Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

►NESBTL
►NPDB
CMandatory_fields_default
CLine_format
CRadius_of_atom
CName_and_radius_of_atom
CName_of_pair
CGeneric_classifier
CWeight_of_atoms
CSelect_by_resname
CSelect_by_atmname
CSelect_by_element
CSelect_by_chainids
CAll_atom_system_builder
CRadius_of_coarse_atom
CColor_of_atom
CColor_of_residues
CCoarse_creator_two_barycenters
CCoarse_creator_closest_to_barycenter
CCoarse_atom
CCoarse_residue
CCoarse_atoms_iterators
CSystem_items_with_coarse_grain
CNot_functor
CAnd_functors
COr_functors
CTraits_for_grid
CGrid_of_cubes
CLine_reader
CLine_reader_with_info
CPDB_line_selector
CPDB_line_selector_two_systems
CPDB_line_selector_chain
CGeneric_line_selector
CMolecular_system
CMolecular_secondary_structure_element
CMolecular_SS_bond
CMolecular_model
CMolecular_chain
CMolecular_residue
CMolecular_atom
CDefault_system_items
CMolecular_chain_with_SSE
CMolecular_residue_with_SSE
CSystem_items_with_SSE
CMolecular_system< System_items_with_SSE, Point >
CNo_occupancy_policy
CAccept_all_occupancy_policy
CAccept_none_occupancy_policy
CMax_occupancy_policy
CMin_occupancy_policy
CAtom_list_occupancy_policy
CSelected_atom_iterator
CSystem_updater_from_xdrfile
CWeighted_atom_iterator
CPoint_3
►NSBL	[includes]
►NBatch_manager
CBM_Dataset
CBM_Database
CBM_Run_specification_tuple
CBM_Run_specification_ensemble
CBM_Batch
►NBinding_affinity_utils
CExec_runner
►NCADS
CT_Tree_solver	A dynamic programming algorithm which solves the D family matching problem for trees
CT_Shelling_diagram_vertex_property	Info attached to a vertex of a T_Cell_complex_shelling_diagram
CT_Cell_complex_shelling_diagram	Diagram representing the shelling order of a cell complex
CT_Container_of_containers_iterator_base	Base representation of an iterator over nested containers
CT_Container_of_containers_iterator	Iterator iterator over nested mutable containers
CT_Container_of_containers_const_iterator	Iterator iterator over nested non-mutable containers
CT_Dijkstra_shortest_paths_with_landmarks	Brief todo
CT_Directed_acyclic_graph	Generic representation of a directed acyclic graph
CDirected_acyclic_graph_default_property	Default data structure containing information associated to an edge or a vertex of a directed acyclic graph
CT_Directed_acyclic_graph_with_layers	Generic representation of a directed acyclic graph with layers
CT_EMD_distance_default	Default distance used by the EMD algorithm returning always the null distance
CT_Earth_mover_distance	Earth mover distance algorithm using lp_solve software for solving linear program problems
CT_Earth_mover_distance_connectivity_constraints_checker	Functor measuring the violation of the connectivity constraints of any Earth Mover Distance algorithm
CT_EMD_LP_LP_format_writer	Writing a LP problem using the LP format
CT_EMD_LP_MPS_format_writer	Writing a LP problem using the MPS format
CT_EMD_CC_stat_triple	Internal data structure used to store information for the transportation plan
CT_Earth_mover_distance_transportation_plan	Transportation plan for the Earth Mover Distance algorithms
CT_Earth_mover_distance_vertices_accessor_graph	Accessors for weighted vertices stored in a boost graph
CT_Earth_mover_distance_vertices_accessor_vector	Accessors for weighted vertices stored in a simple vector with no connectivity
CT_Earth_mover_distance_with_connectivity_constraints	Earth mover distance algorithm with connectivity constraints on the input data
CT_Geodesic_distances_generation	Brief todo
CT_Tree	A superstructure over the Graph used to represent trees
►CT_Sub_graph	A superstructure over the Graph used to represent non-induced sub-graphs
CSub_vertex_property	Sub graph vertex property (wee link it to the vertex it represents in the Graph)
CT_Greedy_selection	Generic greedy selection algorithm of arrangements of cells
CT_Greedy_selection_incremental	Generic Greedy selection algorithm of arrangements of cells
CT_Maximum_clique_finder	Functor returning the vertices of a maximum clique of an input graph
CT_Minimal_oriented_spanning_forest_Boruvka	Minimal Spanning Forest algorithm
CT_Ordered_forest_edit_distance	Generic Forest Edit Distance algorithm for ordered forests
CT_Product_graph_builder	Builder class for product graphs
CT_Vertex_product_graph_builder	Builder class for vertex product graphs
CT_Edge_product_graph_builder	Builder class for edge product graphs
CIs_product_vertex_default	Default functor for product vertex always returning true
CIs_product_edge_default	Default functor for product edge always returning true
CT_Vertex_product_graph_traits	Traits clas defining types for a vertex product graph
CT_Edge_product_graph_traits	Traits clas defining types for an edge product graph
CT_Random_spanning_tree_property	The solution space for the random spanning tree algorithm.
CD_Solution	The solution space for the Maximum Spanning tree algorithm.
CMaximum_spanning_tree_property	The solution space for the maximum spanning tree algorithm.
►CT_Maximum_spanning_tree_generator	Generates a Maximum spanning tree over a given graph (using boost::graph)
CNegative_graph_vertex_property	To compute the Maximum spanning tree, we use a negative version of the original graph
CT_Random_spanning_tree_generator	Generates a Random spanning tree over a given graph (using boost::graph)
CT_Spanning_tree_solver	A heuristic algorithm to solve the D-Family-matching problem by using spanning trees
CT_Union_find_vertex_data_structure_contains	Representation of a vertex in the Union-Find data structure containing a data
CT_Union_find_vertex_data_structure_specializes	Representation of a vertex of the Union-Find data structure inheriting a data type
►CT_Union_find_base	Base class implementing the Union-Find data structure
CDescendants_iterator	Iterator over the descendants of a given vertex
CT_Union_find_contains	Union-Find data structure where the vertices contains a data.
CT_Union_find_contains_with_map	Union-Find data structure where the vertices contains a data
CT_Union_find_specializes	Union-Find data structure where the vertices inherit from a data type.
CUnion_find_vertex_data_structure_base	Base representation of a vertex in the Union-Find data structure
CUnion_find_default	Default Union-Find data structure with no data attached to the vertices.
►NCombinations_of_variables_model_evaluation
CCombinations_of_variables_model_evaluation
COverall_default_anaysis	Overall analysis provided in our paper
CPer_model_default_analysis	Analysis for each model provided in our paper
CPer_model_binding_affinity_analysis	Analysis for each model provided in our paper
►NConnectivity_inference_analysis
CMCI_output_preprocessing
CMCI_analysis
►NConnectivity_inference_data_structures
CMCI_string_tools	Cleaning/Trimming the string before use Endline characters are removed, double spaces to single spaces, space at the beginning of the line are removed
CMCI_regex	A set of static regular expression to parse specification files and results files
CMCI_specification
CMCI_set_of_contacts
CMCI_solutions
►NConnectivity_inference_engine
CMCI_MILP_engine
►NCSB
CT_AD_buffer	Todo
CT_AD_stack	Todo
►CT_Alignment_engine	Base engine for making alignments between structures and sequences. Base engine for making alignments between structures and sequences
CIs_lower_name_pair	Predicate for comparing two pairs whatever the order of Alignment_unit_rep in each pair
CMatrix_function	Functor 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_Default_amino_acid_seqan_sequence_converter	Default converter that justs returns the input name as the seqan amino acid name, and recirpocally
CT_Aligner_sequence_seqan_wrapper	Wrapper of the Seqan algorithm for aligning pairwise sequences
CT_Alignment_engine_sequences_seqan	Engine for making alignments between sequences using Seqan
CT_Alignment_engine_structures	Base engine for making alignments between structures. Base engine for making alignments between structures
CT_Aligner_structure_apurva_wrapper	Wrapper of the Apurva algorithm for aligning pairwise structures
CT_Alignment_engine_structures_apurva	Base engine for making alignments between structures using Apurva
CT_Alignment_engine_structures_identity	Base engine for making alignments between two identical structures (in different conformations)
CT_Alignment_engine_structures_iterative_identity	Base engine for making queries in a identity alignment setting for a best local fit
CT_Alignment_engine_structures_kpax	Base engine for making alignments between structures using Kpax
CT_Alignment_residue	Representation of a residue in the alignement engines Representation of a residue in the alignement engines
CT_Alignment_sequence	Representation of a sequence of residues in the alignement engines Representation of a sequence of residues in the alignement engines
►CT_Particle_vertex_base	Specialized vertex of a 3D triangulation with an attached particle
CRebind_TDS	Rebind data structure for inheriting from a vertex data structure as specified in the CGAL library
CT_Alpha_complex_base_3	Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
CT_Alpha_complex_vertex_base_3	Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
CT_Alpha_complex_cell_base_3	Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes
CT_Alpha_complex_of_molecular_model_traits	Class defining all the types related to the -complex of a molecular model
CT_Triangulation_of_molecular_model	Derived class from CGAL Regular triangulation for filling it with particles
CT_Alpha_complex_of_molecular_model	Derived class from CGAL alpha-complex for filling it with particles
CT_Bicolor_interface_data_structure_base	Container defining what is a bicolor interface between two partners
CT_Binet_Cauchy_kernel_score	Model of Distances for defining distance between two conformations
CT_Buried_surface_area_with_labels	Compute the buried surface area of two given partners
CT_Buried_surface_area_without_label	Compute the buried surface area of two given partners
CT_Canonize_conformation	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	Data structure to handle the contiguous indices of residues/un its in a chain even in the presence of missing residues/units
CCoarse_creator_two_barycenters
CCoarse_creator_closest_to_barycenter
CCoarse_atom
CCoarse_residue
CCoarse_atoms_iterators
CSystem_items_with_coarse_grain
CT_Conformation_builder_cartesian_default	Default builder for conformations with cartesian coordinates,
CT_Conformation_traits	Traits class to be specialized
CT_Conformation_traits< CGAL::Point_d< Kernel > >	Class specializing SBL::CSB::T_Conformation_traits by storing the conformation as Point_d
CT_Conformation_traits< std::vector< NT > >	Class specializing SBL::CSB::T_Conformation_traits by storing the conformation as a vector of coordinates of a user-specified type
CT_Conformation_traits< T_Conformation_as_vector< NT > >
CT_Conformation_with_covalent_structure	Class enhancing a conformation with a covalent structure e.g. from the package Molecular_covalent_structure
CT_Conformation_traits< T_Conformation_with_covalent_structure< ConformationBase, CovalentStructure > >	Class specializing SBL::CSB::T_Conformation_traits by storing the conformation enhanced by a molecular covalent structure (SBL::CSB::T_Conformation_with_covalent_structure)
CT_Conformation_with_height	Struct SBL::CSB::T_Conformation_with_implicit_height which enhances a conformation with coordinates by adding a height
CT_Conformation_traits< T_Conformation_with_height< ConformationBase, HeightType > >	Class specializing SBL::CSB::T_Conformation_traits by storing the conformation enhanced by a height. (SBL::CSB::T_Conformation_with_height)
CT_Conformation_with_implicit_height	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_Conformation_traits< T_Conformation_with_implicit_height< ConformationBase, HeightFunctor > >	Class specializing SBL::CSB::T_Conformation_traits by storing the conformation enhanced by a height and a function applying onto the height. (SBL::CSB::T_Conformation_with_implicit_height)
CDefault_system_items
CT_External_distance	Distance computed from an external executable (sbl-conf-distance.exe) Distance computed from an external executable (sbl-conf-distance.exe)
CT_Get_particle_default	Model of Distance for defining distance between two conformations
CT_Hierarchical_labels_forest	Provides a forest structure associated to the labels defined in MolecularSystemLabelsTraits
CT_Iterative_aligner
CT_Iterative_aligner_identity
CT_Kpax
CT_Least_RMSD_cartesian	Model of Distances for defining distance between two conformations
CT_Least_RMSD_cartesian_with_chirality	Model of Distances for defining distance between two conformations
CT_Mediated_interface_data_structure_base	Container defining what is a mediated interface between two partners and a mediator
CMolecular_alignment_default	Make an alignment between two molecules with the same numbers of atoms, with the same order
CMolecular_atom	A class representing a molecular atom
CT_Molecular_cartesian_coordinates	Computes the cartesian coordinates from the internal coordinates and the covalent structure of a molecular conformation
CMolecular_chain	A class representing a molecular chain
CMolecular_coordinates_utilities	Class with static methods for internal coordinates computations
CT_Molecular_covalent_structure	Representation of the covalent structure of a molecular conformation
CT_Molecular_covalent_structure_builder_for_protein_martini	Builds a covalent structure from a given model
CT_Molecular_covalent_structure_builder_for_proteins	Builds a covalent structure from a given model
CT_Molecular_covalent_structure_constraints_for_proteins	Returns true iff the input conformation respects the input constraints
CT_Molecular_covalent_structure_optimal	Optimized representation of the covalent structure of a molecular conformation
CT_Molecular_geometric_model_classifier_for_alpha_complex	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	Container for interfaces edges of the alpha-complex that are connected and share the same interface
CHave_labels	Predicate 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_data_structure_base	Container for Molecular interface connected components that share the same interface
CT_Molecular_interfaces_builder	Construct all the primitive and hierarchical interfaces associated to a molecular model represented by an alpha-complex
CT_Molecular_interfaces_traits	Traits class defining the different kind of molecular interfaces
CMolecular_model	A class representing a molecular model
CT_Bonded_particles_visitor	Defines iterator over the bonds of a covalent structure
CT_Bond_angles_visitor	Defines iterator over the bond angles of a covalent structure
CT_Dihedral_angles_visitor	Defines iterator over the dihedral angles of a covalent structure
CT_Improper_angles_visitor	Defines iterator over the improper angles of a covalent structure
CT_Phi_psi_dihedral_angles_visitor	Defines iterator over all successive pairs of dihedrals
CT_Unbonded_particles_visitor	Defines iterator over all distinct pairs of particles
CT_Unbonded_particles_with_threshold_visitor	Defines iterator over all distinct pairs of particles
CT_Molecular_potential_energy_bond_length_term_harmonic	Defines the standard term associated to the bond length contribution
CT_Molecular_potential_energy_bond_angle_term_harmonic	Defines the standard term associated to the bond angle contribution
CT_Molecular_potential_energy_bond_angle_term_Urey_Bradley	Defines the Urey-Bradley term associated to a bond angle
CT_Molecular_potential_energy_torsion_angle_term_harmonic	Defines the harmonic term associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_term_periodic	Defines the periodic term associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_term_Fourier	Defines the Fourier term associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_term_Ryckaert_Bellemans	Defines the Ryckaert_Bellemans term associated to the proper dihedral angle contribution.
CT_Molecular_potential_energy_cmap_term	Defines the CMap term associated to a pair of proper dihedral angles.
CT_Molecular_potential_energy_Lennard_Jones_term	Defines the standard term associated to the Lennard Jones contribution
CT_Molecular_potential_energy_electrostatic_term	Defines a standard term associated to the electrostatic contribution
CT_Molecular_potential_energy_contribution	Contribution of an energy term to the potential energy function
CT_Molecular_potential_energy_bonded_contribution	Contribution of all bonded energy terms to the potential energy function
CT_Molecular_potential_energy	Potential energy function adding up all the input contributions (C++11 only)
CT_Molecular_covalent_structure_bond_length_gradient	Defines the gradient associated to the bond length
CT_Molecular_covalent_structure_bond_angle_gradient	Defines the gradient associated to the bond angle
CT_Molecular_covalent_structure_torsion_angle_gradient	Defines the gradient associated to the torsion angle
CT_Molecular_potential_energy_bond_length_gradient_harmonic	Defines the standard gradient associated to the bond length contribution
CT_Molecular_potential_energy_bond_angle_gradient_harmonic	Defines the standard gradient associated to the bond angle contribution
CT_Molecular_potential_energy_bond_angle_gradient_Urey_Bradley	Defines the Urey-Bradley gradient associated to a bond angle
CT_Molecular_potential_energy_torsion_angle_gradient_harmonic	Defines the harmonic gradient associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_gradient_periodic	Defines the periodic gradient associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_gradient_Fourier	Defines the Fourier gradient associated to the proper dihedral angle contribution
CT_Molecular_potential_energy_torsion_angle_gradient_Ryckaert_Bellemans	Defines the Ryckaert_Bellemans gradient associated to the proper dihedral angle contribution.
CT_Molecular_potential_energy_torsion_angle_gradient_in_linear_structure	Defines the gradient associated to the torsion angle contribution in a linear structure
CT_Molecular_potential_energy_Lennard_Jones_gradient	Defines the standard gradient associated to the Lennard Jones contribution
CT_Molecular_potential_energy_electrostatic_gradient	Defines a standard gradient associated to the electrostatic contribution
CT_Molecular_potential_energy_gradient_contribution	Contribution of an energy gradient term to the potential energy gradient function
CT_Molecular_potential_energy_gradient	Sum of the contributions of an energy gradient term to the potential energy gradient function
CT_Molecular_potential_energy_numerical_gradient	Computes numerically the gradient of a potential energy function
CT_Molecular_potential_energy_torsion_angle_in_linear_structure_term	Defines the term associated to the torsion angle contribution in a linear structure
CT_Molecular_primitive_internal_coordinates	Computes the internal coordinates from the covalent structure of a molecular conformation
CMolecular_residue	A class representing a molecular residue
CMolecular_secondary_structure_element	A class representing a secondary structure element
CMolecular_SS_bond	A class representing a SS bond between two residues
CT_Molecular_structure_classifier	Classify the particles of molecular systems that are at a given interface
CT_Molecular_structure_traits	Traits clas defining types used for the Molecular Structure Classifier
CMolecular_system	A class representing a molecular system
CT_Multiple_sequence_alignment_DS
CT_Multiple_sequence_alignment_DS_filtered
CT_Particle_info_for_proteins	Information on the particle to attach to the vertices of the covalent structure when using it with force fields
CT_Particle_info_traits	Concept for manipulating particle info attached to a covalent structure
CT_Polypeptide_chain_contacts_finder	Class to find pairwise atomic contacts withing a polypeptide chain
CContact_map_for_one_ctype	Records pairs of interacting residues for one contact type
CPairwise_contacts_for_polypeptide_chain
►CT_Polypeptide_chain_representation	Reprenstation of a single polypeptidic chain within a protein representation
CBackbone_const_iterator	Iterator through the atoms of the polypeptide chain backbone (const)
CBackbone_iterator	Iterator through the atoms of the polypeptide chain backbone
CBond	Representation of a bond between two atoms
CBond_angle	Representation of a valence angle between three atoms
CBond_angle_const_iterator	Iterator through all the valence angles in the polypeptide chain (const)
CBond_angle_iterator	Iterator through all the valence angles in the polypeptide chain
CBond_const_iterator	Iterator through all the bonds in the polypeptide chain (const)
CBond_iterator	Iterator through all the bonds in the polypeptide chain
CDihedral_angle	Representation of a proper dihedral angle between four atoms
CDihedral_angle_const_iterator	Iterator through all the proper dihedral angles in the polypeptide chain (const)
CDihedral_angle_iterator	Iterator through all the proper dihedral angles in the polypeptide chain
CIncident_atoms_const_iterator	Iterator through bonded atoms to an input atom (const)
CIncident_atoms_iterator	Iterator through bonded atoms to an input atom
CResidue_atoms_const_iterator	Iterator through all the atoms of an input residue (const)
CResidue_atoms_iterator	Iterator through all the atoms of an input residue
CT_Protein_representation	Representaiton of a protein with its polypeptide chains
CT_Minimizer_parameters_without_constraint	Constraints for minimizing without any constraint
CT_Real_value_function_minimizer	Minimizer of a real valued function
CT_Minimizer_Ipopt_parameters_without_constraint	Constraints for minimizing without any constraint
CT_Real_value_function_minimizer_Ipopt	Minimizer of a real valued function
CT_Real_value_function_minimizer_LBFGS	Minimizer of a real valued function using the header-only library LBFGS++
►CT_RMSD_comb_edge_weighted	Given a set of motifs instantiates the motif graph and computes the associated combined RMSD
CVertex_property	Vertex property for the motif graph
CT_Score_computer_K
CT_Seeder_basic	Given two structures, align them using Kpax_seeder
CT_Seeder_DP_score	Given two structures, align them using Seeder_DP_score
CT_Squared_angular_internal_distance	Model of distance between angles of two conformations given with their internal coordinates
CT_Angular_internal_distance	Model of Distance between angles of two conformations given with their internal coordinates
CT_Squared_RMSD_internal_distance	Model of Distance for defining distance between two conformations
►CT_Tertiary_quaternary_structure_annotator	Builds a graph representing the biochemical interactions between units of a protein
CEdge_label_writer	Functor allowing to write two properties associated to a vertex or an edge into a dot file representing a graph
CVertex_label_writer	Functor allowing to write two properties associated to a vertex into a dot file representing a graph
CT_Transition_graph_traits_compressed	Note that all methods are static – no member data
CT_Transition_graph_traits_standard	TG representation with explicit storage of the saddles as vertices of the TG
CT_Tricolor_interface_data_structure_base	Container defining what is a tricolor interface between two partners
CT_Tripeptide_loop_closure	Computes the backbone coordinates of solutions to the Tripeptide loop closure with only phi and psi bond angles changing in internal coordinates
CT_Tripeptide_constraints_to_polynomial	Converts the Tripeptide contraints given to a 16th degree polynomial
CT_Polynomial_solver_interface	Interface to the CGAL polynomial solver using Algebraic Number types
CT_TLC_polynomial_roots_to_embedings	Converts polynomial roots to embeddings using values defined in T_Tripeptide_constraints_to_polynomial
CT_Tripeptide_anchors	Anchor atoms around the moving atoms for the tripeptide loop closure
CT_Tripeptide_constraints	Constraints used to solve the tripeptide loop closure
CContants_for_embedding	Values obtained when converting constraints to polynomial coefficients and used once more to convert roots to cartesian embeddings of solution in tripeptide loop closure
CT_Molecular_interface_connected_component_oserialization	Serialization of a connected component of a molecular interface
CT_Molecular_interface_oserialization	Serialization of a molecular interface
CT_Bicolor_interface_oserialization	Serialization of a bicolor interface
CT_Mediated_interface_oserialization	Serialization of a mediated interface
CT_Tricolor_interface_oserialization	Serialization of a tricolor interface
►NDB_hit_manager
CHit_info
CHits_manager
CHits_manager_no_annotations
►NDB_manipulators
CUniprot_wrapper
CNCBI_wrapper
►NGT
CWL_histo_change_measure	Change from measure pi to measure mu, see paper
CT_Combined_Move_Params	Collect into a tuple the params of all move sets
CT_Combined_Move_Stats	Collect into a tuple the stats of all move sets
CCombined_WL_Move_Set_Data_Interface	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
CT_Combined_Move_Set_Controller	Contoler : controls the MS WL calls the controller of the combined MS, which (recursively, thanks to templates) calls the defered controllers
CT_Combined_Move_Set	As above, but for move sets rather than controllers
CDarting_Move_Params	Darting Move set Params
CDarting_Move_Stats	Darting Move set Stats
CT_Darting_Move_Set_Controller	Darting Move set Controller
CT_Darting_Move_Set	Darting Move set. Physical conformation needs a function get_grad, compute_energy and get_energy and a member data
CDarting_Move_Set_Traits	Darting Move set traits (see paper for details of internal working)
CGaussian_Move_Params	Gaussian Move params
CGaussian_Move_Stats	Gaussian Move Set stats
CT_Gaussian_Move_Set_Controller	Gaussian Move Set controller
CT_Gaussian_Move_Set	Gaussian Move Set
CGaussian_Move_Set_Traits	Gaussian Move Set, simplest move set provided. Propose a move sampled from a normal distribution centered on the starting point
CNo_Overstep_Cone_Move_Params	No overstep cone move set params
CNo_Overstep_Cone_Move_Stats	No overstep cone move set stats
CT_No_Overstep_Cone_Move_Set_Controller	No overstep cone move set controller
CT_No_Overstep_Cone_Move_Set	No overstep cone move set
CNo_Overstep_Cone_Move_Set_Traits	No 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_Move_Params	No overstep move set params
CNo_Overstep_Move_Stats	No overstep move set stats
CT_No_Overstep_Move_Set_Controller	No overstep move set controller
CT_No_Overstep_Move_Set	No overstep move set
CNo_Overstep_Move_Set_Traits	No overstep move set traits: a move set that aims to sample neighbourings energy strata. See paper for details
►CT_Wang_Landau	This is the main class that runs a Wang-Landau simulation
CRoll_Back_Restoration_Point	Informotion used to roll back, including the states for random number generators
CWL_DS_Interface	Class 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_MS	This class specializes its internal counterpart to record additional info used by move sets
CT_Bin_properties	This class extends Bin_properties to record info from the move sets
CT_DS_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	A class storing the main pieces of information, at a given time stamp in the course of the algorithm
CT_WL_Data_Structure_Internal	Bin management: main data structure used by Wang_landau algorithm
CBin_properties_Internal	The Bin_properties struct defines which properties are stored per bin. by default, the density and the histogram, plus some custom user-defined stats
CWL_stats_serializer	Helper class which stores into files:
CT_WL_Simulation
CT_WL_Simulation_Gaussian	Specialisation of T_WL_Simulation for Gaussian move set
CT_WL_Simulation_No_Overstep	Specialisation of T_WL_Simulation for No overstep move set
CT_ANN_FLANN_wrapper	Nearest neighbor engine from FLANN library
CT_ANN_meta	Nearest neighbor engine designed for metric spaces
CT_ANN_metric_space_LAESA	Nearest neighbor engine designed for metric spaces
CT_ANN_metric_space_proximity_tree	Nearest neighbor engine designed for metric spaces
CT_Betti_numbers_1	Compute the Betti numbers of a Graph
CT_Betti_numbers_2	Compute the Betti numbers of a 3D Cell Complex from its alpha-complex
CT_Cluster_engine_k_means_center_of_mass	Representation of a center of mass in k-means algorithm
CT_Cluster_engine_k_means_point_selector_random	Select randomly the initial centers of mass for k-means algorithm
CT_Cluster_engine_k_means_point_selector_plus_plus	Select initial centers of mass using the ++ strategy
CT_Cluster_engine_k_means_point_selector_minimax	Select initial centers of mass by maximizing the min distance between centers of mass at each selection step
CT_Cluster_engine_k_means	K-means algorithm
CT_Cluster_engine_k_means_com_euclidean	Representation of a center of mass for k-means in Euclidean spaces
CT_Cluster_engine_k_means_com_Sd	Representation of a center of mass in k-means algorithm
CK_means_scores	Various scores for K_means
CT_Cluster_engine_Morse_theory_based	Morse theory based clustering algorithm
CT_Spectral_clustering	Spectral clustering algorithm from Ng et al at NeurIPS 2001
►CT_Delaunay_triangulation_extension_3	Defines simple predicates and constructions structure over a triangulation
CGet_area_of_dual_of_edge	Given the dual of an edge, compute its area
CGet_dual_of_edge	Given an edge, return its dual as a container of points
CGet_dual_of_facet	Given a facet, return its dual as a segment
CGet_squared_length_of_dual_of_facet	Given a facet, return the squared length of its dual segment
►CT_Delaunay_triangulation_spherical_traits_3_base	Model for the base of a geometric kernel for T_Delaunay_triangulation_spherical_traits_3
CBase	Base for the kernel
CT_Delaunay_triangulation_spherical_traits_3	Kernel used for computations involving exact number types for coordinates of boundary points
CT_Frechet_mean_S1	This class computes local and global minimums of the sum of p exponent distance function
CT_Stable_manifold_as_list_traits	Simple representation of a stable manifold as a list of points
CT_Morse_Smale_Witten_chain_complex	Representation of the complex of the same name
CT_Distance_default_for_graph	Base distance over vertices of a graph
CT_Morse_Smale_Witten_chain_complex_from_NNG_builder	Builds the Morse Smale Witten chain complex from a NNG
CT_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder	Builds the Morse Smale Witten chain complex from a weighted graph
CT_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder	Builds the Morse Smale Witten chain complex from a vertex weighted graph
CT_Morse_theory_based_analyzer	Analysis of a Morse Smale Witten chain complex
CNearest_neighbors_graph_builder	Builder for nearest neighbors graphs
CNearest_neighbors_graph_builder_with_edge_weight	Builder for nearest neighbors graphs
CT_NN_linear_scan	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_Splitter_default	Nearest neighbor engine designed for metric spaces
CT_NN_metric_tree	Nearest neighbor engine designed for metric spaces
CT_Point_cloud_rigid_registration_3	Model of Distances for defining distance between two point clouds
CT_Squared_RMSD_cartesian_3	Squared RMSD distance between two 3D point clouds
CT_RMSD_cartesian_3	RMSD distance between two 3D point clouds
CT_Squared_Least_RMSD_cartesian_3	Perform a 3D rigid registration between two 3D point clouds, then computes the squared RMSD distance between the two aligned clouds
CT_Least_RMSD_cartesian_3	Perform a 3D rigid registration between two 3D point clouds, then computes the RMSD distance between the two aligned clouds
CT_Rotation_3	Static 3d rotation methods
►CT_Spherical_kernel_extension_3	Extension completing the 3D Spherical kernel of CGAL.
CIs_counter_clockwise_oriented	Check that an oriented edge and a point on the circular arc represented by this edge defines a counter clockwise orientation
CIs_largest_circular_arc_3	Returns 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
COrientation_with_roots_3	Orientation predicate allowing input numbers as Root_of_2
►CT_Triangulation_extension_3_base	Defines simple predicates and constructions structure over a triangulation
CCanonical_edge	Canonical representation of an edge in the 3D Triangulation
CCanonical_facet	Canonical representation of a facet in the 3D Triangulation
CGet_common_facet	Given two cells, return the common facet of the two cells
CGet_other_two_edges	Given an edge and a facet bounding it, return the two other edges of the facet
CIs_coface	Check that a simplex is the coface of a second simplex
CIs_counter_clockwise_oriented	Predicate checking that a facet of the 3D triangulation is counter-clockwise oriented
CT_Vertex_handle_with_order	Check that a simplex is the coface of a second simplex
CT_Triangulation_extension_3	Defines simple predicates and constructions structure over a triangulation
CT_Union_of_balls_boundary_3_builder	Functor filling a HDS of the Boundary of an union of balls
CT_Union_of_balls_boundary_3_item_info	Attached a simplex of the -complex to an item of the half-edge data structure
CT_Union_of_balls_boundary_3_vertex	Representation of a vertex in the half-edge data structure
CT_Union_of_balls_boundary_3_half_edge	Representation of a half-edge in the half-edge data structure
CT_Union_of_balls_boundary_3_face	Representation of a face in the half-edge data structure
CT_Union_of_balls_boundary_3_items	Instantiation of face, half-edge and vertex tpes of the half-edge data structure
CT_Union_of_balls_boundary_3_data_structure	Representation of the boundary of the union of balls
CT_Union_of_balls_boundary_3_side	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	Shelling diagram of a patch on the boundary of the union of 3D balls
CT_Union_of_balls_epsilon_mesh_3	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	Algorithm constructing the medial axis of an union of balls
CT_Union_of_balls_medial_axis_3_face	Representation of a face in the half-edge data structure
CT_Union_of_balls_medial_axis_3_items	Instantiation of face, half-edge and vertex tpes of the half-edge data structure
CT_Union_of_balls_medial_axis_3_data_structure	Representation of the medial-axis of the union of balls
CT_Union_of_balls_medial_axis_3_vertex	Representation of a vertex in the half-edge data structure
CT_Union_of_balls_medial_axis_3_halfedge	Representation of a half-edge in the half-edge data structure
CT_Union_of_balls_surface_volume_3	Algorithm computing the surface area and the volume of the union of 3D balls
►NHMMER_Wrapper
CHMM
►NIO
CMolecular_view< Viewer, CGAL::Fixed_alpha_shape_vertex_base_3< Gt, Vb > >	Uses the Molecular viewer of the base vertex of the fixed 3D -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 -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 -complex
CMolecular_view< Viewer, CGAL::Fixed_alpha_shape_3< Dt > * >	Views in Molecular format the edges and facets of the input fixed 3D -complex for its value
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 -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 -complex, using the underlaying Delaunay triangulation
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 -complex
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 -complex
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 -complex
CMolecular_view< Viewer, CGAL::Alpha_shape_3< Dt, ExactAlphaComparisonTag > * >	Views in Molecular format the edges and facets of the input 3D -complex for its value
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 -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 -complex, using the underlaying Delaunay triangulation
CT_Archive_file_loader	Loader for one or more boost archive files
CT_Conformation_loader	Class for loading conformations from a list of PDB / cif files, or from a plain txt file listing the conformations as Point_d. Class for loading conformations from a list of PDB / cif files, or from a plain txt file listing the conformations as Point_d
CT_Index_wrapper	Wrapper for indices where the IO dumping may be different from the index itself
CLoader_base	Base loader from which any loader should inherit
CT_Molecular_covalent_structure_loader	Loader for covalent structures from PDB / mmCIF files
CT_Molecular_covalent_structure_loader_from_MOL	Loader for covalent structures from MOL files
CT_Molecular_covalent_structure_loader_from_PDB	Loader for covalent structures from PDB files using ESBTL
CT_Molecular_system_loader	Class for loading molecular systems
CMolecular_view	Base class for viewing an object in one of the available format (VMD, PyMOL)
CT_Multiple_archives_serialization_xml_iarchive	XML input archive coupling the data from a secondary archive to the main xml archive
CT_Multiple_archives_serialization_xml_oarchive	XML output archive decoupling the data to put in the archive and data to possibly put in a secondary file
CT_Multiple_archives_xml_archive_file_loader	Loader for one or more multiple archives xml archive files
CT_Numbers_file_loader	Loader for files listing numbers
CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Point_3< K > >	Views a 3D point in VMD format
CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Point_3< K > >	Views a 3D point in PyMOL format
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_PyMOL_viewer< Dummy >, std::pair< CGAL::Point_3< K >, CGAL::Point_3< K > > >	Views a 3D segment in PyMOL format
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_PyMOL_viewer< Dummy >, CGAL::Triple< CGAL::Point_3< K >, CGAL::Point_3< K >, CGAL::Point_3< K > > >	Views a 3D triangle in PyMOL format
CT_Primitive_labels_loader	Loader for systems' labels specification. Loader for systems' labels specification
CT_Protein_representation_loader	Loader for proteins from PDB and mmCIF files using SBL
CT_PyMOL_viewer	Viewer writing in PyMOL file format
CPyMOL_viewer	Viewer writing in PyMOL file format
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::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, 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, CGAL::Regular_triangulation_3< Gt, Tds > * >	Views in Molecular format the edges and facets 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 >::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
CMolecular_view< T_VMD_viewer< Dummy >, CGAL::Sphere_3< K > >	Views in VMD format a 3D sphere.
CMolecular_view< T_PyMOL_viewer< Dummy >, CGAL::Sphere_3< K > >	Views in PyMOL format a 3D sphere.
CT_Transition_graph_loader	Loader for one or more boost archive files
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::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::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, CGAL::Triangulation_3< Gt, Tds > * >	Views in Molecular format the edges and facets of the input 3D triangulation
CVMD_viewer	Viewer writing in VMD file format
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_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_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< 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::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_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
►Nmcibootstrap_iterative
CMCI_bootstrap
►NModels
CAB_label_traits	Traits class defining partners' labels for binary molecular complexes A and B. Traits class defining partners' labels for binary molecular complexes A and B
►CT_Atom_with_flat_info_and_annotations_traits	Defines a generic serializable atom with annotations (default is name, radius and optional annotations)
CGet_geometric_representation	Functor returning a weighted point representing the atom
CT_Atom_with_flat_info	Wrapper representing the atom
►CT_Atom_with_flat_info_traits	Traits class defining atoms traits (biophysical and geometric properties). Traits class defining atoms traits (biophysical and geometric properties)
CAtom_with_flat_infos_builder	Builder for containers of Particle_type
CGet_geometric_representation	Functor returning a weighted point representing the atom
►CT_Atom_with_hierarchical_info_and_annotations_traits	Traits class defining atoms traits with annotations (at least name and radius). Traits class defining atoms traits with annotations (at least name and radius)
CGet_geometric_representation	Functor returning a weighted point representing the atom
►CT_Atom_with_hierarchical_info_traits	Traits class defining atoms traits (biophysical and geometric properties). Traits class defining atoms traits (biophysical and geometric properties)
CGet_geometric_representation	Functor returning a weighted point representing the atom
►CT_Chain_label_traits	Model of MolecularSystemLabelTraits for chains
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CChain_label_traits	Model of MolecularSystemLabelTraits for chains
CT_Conformation_builder_cartesian_default	Default builder for conformations with cartesian coordinates Default builder for conformations with cartesian coordinates
CT_Conformations_file_loader	Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d
CDefault_radii_for_particles_with_annotated_name	Default radii for atoms and pseudo-atoms as residues
CT_Domain_annotator_for_particles	Model of ParticleAnnotator for attributing a domain to atoms. Model of ParticleAnnotator for attributing a domain to atoms
►CT_Domain_label_traits	Model of MolecularSystemLabelTraits for molecular complexes defined in a file.
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CDomain_label_traits	Model of MolecularSystemLabelTraits for molecular complexes defined in a file
►CT_Dynamic_annotator_for_atoms	Model of ParticleAnnotator for attributing any annotation to a particle dynamically
CT_Annotations_with_dynamic	Default class for representing dynamic annotations (it refines a base class of annotations)
CT_Annotations_with_dynamic< void, DynamicAnnotation >	Default class for representing dynamic annotations (it is a base class of annotations)
CSet_dynamic_annotation_default	Default data structure adding a dynamic annotation to a particle
CT_Dynamic_annotator_for_residues	Model of ParticleAnnotator for attributing any annotation to a particle dynamically
►CExtra_label_traits	Traits class defining one extra's label. Traits class defining one extra's label
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CT_Generic_annotator	Model of ParticleAnnotator for attributing any annotation to a particle
CT_Generic_annotator_without_file	Model of ParticleAnnotator for attributing any annotation to a particle without loading a file
CGet_annotator_option_name_default	Returns a string that is the default option name for generic annotators
CGet_annotator_option_help_default	Returns a string that is the default option help for generic annotators
CGet_annotator_option_display_name_default	Returns a string that is the default display name of options for generic annotators
CMake_no_annotation_key	Returns false, whatever is the entry
►CT_Geometric_particle_traits	Particle represented by a simple geometric object (a 3D point, a 3D sphere or a 3D weighted point)
CGet_geometric_representation	Functor returning a weighted point representing the atom
►CT_IG_label_traits	[definition]
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CIG_label_traits	Traits class defining hierarchical partners' labels for immunoglobulin (IG). Traits class defining hierarchical partners' labels for immunoglobulin (IG)
CIGAg_label_traits	Traits 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)
CT_Moveset_atomic	Moveset from each particle of a conformation
CT_Moveset_global	Moveset of the conformation as a whole
CT_Moveset_interpolation	Moveset of the conformation by interpolation between two conformations
CT_Name_annotator_for_atoms	Model of ParticleAnnotator for attributing a name to an atom
CName_annotator_for_atoms_setter_default	Default annotated name setter, using the method set_annotated_name of the input particle
CT_Name_annotator_for_pseudo_atoms	Model of ParticleAnnotator for attributing a name to a pseudo-atom
CName_annotator_for_pseudo_atoms_setter_default	Default annotated name setter, using the method set_annotated_name of the input particle
►CNo_label_traits	Traits class defining no system's label. Traits class defining no system's label
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CNo_particle_annotator	Annotator that does not do anything
►COne_label_traits	Traits class defining one partner's label. Traits class defining one partner's label
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CT_Particle_annotator_collector	Collector for models of ParticleAnnotator
CT_Particle_with_annotations	Traits class defining particles traits with annotations
CT_Particle_with_annotations_traits	Traits class defining patricles traits with annotations
►CT_Particle_with_system_label	Model of Particle with a system's label
CSystem_label	Representation of a system's label, that can be either a partner, a mediator or an extra label
CT_Particle_with_system_label_traits	Model of ParticleTraits for defining particles with a system's label
CT_PDB_file_loader	Loader for one or more PDB files, even listed in a file. Loader for one or more PDB files, even listed in a file
CT_Points_d_file_loader	Loader for one or more txt files listing dD points Loader for one or more txt files listing dD points
►CT_Pseudo_atom_per_residue_spec_with_flat_info_and_annotations_traits	Traits class defining pseudo-atoms traits (biophysical and geometric properties). Traits class defining pseudo-atoms traits (biophysical and geometric properties)
CGet_geometric_representation	Functor returning a weighted point representing the coarse atom
CT_Pseudo_atom_per_residue_spec_with_flat_info	Wrapper representing the coarse atom
►CT_Pseudo_atom_per_residue_spec_with_flat_info_traits	Traits class defining pseudo-atoms traits (biophysical and geometric properties). Traits class defining pseudo-atoms traits (biophysical and geometric properties)
CGet_geometric_representation	Functor returning a weighted point representing the atom
CT_Name_and_radius_annotations	Base annotations for a default atom (name and radius)
CT_Radius_annotator_for_particles_with_annotated_name	Model of ParticleAnnotator for attributing a radius to an atom
CRadius_annotator_for_particles_with_annotated_name_setter_default	Default radius setter, using the method set_radius of the input particle
CT_Spheres_3_file_loader	Loader for one or more txt files listing 3D spheres
CT_Unit_system_traits_AKMA	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	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	Traits class defining dimensionless types for AKMA Traits class defining dimensionless types for AKMA
CT_Unit_system_traits_none_MD	Traits class defining dimensionless types for MD Traits class defining dimensionless types for MD
►CWater_label_traits	Traits class defining mediators' labels for water. Traits class defining mediators' labels for water
CPrimitive_label_classifier	Functor returning a pair classifying a particle
CT_XTC_file_loader	Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d
►NModules
CT_Alignment_sequences_module	Module which computes a pairwise alignment of two sequences Module which computes a pairwise alignment of two sequences
CT_Alignment_structures_module	Module which computes a pairwise alignment of two structures Module which computes a pairwise alignment of two structures
CT_Alpha_complex_of_molecular_model_module	Module building the alpha-complex of an input set of particles. Module building the alpha-complex of an input set of particles
CT_Buried_surface_area_with_labels_module	Module building the buried surface areas from the alpha-complex of a molecular model. Module building the buried surface areas from the alpha-complex of a molecular model
CT_Buried_surface_area_without_label_module	Module building the buried surface area of a partner from the alpha-complex of a molecular model. Module building the buried surface area of a partner from the alpha-complex of a molecular model
CT_Cluster_engine_module	Module which computes clusters from a cloud of points Module which computes clusters from a cloud of points
CT_Earth_mover_distance_module	Application's module instantiating the eartyh mover distance algorithm
CT_Module_option_description	Base module from which any module should inherit
CModule_base	Base module from which any module should inherit
►CT_Module_based_workflow	Internal base for the workflow
CEdge_property_label_writer	Writer of properties of an edge of the graph in .dot format
CGraph_property_label_writer	Writer of properties of the graph in .dot format
CVertex_property_label_writer	Writer of properties of a vertex of the graph in .dot format
CModule_based_workflow	Representaiont of the workflow of an application enriched with default options
CT_Module_condition	Condition module for selecting one of two possible outflows
CT_Module_conjunction	Conjunction module linking two input modules or loaders with an and operator
CT_Molecular_interfaces_module	Module building the bicolor, mediated and tricolor interfaces of a molecular structure. Module building the bicolor, mediated and tricolor interfaces of a molecular structure
CT_Bicolor_interface_oserialization	Serialization of a bicolor interface
CT_Mediated_interface_oserialization	Serialization of a mediated interface
CT_Tricolor_interface_oserialization	Serialization of a tricolor interface
CT_Molecular_interfaces_module_statistics	Application's module_statistics for building the alpha-complex of a molecular model.
CT_Molecular_structure_classifier_module	Module classifying the particles of a molecular structure following their system's labels. Module classifying the particles of a molecular structure following their system's labels
CT_Morse_theory_based_analyzer_module	Generic manager for reading arguments of the program and run the calculations
CT_Morse_theory_based_analyzer_for_NNG_module	Generic manager for reading arguments of the program and run the calculations
CT_Morse_theory_based_analyzer_for_vertex_weighted_graph_module	Generic manager for reading arguments of the program and run the calculations
CT_Morse_theory_based_analyzer_for_weighted_graph_module	Generic manager for reading arguments of the program and run the calculations
CT_Nearest_neighbors_graph_builder_module	Generic manager for reading arguments of the program and run the calculations
CT_RMSD_comb_edge_weighted_module	Undefined. Undefined
CT_Spatial_search_module	Module building a data base for spatial-search from an input set of points. Module building a data base for spatial-search from an input set of points
CT_Tertiary_quaternary_structure_annotator_module	Module building the Biochemical Interfaces Graph of a molecular structure
CT_Union_of_balls_boundary_3_module	Module building the boundary of the union of input 3D balls. Module building the boundary of the union of input 3D balls
CT_Union_of_balls_boundary_patch_shelling_3_module	Module computing the shelling order forests of particles in a binding patch. Module computing the shelling order forests of particles in a binding patch
CT_Union_of_balls_mesh_3_module	Module computing a sampling of an input boundary of the union of 3D balls. Module computing a sampling of an input boundary of the union of 3D balls
►CT_Union_of_balls_surface_volume_3_module	Module computing the surface area and the volume of the union of an input set of 3D balls. Module computing the surface area and the volume of the union of an input set of 3D balls
CUnion_of_balls_surface_volume_3	Contains pointers over two functors for computing the volumes and surfaces areas with different level of exactness
►NMolecular_cradle_step1
CCradle_step1
►NMolecular_cradle_step2
CCradle_step2
►NMolecular_cradle_step2_selected
CCradle_step2_selected
►NMolecular_cradle_step3
CCradle_step3
►NMolecular_cradle_utils_dendogram
CMatrix_processor
CDendogram_processor
►NMolecular_cradle_utils_distance
CDistance_calculator
►NMolecular_cradle_utils_label_selection
CLabel_selector
►NMultiple_interface_string_alignment
CResidue_mapping
CChain_instances
CInterface_oneside
CInterface_strings
CInterface_pool
CMISA
CMISA_constructor
►NPALSE
CPython_dico_vs_XML_Etree
CBioPDB_vs_XML_Etree
CPALSE_xml_DB
CPALSE_DS_manipulator
CPALSE_statistic_handle
►NPDB_complex_to_unbound_partners_matchings
CPDB_complex_to_unbound_partners_matcher
►NProtein_complex_analysis_molecular_data_structures
CAtom_data	The properties of an atom as given by vorshell + vorlume
CResidue_contact_data	The properties of a residue as given by vorshell + vorlume
CAtomic_contact_data	Information about contacts between atoms
CResidue_data	The properties of a residue as given by vorshell + vorlume
CChain_data	Essentially a collection of Residue_data
CFile_data	Essentially a collection of Chain_data
CComplex_data_collector
►NSBL_Genetrank_gene_radar_scatter_plot
CGenetrank_gene_radar
►NSBL_Genetrank_gene_to_protein
CGenetrank_Translations
CGenetrank_GeneProteinTranslator
►NSBL_Genetrank_network_statistical_analysis
CGenetrank_network_statistical_analysis
►NSequence_annotators
CFeature	Undefined
CAnnotated_sequence
CPhobius_annotator
►NSequence_filters
CTransmembrane_filter
CClass_II_filter
CSBL_init_tools	Accessing env variable
Cbranch_and_bound
Cdp_mat_apurva
CGet_not_annotator_option_name	Returns empty option name
Clambda_matrix
CModules_collection	Base module from which any module should inherit
Cparameters
Cproblem
CMCI_Contact
CMCI_Oligomers
CB_factor_color_engine
CB_factor_coloring_parser
CBSA_color_engine
CBSA_coloring_parser
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
CMISA_input_specification_parser
CPlot_tools
CResSelector
CSSE_color_engine
CSSE_coloring_parser
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
CT_Minimal_oritend_spanning_forest_module	Module building the minimal spanning forest of a weighted bipartite graph Module building the minimal spanning forest of a weighted bipartite graph