views in Molecular format the point represented by the input vertex of a 3D triangulation
 CMolecular_view< Viewer, CGAL::Triangulation_3< Gt, Tds > * >Views in Molecular format the edges and facets of the input 3D triangulation
 CMolecular_view< Viewer, CGAL::Triangulation_vertex_base_3< Gt, Vb > >Views in Molecular format the point represented by the input vertex of a 3D triangulation
 CMolecular_view< Viewer, CGAL::Triangulation_vertex_base_with_info_3< Info, Gt, Vb > >Views in Molecular format the point represented by the input vertex of a 3D triangulation (when info is attached)
 CMolecular_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 > >Views in Molecular format the segment represented by the input edge of a 3D $\alpha$-complex
 CMolecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Fixed_alpha_shape_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > >Views in Molecular format the segment represented by the input edge of a fixed 3D $\alpha$-complex
 CMolecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Regular_triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > >Views in molecular format the segment represented by the input edge of a 3D regular triangulation
 CMolecular_view< Viewer, CGAL::Triple< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int, int > >Views in Molecular format the segment represented by the input edge of a 3D triangulation
 CMolecular_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 > >Views in Molecular format the triangle represented by the input facet of a 3D $\alpha$-complex
 CMolecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Fixed_alpha_shape_cell_base_3< Gt, Cb >, Allocator >, Const >, int > >Views in Molecular format the triangle represented by the input facet of a fixed 3D $\alpha$-complex
 CMolecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Regular_triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int > >Views in Molecular format the triangle represented by the input facet of a 3D triangulation
 CMolecular_view< Viewer, std::pair< CGAL::internal::CC_iterator< CGAL::Compact_container< CGAL::Triangulation_cell_base_3< Gt, Cb >, Allocator >, Const >, int > >Views in Molecular format the triangle represented by the input facet of a 3D triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > *, typename CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag >::Edge > >Views in Molecular format the facet dual of the input edge of a 3D $\alpha$-complex, using the underlaying Delaunay triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > *, typename CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag >::Facet > >Views in Molecular format the edge dual of the input facet of a 3D $\alpha$-complex, using the underlaying Delaunay triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Fixed_alpha_shape_3< Dt > *, typename CGAL::Fixed_alpha_shape_3< Dt >::Edge > >Views in Molecular format the facet dual of the input edge of a fixed 3D $\alpha$-complex, using the underlaying Delaunay triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Fixed_alpha_shape_3< Dt > *, typename CGAL::Fixed_alpha_shape_3< Dt >::Facet > >Views in Molecular format the edge dual of the input facet of a fixed 3D $\alpha$-complex, using the underlaying Delaunay triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Regular_triangulation_3< Gt, Tds > *, typename CGAL::Regular_triangulation_3< Gt, Tds >::Edge > >Views in Molecular format the facet dual of the input edge of the input 3D regular triangulation
 CMolecular_view< Viewer, std::pair< const CGAL::Regular_triangulation_3< Gt, Tds > *, typename CGAL::Regular_triangulation_3< Gt, Tds >::Facet > >Views in Molecular format the edge dual of the input facet of the input 3D regular triangulation
 CT_Index_wrapper< IndexType, PrintedIndexType >Wrapper for indices where the IO dumping may be different from the index itself
 CT_Multiple_archives_serialization_xml_iarchive< DataType, InputArchive >XML input archive coupling the data from a secondary archive to the main xml archive
 CT_Multiple_archives_serialization_xml_iarchive< DataType, InputArchive >
 CT_Multiple_archives_serialization_xml_iarchive< SecondaryData, SecondaryArchive >
 CT_Multiple_archives_serialization_xml_oarchive< DataType, OutputArchive, IsLessData >XML output archive decoupling the data to put in the archive and data to possibly put in a secondary file
 CT_Multiple_archives_serialization_xml_oarchive< DataType, OutputArchive, IsLessData >
 CT_PyMOL_viewer< Dummy >Viewer writing in PyMOL file format
 CVMD_viewerViewer writing in VMD file format
 CKpaxAlignmentGraph
 CKpaxPostAnalyzer
 CMCI_bootstrap
 CAB_label_traitsTraits class defining partners' labels for binary molecular complexes A and B. Traits class defining partners' labels for binary molecular complexes A and B
 CDefault_radii_for_particles_with_annotated_nameDefault radii for atoms and pseudo-atoms as residues
 CExtra_label_traitsTraits class defining one extra's label. Traits class defining one extra's label
 CExtra_label_traits::Primitive_label_classifierFunctor returning a pair classifying a particle
 CGet_annotator_option_display_name_defaultReturns a string that is the default display name of options for generic annotators
 CGet_annotator_option_help_defaultReturns a string that is the default option help for generic annotators
 CGet_annotator_option_name_defaultReturns a string that is the default option name for generic annotators
 CIGAg_label_traitsTraits class defining hierarchical partners' labels for immunoglobulin (IG) with an antigen (Ag). Traits class defining hierarchical partners' labels for immunoglobulin (IG) with an antigen (Ag)
 CMake_no_annotation_keyReturns false, whatever is the entry
 CName_annotator_for_atoms_setter_defaultDefault annotated name setter, using the method set_annotated_name of the input particle
 CName_annotator_for_pseudo_atoms_setter_defaultDefault annotated name setter, using the method set_annotated_name of the input particle
 CNo_label_traitsTraits class defining no system's label. Traits class defining no system's label
 CNo_label_traits::Primitive_label_classifierFunctor returning a pair classifying a particle
 COne_label_traitsTraits class defining one partner's label. Traits class defining one partner's label
 COne_label_traits::Primitive_label_classifierFunctor returning a pair classifying a particle
 CRadius_annotator_for_particles_with_annotated_name_setter_defaultDefault radius setter, using the method set_radius of the input particle
 CSet_dynamic_annotation_defaultDefault data structure adding a dynamic annotation to a particle
 CT_AB_label_traits< Dummy >::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_Atom_with_flat_info< NT >Wrapper representing the atom
 CT_Atom_with_flat_info_and_annotations_traits< Annotations, GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_Atom_with_flat_info_traits< GeometricKernel, SystemItems >Traits class defining atoms traits (biophysical and geometric properties). Traits class defining atoms traits (biophysical and geometric properties)
 CT_Atom_with_flat_info_traits< GeometricKernel, SystemItems >::Atom_with_flat_infos_builderBuilder for containers of Particle_type
 CT_Atom_with_flat_info_traits< GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_Atom_with_flat_info_traits< CGAL::Exact_predicates_inexact_constructions_kernel, SBL::CSB::Default_system_items >
 CT_Atom_with_flat_info_traits< GeometricKernel, SystemItems >
 CT_Atom_with_hierarchical_info_and_annotations_traits< Annotations, GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_Atom_with_hierarchical_info_traits< GeometricKernel, SystemItems >Traits class defining atoms traits (biophysical and geometric properties). Traits class defining atoms traits (biophysical and geometric properties)
 CT_Atom_with_hierarchical_info_traits< GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_Atom_with_hierarchical_info_traits< CGAL::Epick, T_System_items_with_annotations< T_Name_and_radius_annotations< CGAL::Epick::FT, SBL::Models::T_Dynamic_annotator_for_atoms<>::template T_Annotations_with_dynamic< void > >, SBL::CSB::Default_system_items > >
 CT_Chain_label_traits< Dummy >Model of MolecularSystemLabelTraits for chains
 CT_Chain_label_traits< Dummy >::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_Conformation_builder_cartesian_default< ConformationType >Default builder for conformations with cartesian coordinates
 CT_Domain_label_traits< Dummy >Model of MolecularSystemLabelTraits for molecular complexes defined in a file.
 CT_Domain_label_traits< Dummy >::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_Dynamic_annotator_for_atoms< SetDynamicAnnotation >::T_Annotations_with_dynamic< AnnotationBase, DynamicAnnotation >Default class for representing dynamic annotations (it refines a base class of annotations)
 CT_Dynamic_annotator_for_atoms< SetDynamicAnnotation >::T_Annotations_with_dynamic< void, DynamicAnnotation >Default class for representing dynamic annotations (it is a base class of annotations)
 CT_Geometric_particle_traits< GeometricKernel, GeometricRepresentation >Particle represented by a simple geometric object (a 3D point, a 3D sphere or a 3D weighted point)
 CT_Geometric_particle_traits< GeometricKernel, GeometricRepresentation >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_IG_label_traits< Dummy >[definition]
 CT_IG_label_traits< Dummy >::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_IGAg_label_traits< Dummy >::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_Moveset_atomic< ConformationType >Moveset from each particle of a conformation
 CT_Moveset_global< ConformationType >Moveset of the conformation as a whole
 CT_Moveset_interpolation< ConformationType, Distance >Moveset of the conformation by interpolation between two conformations
 CT_Name_and_radius_annotations< FT, AnnotationsBase >Base annotations for a default atom (name and radius)
 CT_Particle_with_annotations< ParticleBase, AnnotationsType >Traits class defining particles traits with annotations
 CT_Particle_with_annotations< typename Base::Particle_type, AnnotationsType >
 CT_Particle_with_annotations_traits< ParticleTraitsBase, AnnotationsType >Traits class defining patricles traits with annotations
 CT_Particle_with_system_label< ParticleBase, PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits, IsSerializedLabel >Model of Particle with a system's label
 CT_Particle_with_system_label< ParticleBase, PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits, IsSerializedLabel >::System_labelRepresentation of a system's label, that can be either a partner, a mediator or an extra label
 CT_Particle_with_system_label< typename ParticleTraitsBase::Particle_type, PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits, IsSerializedLabel >
 CT_Particle_with_system_label_traits< ParticleTraitsBase, PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits, IsSerializedLabel >Model of ParticleTraits for defining particles with a system's label
 CT_Pseudo_atom_per_residue_spec_with_flat_info< NT >Wrapper representing the coarse atom
 CT_Pseudo_atom_per_residue_spec_with_flat_info_and_annotations_traits< Annotations, GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the coarse atom
 CT_Pseudo_atom_per_residue_spec_with_flat_info_traits< GeometricKernel, SystemItems >Traits class defining pseudo-atoms traits (biophysical and geometric properties). Traits class defining pseudo-atoms traits (biophysical and geometric properties)
 CT_Pseudo_atom_per_residue_spec_with_flat_info_traits< GeometricKernel, SystemItems >::Get_geometric_representationFunctor returning a weighted point representing the atom
 CT_Pseudo_atom_per_residue_spec_with_flat_info_traits< CGAL::Exact_predicates_inexact_constructions_kernel, SBL::CSB::System_items_with_coarse_grain >
 CT_Pseudo_atom_per_residue_spec_with_flat_info_traits< GeometricKernel, SystemItems >
 CT_Unit_system_traits_AKMA< NT >Traits class defining the types used in the AKMA unit system Traits class defining the types used in the AKMA unit system
 CT_Unit_system_traits_for_potential_energy< UnitSystemTraitsBase >Traits class defining the types used in an input system with eneriched types used in potential energy calculations Traits class defining the types used in an input system with eneriched types used in potential energy calculations
 CT_Unit_system_traits_none_AKMA< NT >Traits class defining dimensionless types for AKMA Traits class defining dimensionless types for AKMA
 CT_Unit_system_traits_none_AKMA< FT >
 CT_Unit_system_traits_none_AKMA< NT >
 CT_Unit_system_traits_none_MD< NT >Traits class defining dimensionless types for MD Traits class defining dimensionless types for MD
 CT_Unit_system_traits_none_MD< NT >
 CWater_label_traitsTraits class defining mediators' labels for water. Traits class defining mediators' labels for water
 CWater_label_traits::Primitive_label_classifierFunctor returning a pair classifying a particle
 CT_Bicolor_interface_oserialization< MolecularInterfaceBuilder >Serialization of a bicolor interface
 CT_Mediated_interface_oserialization< MolecularInterfaceBuilder >Serialization of a mediated interface
 CT_Module_based_workflow< Dummy >::Edge_property_label_writerWriter of properties of an edge of the graph in .dot format
 CT_Module_based_workflow< Dummy >::Graph_property_label_writerWriter of properties of the graph in .dot format
 CT_Module_based_workflow< Dummy >::Vertex_property_label_writerWriter of properties of a vertex of the graph in .dot format
 CT_Module_option_description< Dummy >Base module from which any module should inherit
 CT_Molecular_interfaces_module_statistics< MolecularStructureClassifier >Application's module_statistics for building the alpha-complex of a molecular model.
 CT_Tricolor_interface_oserialization< MolecularInterfaceBuilder >Serialization of a tricolor interface
 CT_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >::Union_of_balls_surface_volume_3Contains pointers over two functors for computing the volumes and surfaces areas with different level of exactness
 CCradle_step1
 CCradle_step2
 CCradle_step2_selected
 CCradle_step3
 CDendogram_processor
 CMatrix_processor
 CDistance_calculator
 CLabel_selector
 CB_factor_color_engine
 CB_factor_coloring_parser
 CBSA_color_engine
 CBSA_coloring_parser
 CChain_instances
 CcMISA_constructor
 CcMISA_recorder
 CColorbarTools
 CColored_MISA
 CCompute_interface_lRMSD
 CCreate_And_Compute_iRMSD
 CDefault_color_engine
 CDelta_ASA_color_engine
 CDelta_ASA_coloring_parser
 CExtract_shared_PDB_interface
 CInterface_oneside
 CInterface_pool
 CInterface_strings
 CMISA
 CMISA_constructor
 CMISA_input_specification_parser
 CPlot_tools
 CResidue_mapping
 CResSelector
 CSSE_color_engine
 CSSE_coloring_parser
 CBioPDB_vs_XML_Etree
 CPALSE_DS_manipulator
 CPALSE_statistic_handle
 CPALSE_xml_DB
 CPython_dico_vs_XML_Etree
 CIOI_tuple\sbl_add_package_main_class{Script_design, SBL.Params_base.IOI_tuple, Long: A dataclass storing the data members to initialize IO and interaction Short: A dataclass storing the data members to initialize IO and interaction } i################################################################################
 CParams_IOI\sbl_add_package_main_class{Script_design, SBL::Params_base::Params_IO, Long: A base class handling paths and filenames for outputs Short: A base class handling paths and filenames for outputs } i################################################################################
 CParams_zero\sbl_add_package_main_class{Script_design, SBL.Params_base.Params_zero, Long: A base class to automatically setup data members from kwargs Short: A base class to automatically setup data members from kwargs } i################################################################################
 CSBL_base_parser\sbl_add_package_main_class{Script_design, SBL.Params_base.SBL_base_parser, Long: A base parser providing default ubiquitous options Short: A base parser providing default ubiquitous options } i################################################################################
 CPDB_complex_to_unbound_partners_matcher
 CAtom_dataThe properties of an atom as given by vorshell + vorlume
 CAtomic_contact_dataInformation about contacts between atoms
 CChain_dataEssentially a collection of Residue_data
 CComplex_data_collector
 CFile_dataEssentially a collection of Chain_data
 CResidue_contact_dataThe properties of a residue as given by vorshell + vorlume
 CResidue_dataThe properties of a residue as given by vorshell + vorlume
 CGenetrank_gene_radar
 CGenetrank_GeneProteinTranslator
 CGenetrank_Translations
 CGenetrank_network_statistical_analysis
 CSBL_init_toolsAccessing env variable
 CPPIN_application
 CPPIN_gene_radar_scatter_plot
 CGenetrank_simulation_input
 CPPIN_simulation
 CPPIN_simulation_result
 CPPIN_multiple_simulation_statistics
 CPPIN_simulation_statistics
 CPPIN_simulation_visualizations
 CSBL_pytools\sbl_add_package_main_class{Script_design, SBL.SBL_pytools.SBL_pytools, Long: class providing utilities to handles files and directories Short: class providing utilities to handles files and directories } i################################################################################
 CSBL_pytools_latex\sbl_add_package_main_class{Script_design, SBL.SBL_pytools.SBL_pytools_latex, Long: class providing utilities to generated latex reports Short: class providing utilities to generated latex reports } i################################################################################
 CAnnotated_sequence
 CFeatureUndefined
 CPhobius_annotator
 CClass_II_filter
 CTransmembrane_filter
 CSpherical_outlier_detector\sbl_add_package_main_class{Cluster_ksubspace, SBL::Cluster_ksubspace::SESC_model , Long: Class implementing the spherical cluster model Short: Class implementing the spherical cluster model} i################################################################################
 CTraj_typeTodo:
 CSpectraldomPostAnalyzer
 CCluster_challenger1 cluster challenge i################################################################################
 CCluster_challenger_two2 clusters challenge i################################################################################
 CUnion_find_DS\sbl_add_package_main_class{Union_find, SBL.Union_find.Union_find_DS , Long: Union-find data structure Short: Union-find data structure} i################################################################################
 CUnion_find_wrapper\sbl_add_package_main_class{Union_find, SBL.Union_find.Union_find_wrapper , Long: wrapper for the Union-find data structure Short: warpper for the Union-find data structure} i################################################################################
 CUF_null_model\sbl_add_package_main_class{PDB_utilities, SBL::PDB_utilities::UF_null_model , Long: this class implements the null model for filtrations Short: this class implements the null model for filtrations } i################################################################################
 CT_Biopolymer_chain_representationRepresentation of a single biopolymer chain
 CT_Minimal_oritend_spanning_forest_moduleModule building the minimal spanning forest of a weighted bipartite graph Module building the minimal spanning forest of a weighted bipartite graph