►NProtein_complex_analysis_molecular_data_structures | |
CAtom_data | The properties of an atom as given by vorshell + vorlume |
CAtomic_contact_data | Information about contacts between atoms |
CChain_data | Essentially a collection of Residue_data |
CComplex_data_collector | Class responsible for parsing the directory structure output by sbl-binding-affinity-run-applications.py and filling the data structures with the gathered information |
CFile_data | Essentially a collection of Chain_data |
CResidue_contact_data | The properties of a residue as given by vorshell + vorlume |
CResidue_data | The properties of a residue as given by vorshell + vorlume |
►NSBL | |
►NBatch_manager | |
CBM_Batch | Definition of a batch with a data set, and specification of runs |
CBM_Database | Data structure representing a set of datasets |
CBM_Dataset | Data structure representing a dataset, i.e a collection of files |
CBM_Dataset_association_rules | Associate a rule between files of a dataset |
CBM_IFO_set | Set of input file options with multiple values |
CBM_NFO_set | Set of non-file options with multiple values |
CBM_Run_specification_ensemble | A list of run specifications |
CBM_Run_specification_tuple | A list of name-value-pairs to specify one run |
►NBinding_affinity_utils | |
CExec_runner | Runs a set of commands with their corresponding parameters.Possible on multiple processes |
►NCADS | |
CD_Solution | The solution space for the Maximum Spanning tree algorithm |
CDirected_acyclic_graph_default_property | Default data structure containing information associated to an edge or a vertex of a directed acyclic graph |
CIs_product_edge_default | Default functor for product edge always returning true |
CIs_product_vertex_default | Default functor for product vertex always returning true |
CMaximum_spanning_tree_property | The solution space for the maximum spanning tree algorithm |
CT_Cell_complex_shelling_diagram | Diagram representing the shelling order of a cell complex |
CT_Container_of_containers_const_iterator | Iterator iterator over nested non-mutable containers |
CT_Container_of_containers_iterator | Iterator iterator over nested mutable containers |
CT_Container_of_containers_iterator_base | Base representation of an iterator over nested containers |
CT_Dijkstra_shortest_paths_with_landmarks | Brief todo |
CT_Directed_acyclic_graph | Generic representation of a directed acyclic graph |
CT_Directed_acyclic_graph_with_layers | Generic representation of a directed acyclic graph with layers |
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_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_Edge_product_graph_builder | Builder class for edge product graphs |
CT_Edge_product_graph_traits | Traits clas defining types for an edge product graph |
CT_EMD_CC_stat_triple | Internal data structure used to store information for the transportation plan |
CT_EMD_distance_default | Default distance used by the EMD algorithm returning always the null distance |
CT_Geodesic_distances_generation | Brief todo |
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_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_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_Random_spanning_tree_generator | Generates a Random spanning tree over a given graph (using boost::graph) |
CT_Random_spanning_tree_property | The solution space for the random spanning tree algorithm |
CT_Shelling_diagram_vertex_property | Info attached to a vertex of a T_Cell_complex_shelling_diagram |
CT_Spanning_tree_solver | A heuristic algorithm to solve the D-Family-matching problem by using spanning 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_Tree | A superstructure over the Graph used to represent trees |
CT_Tree_solver | A dynamic programming algorithm which solves the D family matching problem for trees |
►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 |
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_Vertex_product_graph_builder | Builder class for vertex product graphs |
CT_Vertex_product_graph_traits | Traits clas defining types for a vertex product graph |
CUnion_find_default | Default Union-Find data structure with no data attached to the vertices |
CUnion_find_vertex_data_structure_base | Base representation of a vertex in the Union-Find data structure |
►NCombinations_of_variables_model_evaluation | |
CCombinations_of_variables_model_evaluation | Builds, evaluates and ranks statistical models from a set of variables |
COverall_default_anaysis | Overall analysis provided in our paper |
CPer_model_binding_affinity_analysis | Analysis for each model provided in our paper |
CPer_model_default_analysis | Analysis for each model provided in our paper |
►NConnectivity_inference_analysis | |
CMCI_analysis | A class to analyze the solutions of a connectivity inference problem |
CMCI_output_preprocessing | A class to preprocess the output of a connectivity inference problem |
►NConnectivity_inference_data_structures | |
CMCI_regex | A set of static regular expression to parse specification files and results files |
CMCI_set_of_contacts | A class to specify a set of contacts |
CMCI_solutions | A class to store solutions, each as a triple (cost, set of contacts, running time per solution) |
CMCI_specification | A class to specify the input of a connectivity inference problem |
►NConnectivity_inference_engine | |
CMCI_MILP_engine | A class implementing the Mixed Integer Linear Program (MILP) to solve Connectivity inference problems |
►NCSB | |
CMolecular_alignment_default | Make an alignment between two molecules with the same numbers of atoms, with the same order |
CParticle_info_for_force_field | Information on the particle to attach to the vertices of the covalent structure when using it with force fields |
CT_AD_buffer | Todo |
CT_AD_stack | Todo |
CT_Aligner_sequence_seqan_wrapper | Wrapper of the Seqan algorithm for aligning pairwise sequences |
CT_Aligner_structure_apurva_wrapper | Wrapper of the Apurva algorithm for aligning pairwise structures |
►CT_Alignment_engine | 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_Alignment_engine_sequences_seqan | Engine for making alignments between sequences using Seqan |
CT_Alignment_engine_structures | Base engine for making alignments between structures |
CT_Alignment_engine_structures_apurva | Base engine for making alignments between structures using Apurva |
CT_Alpha_complex_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 | Derived class from CGAL alpha-complex for filling it with particles |
CT_Alpha_complex_of_molecular_model_traits | Class defining all the types related to the -complex of a molecular model |
CT_Alpha_complex_vertex_base_3 | Class allowing to have identical template parameters for Alpha_shape and Fixed_alpha_shape classes |
CT_Angular_internal_distance | Model of Distance between angles of two conformations given with their internal coordinates |
CT_Bicolor_interface_data_structure_base | Container defining what is a bicolor interface between two partners |
CT_Bicolor_interface_oserialization | Serialization of a bicolor interface |
CT_Bond_angles_visitor | Defines iterator over the bond angles of a covalent structure |
CT_Bonded_particles_visitor | Defines iterator over the bonds of a covalent structure |
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_Default_amino_acid_seqan_sequence_converter | Default converter that justs returns the input name as the seqan amino acid name, and recirpocally |
CT_Dihedral_angles_visitor | Defines iterator over the dihedral angles of a covalent structure |
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_Improper_angles_visitor | Defines iterator over the improper angles of a covalent structure |
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 |
CT_Mediated_interface_oserialization | Serialization of a mediated interface |
CT_Metropolis_predicate | Metropolis based predicate |
CT_Minimizer_Ipopt_parameters_without_constraint | Constraints for minimizing without any constraint |
CT_Minimizer_parameters_without_constraint | Constraints for minimizing without any constraint |
CT_Molecular_cartesian_coordinates | Computes the cartesian coordinates from the internal coordinates and the covalent structure of a molecular conformation |
CT_Molecular_covalent_structure | Representation of the covalent structure of a molecular conformation |
CT_Molecular_covalent_structure_bond_angle_gradient | Defines the gradient associated to the bond angle |
CT_Molecular_covalent_structure_bond_length_gradient | Defines the gradient associated to the bond length |
CT_Molecular_covalent_structure_builder_for_proteins | Builds a covalent structure from a given structure |
CT_Molecular_covalent_structure_optimal | Optimized representation of the covalent structure of a molecular conformation |
CT_Molecular_covalent_structure_torsion_angle_gradient | Defines the gradient associated to the torsion angle |
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_connected_component_oserialization | Serialization of a connected component of a molecular interface |
CT_Molecular_interface_data_structure_base | Container for Molecular interface connected components that share the same interface |
CT_Molecular_interface_oserialization | Serialization of a molecular 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 |
CT_Molecular_potential_energy | Potential energy function adding up all the input contributions (C++11 only) |
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_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_bond_length_gradient_harmonic | Defines the standard gradient associated to the bond length contribution |
CT_Molecular_potential_energy_bond_length_term_harmonic | Defines the standard term associated to the bond length contribution |
CT_Molecular_potential_energy_bonded_contribution | Contribution of all bonded energy terms to the potential energy function |
CT_Molecular_potential_energy_cmap_term | Defines the CMap term associated to a pair of proper dihedral angles |
CT_Molecular_potential_energy_contribution | Contribution of an energy term to the potential energy function |
CT_Molecular_potential_energy_electrostatic_gradient | Defines a standard gradient associated to the electrostatic contribution |
CT_Molecular_potential_energy_electrostatic_term | Defines a standard term associated to the electrostatic contribution |
CT_Molecular_potential_energy_gradient | Sum of the contributions of an energy gradient term to the potential energy gradient function |
CT_Molecular_potential_energy_gradient_contribution | Contribution of an energy gradient term to the potential energy gradient function |
CT_Molecular_potential_energy_Lennard_Jones_gradient | Defines the standard gradient associated to the Lennard Jones contribution |
CT_Molecular_potential_energy_Lennard_Jones_term | Defines the standard term associated to the Lennard Jones contribution |
CT_Molecular_potential_energy_numerical_gradient | Computes numerically the gradient of a potential energy function |
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_harmonic | Defines the harmonic 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_torsion_angle_gradient_periodic | Defines the periodic 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_in_linear_structure_term | Defines the term associated to the torsion angle contribution in a linear structure |
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_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_Ryckaert_Bellemans | Defines the Ryckaert_Bellemans term associated to the proper dihedral angle contribution |
CT_Molecular_primitive_internal_coordinates | Computes the internal coordinates from the covalent structure of a molecular conformation |
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 |
►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_Phi_psi_dihedral_angles_visitor | Defines iterator over all successive pairs of dihedrals |
CT_Real_value_function_minimizer | Minimizer of a real valued function |
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_Squared_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 |
C Edge_label_writer | Functor allowing to write two properties associated to a vertex or an edge into a dot file representing a graph |
C Vertex_label_writer | Functor allowing to write two properties associated to a vertex into a dot file representing a graph |
CT_Transition_graph_traits_compressed | Compressed means that vertices are the minima and edges are the transitions |
CT_Transition_graph_traits_standard | Standard means that the vertices are the minima and transitions, and the edges link minima to transitions |
CT_Triangulation_of_molecular_model | Derived class from CGAL Regular triangulation for filling it with particles |
CT_Tricolor_interface_data_structure_base | Container defining what is a tricolor interface between two partners |
CT_Tricolor_interface_oserialization | Serialization of a tricolor interface |
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 |
►NGT | |
CNearest_neighbors_graph_builder | Builder for nearest neighbors graphs |
CNearest_neighbors_graph_builder_with_edge_weight | Builder for nearest neighbors graphs |
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 | K-means algorithm |
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_minimax | Select initial centers of mass by maximizing the min distance between centers of mass at each selection step |
CT_Cluster_engine_k_means_point_selector_plus_plus | Select initial centers of mass using the ++ strategy |
CT_Cluster_engine_k_means_point_selector_random | Select randomly the initial centers of mass for k-means algorithm |
CT_Cluster_engine_Morse_theory_based | Morse theory based clustering algorithm |
►CT_Delaunay_triangulation_extension_3 | Defines simple predicates and constructions structure over a triangulation |
C Get_area_of_dual_of_edge | Given the dual of an edge, compute its area |
C Get_dual_of_edge | Given an edge, return its dual as a container of points |
C Get_dual_of_facet | Given a facet, return its dual as a segment |
C Get_squared_length_of_dual_of_facet | Given a facet, return the squared length of its dual segment |
CT_Delaunay_triangulation_spherical_traits_3 | Kernel used for computations involving exact number types for coordinates of boundary points |
►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_Distance_default_for_graph | Base distance over vertices of a graph |
CT_Morse_Smale_Witten_chain_complex | Representation of the complex of the same name |
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_vertex_weighted_graph_builder | Builds the Morse Smale Witten chain complex from a vertex weighted graph |
CT_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder | Builds the Morse Smale Witten chain complex from a weighted graph |
CT_Morse_theory_based_analyzer | Analysis of a Morse Smale Witten chain complex |
CT_NN_linear_scan | Naive algorithm looking for the nearest neighbors of a point in a database w.r.t a metric spaceNaive algorithm looking for the nearest neighbors of a point in a database w.r.t a metric space |
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_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_Splitter_default | Nearest neighbor engine designed for metric spaces |
CT_Stable_manifold_as_list_traits | Simple representation of a stable manifold as a list of points |
CT_Triangulation_extension_3 | Defines simple predicates and constructions structure over a triangulation |
►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_Union_of_balls_boundary_3_builder | Functor filling a HDS of the Boundary of an union of balls |
CT_Union_of_balls_boundary_3_data_structure | Representation of the boundary of the union of balls |
CT_Union_of_balls_boundary_3_face | Representation of a face 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_item_info | Attached a simplex of the -complex to an item of 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_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_3_vertex | Representation of a vertex in the half-edge data structure |
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_data_structure | Representation of the medial-axis of the 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_halfedge | Representation of a half-edge 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_vertex | Representation of a vertex 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 |
►NIO | |
CLoader_base | Base loader from which any loader should inherit |
CMolecular_view | 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 >, 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 >, 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 -complex for its 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 -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, 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::Regular_triangulation_3< Gt, Tds > * > | Views in Molecular format the edges and facets of the input 3D regular 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 -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, 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 -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, 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 -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 |
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, 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 |
CPyMOL_viewer | Viewer writing in PyMOL file format |
CT_Archive_file_loader | Loader for one or more boost archive files |
CT_Graph_loader | Loader for one or more txt files listing weights |
CT_Index_wrapper | Wrapper for indices where the IO dumping may be different from the index itself |
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_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 |
CT_Primitive_labels_loader | Loader for systems' labels specification |
CT_PyMOL_viewer | Viewer writing in PyMOL file format |
CT_Sequences_loader | Loader for exactly two sequences |
CT_Transition_graph_loader | Loader for one or more boost archive files |
CT_Weighted_vertex_graph_loader | Loader for one or more txt files listing weights |
CVMD_viewer | Viewer writing in VMD file format |
►Nmciboot | |
CMinimum_connectivity_inference | A class to perform compute the solutions of a connectivity inference problem and the analysis of the solutions returned |
►Nmcibootstrap | |
CMinimum_connectivity_inference_bootstrap | A class to enrich set of initial consensus contacts by bootstraping procedure |
►Nmcibootstrap_iterative | |
CMCI_bootstrap | A class to enrich set of initial consensus contacts by bootstraping procedure |
►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 |
CChain_label_traits | Model of MolecularSystemLabelTraits for chains |
CDefault_radii_for_particles_with_annotated_name | Default radii for atoms and pseudo-atoms as residues |
CDomain_label_traits | Model of MolecularSystemLabelTraits for molecular complexes defined in a file |
►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 |
CGet_annotator_option_display_name_default | Returns a string that is the default display name of options for generic annotators |
CGet_annotator_option_help_default | Returns a string that is the default option help for generic annotators |
CGet_annotator_option_name_default | Returns a string that is the default option name for generic annotators |
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) |
CMake_no_annotation_key | Returns false, whatever is the entry |
CName_annotator_for_atoms_setter_default | Default annotated name setter, using the method set_annotated_name of the input particle |
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 |
CRadius_annotator_for_particles_with_annotated_name_setter_default | Default radius setter, using the method set_radius of the input particle |
CSet_dynamic_annotation_default | Default data structure adding a dynamic annotation to a particle |
CT_Atom_with_flat_info | Wrapper representing the atom |
►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_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 |
CT_Conformation_builder_cartesian_default | 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 |
►CT_Domain_label_traits | Model of MolecularSystemLabelTraits for molecular complexes defined in a file. |
CPrimitive_label_classifier | Functor returning a pair classifying a particle |
►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) |
CT_Dynamic_annotator_for_residues | Model of ParticleAnnotator for attributing any annotation to a particle dynamically |
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 |
►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_Graph_loader | Loader for one or more txt files listing weights |
►CT_IG_label_traits | [definition] |
CPrimitive_label_classifier | Functor returning a pair classifying a particle |
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_and_radius_annotations | Base annotations for a default atom (name and radius) |
CT_Name_annotator_for_atoms | Model of ParticleAnnotator for attributing a name to an atom |
CT_Name_annotator_for_pseudo_atoms | Model of ParticleAnnotator for attributing a name to a pseudo-atom |
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 |
CT_Points_d_file_loader | Loader for one or more txt files listing dD points |
CT_Pseudo_atom_per_residue_spec_with_flat_info | Wrapper representing the coarse atom |
►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_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_Radius_annotator_for_particles_with_annotated_name | Model of ParticleAnnotator for attributing a radius to an atom |
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 systemTraits 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 calculationsTraits 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 AKMATraits class defining dimensionless types for AKMA |
CT_Unit_system_traits_none_MD | Traits class defining dimensionless types for MDTraits class defining dimensionless types for MD |
CT_Weights_file_loader | Loader for one or more txt files listing weights |
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 |
►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 |
►NModules | |
CModule_base | Base module from which any module should inherit |
CModule_based_workflow | Representaiont of the workflow of an application enriched with default options |
CT_Acceptance_test_module | Module for checking if a sample is accepted duringthe explorer algorithm |
CT_Alignment_sequences_module | Module which computes a pairwise alignment of two sequences |
CT_Alignment_structures_module | 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 |
CT_Bicolor_interface_oserialization | Serialization of a bicolor interface |
CT_Buried_surface_area_with_labels_module | 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 |
CT_Cluster_engine_module | Module which computes clusters from a cloud of points |
CT_Conformational_ensemble_MST_module | Module for computing the MST of an input NNG |
CT_Conformational_ensemble_pairwise_distances_module | Module for computing all the pairwise distances of an input conformational ensemble |
CT_Conformational_ensemble_sampling_diversity_analysis_module | Module for analyzing the diversity of a conformational ensemble |
CT_Conformational_ensemble_symmetric_difference_module | Module for comparing two conformation ensembles w.r.t an input distance between conformations |
CT_Earth_mover_distance_module | Application's module instantiating the eartyh mover distance algorithm |
CT_Energy_landscape_transition_graph_landmarks_paths_module | Module computing shortes paths in a graph passing through selected landmarks |
CT_Energy_landscape_transition_graph_topology_module | Module analyzingthe topology of a transition graph |
CT_Enriched_nearest_neighbors_graph_builder_module | Module inheriting from the NNG module and adding points linked to specified vertices of the constructed NNG |
CT_Exploration_parameters_update_module | Module for tuning the exploration parameters after the acceptance test |
CT_Mediated_interface_oserialization | Serialization of a mediated interface |
►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 |
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_Module_option_description | Base module from which any module should inherit |
CT_Molecular_interfaces_module | Module building the bicolor, mediated and tricolor interfaces of a molecular structure |
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 |
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_Morse_theory_based_analyzer_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_Point_cloud_hausdorff_distance_d_module | Module computing the Hausdorff distance between conformations of two ensembles |
CT_Record_new_sample_module | Module for recording a new sample in the exploration engine |
CT_Sample_extender_module | Module for extending a selected sample using a given moveset strategy |
CT_Sample_selector_module | Module for selecting a sample to extend during the explorer algorithm |
CT_Space_filling_model_inner_approximation_module | Module building the inner approximation of a set of particles using their medial-axis and a greedy selection algorithm |
CT_Space_filling_model_interpolated_approximation_module | Module building the interpolated approximation of an input set of particles from their inner and outer approximations |
CT_Space_filling_model_outer_approximation_module | Module building the outer approximation of a set of particles from an inner approximation |
CT_Space_filling_model_packing_module | Computes packing properties of particles of at an interface w.r.t to their volume |
CT_Space_filling_model_shelling_diagram_comparison_module | Module comparing two input shelling forests using the ordered forest edit distance |
CT_Spatial_search_module | Module building a data base for spatial-search from an input set of points |
CT_Stop_criterion_module | Module for checking if the explorer algorithm should stop |
CT_Tertiary_quaternary_structure_annotator_module | Module building the Biochemical Interfaces Graph of a molecular structure |
CT_Transition_graph_builder_from_DB_of_critical_points_module | Module building a transition graph from a data base of minima, transitions and weights over those conformations |
CT_Tricolor_interface_oserialization | Serialization of a tricolor interface |
CT_Union_of_balls_boundary_3_module | 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 |
CT_Union_of_balls_mesh_3_module | 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 |
C Union_of_balls_surface_volume_3 | Contains pointers over two functors for computing the volumes and surfaces areas with different level of exactness |
►NPALSE | |
CBioPDB_vs_XML_Etree | A class performing manipulations between the PDB format from BioPython and XML Etrees |
CPALSE_DS_manipulator | A class providing functions to manipulate python Data Structures in general, and lists of strings / native python data types in particular |
CPALSE_statistic_handle | A class providing elementary statistics and plotting facilities |
CPALSE_xml_DB | A class to represent XML files having the same hierarchical structure |
CPython_dico_vs_XML_Etree | A class performing manipulations between python dictionaries and XML Etrees |
►NPDB_complex_to_unbound_partners_matchings | |
CPDB_complex_to_unbound_partners_matcher | Given two PDB files and their respective selected chains, infers the matchings at the chain, residue and atom level |
Cbranch_and_bound | |
Cdp_mat_apurva | |
CGet_not_annotator_option_name | Returns empty option name |
Clambda_matrix | |
CMCI_Contact | A class to store a contact between two subunits of an assembly |
CMCI_Oligomers | A class to store a set of oligomers of an assembly |
CModules_collection | Base module from which any module should inherit |
Cparameters | |
Cproblem | |
CT_Conformational_ensemble_analysis_traits | Traits class for instantiating the workflow T_Conformational_ensemble_analysis_workflow |
CT_Conformational_ensemble_analysis_workflow | Generic workflow of Conformational_ensemble_analysis for reading the command line options of the applications and running the calculations |
CT_Conformational_ensemble_comparison_traits | Traits class for instantiating the workflow T_Conformational_ensemble_comparison_workflow |
CT_Conformational_ensemble_comparison_workflow | Generic workflow of Conformational_ensemble_comparison for reading the command line options of the applications and running the calculations |
CT_Energy_landscape_analysis_traits | Traits class for instantiating the workflow T_Energy_landscape_analysis_workflow |
CT_Energy_landscape_analysis_workflow | Generic workflow of Energy_landscape_analysis for reading the command line options of the applications and running the calculations |
CT_Energy_landscape_comparison_traits | Traits class for instantiating the workflow T_Energy_landscape_comparison_workflow |
CT_Energy_landscape_comparison_workflow | Generic workflow of Energy_landscape_comparison for reading the command line options of the applications and running the calculations |
CT_Euclidean_distance | Euclidean distance between two conformations |
CT_Exploration_algorithm_basins_hopping | Model of exploration algorithm for basins hopping |
CT_Exploration_algorithm_TRRT | Model of exploration algorithm for TRRT |
CT_Exploration_algorithm_TRRT_with_quench | Model of exploration algorithm for TRRT where samples are quenched before inserted |
CT_Exploration_parameters_default | Default representation of the parameters of the exploration algorithm |
CT_Exploration_parameters_with_layers | Representation of the parameters of the exploration algorithm by layers |
CT_Exploration_parameters_with_memory | Representation of the parameters with a map from the samples of the algorithm database to the value of the parameters when the corresponding sample was inserted |
CT_Exploration_parameters_with_reinit | Representation of the parameters with a reinitialization of temperature and displace delta in a fixed interval |
CT_Exploration_parameters_with_sample_map | Representation of the parameters with a map from the samples to their representation in the database of the algorithm |
CT_Gauss6A_function_traits | Traits class defining a mixture of gaussians and its gradient |
CT_Gauss6B_function_traits | Traits class defining a mixture of gaussians and its gradient |
CT_Himmelbleau_function_traits | Traits class defining the Himmelbleau function and its gradient |
CT_Landscape_explorer_traits | Traits class for instantiating the workflow T_Landscape_explorer_workflow |
CT_Landscape_explorer_workflow | Generic workflow of Landscape_explorer for reading the command line options of the applications and running the calculations |
CT_Lrmsd_distance | Least RMSD between two conformations |
CT_Minimal_oritend_spanning_forest_module | Module building the minimal spanning forest of a weighted bipartite graph |
CT_Monkey_function_traits | Traits class defining the Monkey function (function with a monkey saddle) and its gradient |
CT_Morse_function_for_elevated_NNG | Density function where values are already computed and stored in the NNG |
CT_Morse_function_for_NNG_density_from_distance_to_neighbors | Density function proportional to the mean distance between a given vertex and all his neighbors |
CT_Morse_function_for_NNG_density_from_gaussian | Density function proportional to a normal Gaussian estimation over the distances between a given vertex and all his neighbors |
CT_Morse_function_for_NNG_density_from_inverse_distance_to_neighbors | Density function inversely proportional to the distance sum between a given vertex and all his neighbors |
CT_Morse_function_for_NNG_density_from_neighbors | Density function proportional to the number of neighbors of a vertex in the NNG |
CT_Peaks_function_traits | Traits class defining the Peaks function and its gradient |
CT_PeaksE_function_traits | Traits class defining the PeaksE function and its gradient |
CT_Rastrigin_function_traits | Traits class defining the Rastrigin function and its gradient |
CT_Sample_extender_for_BH | Model of extender engine for BH |
CT_Sample_extender_for_BH_with_energy_filter | Model of extender engine for BH using the energy filter of the selector |
CT_Sample_extender_for_TRRT | Model of extender engine for TRRT |
CT_Sample_extender_for_TRRT_with_Voronoi_extender | Model of extender engine for TRRT with the insurance the extended point belongs to the Voronoi cell of the selected conformation |
CT_Sample_selector_for_BH | Model of selector engine for BH |
CT_Sample_selector_for_BH_with_energy_filter | Model of selector engine for BH using energy filters |
CT_Sample_selector_for_stratified | Model of selector engine with several layers of selectors |
CT_Sample_selector_for_TRRT | Model of selector engine for TRRT |
CT_Sample_selector_hybrid_for_BH | Model of selector engine for hybridizing basins hopping |
CT_Space_filling_model_coarse_graining_interpolated_cover | Engine computing the interpolated cover between given inner and outer covers |
►CT_Space_filling_model_coarse_graining_outer_cover | Engine computing the outer cover of a set of balls from its inner cover |
CApollonius_cell | Representation of a cell in the Apollonius diagram |
CLarger_distance_priority | Functor comparing the distance of two points to the center of an input sphere |
CLarger_increment_priority | Sort the Apollonius cells by decreasing volume constribution of their associated sphere |
CT_Space_filling_model_coarse_graining_traits | Traits class for instantiating the workflow T_Space_filling_model_coarse_graining_workflow |
CT_Space_filling_model_coarse_graining_workflow | Generic workflow of Space_filling_model_coarse_graining for reading the command line options of the applications and running the calculations |
►CT_Space_filling_model_interface_finder | Compute the interfaces graph of an input molecular complex |
CParticle_for_union_find | Wrapper for a particle for Union-Find |
CT_Space_filling_model_interface_finder_module | Module building the Interfaces Graph of a molecular structure |
►CT_Space_filling_model_interface_finder_traits | Traits class for instantiating the workflow T_Space_filling_model_interface_finder_workflow |
CGet_label_identifier | Functor returning the identifier of the primitive label of a particle |
CIs_in_partner | Predicate checking that a particle is in a given partner |
CT_Space_filling_model_interface_finder_workflow | Generic workflow of Space_filling_model_interface_finder for reading the command line options of the applications and running the calculations |
CT_Space_filling_model_interface_traits | Traits class for instantiating the workflow T_Space_filling_model_interface_workflow |
CT_Space_filling_model_interface_workflow | Generic workflow of Space_filling_model_interface for reading the command line options of the applications and running the calculations |
CT_Space_filling_model_shelling_diagram_comparison_traits | Traits class for instantiating the workflow T_Space_filling_model_shelling_diagram_comparison_workflow |
CT_Space_filling_model_shelling_diagram_comparison_workflow | Generic workflow of Space_filling_model_shelling_diagram_comparison for reading the command line options of the applications and running the calculations |
►CT_Space_filling_model_shelling_diagram_surface_encoding_traits | Traits class for instantiating the workflow T_Space_filling_model_shelling_diagram_surface_encoding_workflow |
CIs_in_patch | Predicate checking that an input particle is in a given patch |
CT_Space_filling_model_shelling_diagram_surface_encoding_workflow | Generic workflow of Space_filling_model_shelling_diagram_surface_encoding for reading the command line options of the applications and running the calculations |
CT_Space_filling_model_surface_volume_traits | Traits class for instantiating the workflow T_Space_filling_model_surface_volume_workflow |
CT_Space_filling_model_surface_volume_workflow | Generic workflow of Space_filling_model_surface_volume for reading the command line options of the applications and running the calculations |
CT_Transition_graph_builder_from_sampled_energy_landscape_traits | Traits class for instantiating the workflow T_Transition_graph_builder_from_sampled_energy_landscape_workflow |
CT_Transition_graph_builder_from_sampled_energy_landscape_workflow | Generic workflow of Transition_graph_of_energy_landscape_builders for reading the command line options of the applications and running the calculations |
CT_Trigo_terrain_function_traits | Traits class defining a complex function example and its gradient |