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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Base loader from which any loader should inherit. More...
#include <Loader_base.hpp>
Public Types | |
typedef Loader_base | Self |
typedef SBL::Modules::T_Module_option_description | Base |
Public Member Functions | |
Loader_base (void) | |
virtual | ~Loader_base (void) |
virtual boost::program_options::options_description | add_options (void) const |
Virtual method for adding options to the module. More... | |
virtual bool | check_options (std::string &message) const |
Checks that the input options' values are coherent. More... | |
virtual std::string | get_output_prefix (void) const |
Returns a prefix that concatains the input line options used when running the module. More... | |
Static Public Member Functions | |
static boost::program_options::options_description *& | get_options (void) |
Access to the options' description of the module. More... | |
static bool | has_options (void) |
static void | delete_options (void) |
static void | initialize_options (const std::string &caption) |
Requirements | |
virtual bool | load (unsigned verbose, std::ostream &out) |
Loads the data. More... | |
virtual std::string | get_name (void) const |
Return the name of the class itself. More... | |
Management | |
void | set_loader_instance_name (const std::string &loader_instance_name) |
const std::string & | get_loader_instance_name (void) const |
Base loader from which any loader should inherit.
Requirements are...
typedef Loader_base Self |
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inlinevirtual |
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inlinevirtualinherited |
Virtual method for adding options to the module.
Reimplemented in T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Molecular_interfaces_module< ModuleTraits >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< ModuleTraits::Nearest_neighbors_graph, ModuleTraits::Morse_function, ModuleTraits::Distance_graph_function >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Exploration_parameters_update_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Modules_collection< Module, SetIndividualInput >, T_Earth_mover_distance_module< ModuleTraits >, T_Subdomain_comparator_module< ModuleTraits >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Acceptance_test_module< ModuleTraits >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Sample_selector_module< ModuleTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Numbers_file_loader< FT, Tag >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_RST_MST_D_Family_matching_module< ModuleTraits >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Cluster_engine_module< ModuleTraits >, T_Weights_file_loader< FT >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Exploration_parameters_default< NumberType, Distance >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Domain_annotator_for_particles< Annotations >, T_Iterative_alignment_module< ModuleTraits >, T_Weighted_points_d_loader< PointD, WeightType >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Clustering_loader< Graph, Clustering >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, T_Force_field_atomic_traits< TForceFieldFunctionTraits >::Potential_energy_parameters_loader, Conformations_loader, and Space_filling_model_loader.
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inlinevirtualinherited |
Checks that the input options' values are coherent.
Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Molecular_interfaces_module< ModuleTraits >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< ModuleTraits::Nearest_neighbors_graph, ModuleTraits::Morse_function, ModuleTraits::Distance_graph_function >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Exploration_parameters_update_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Module_condition< void, Predicate >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Subdomain_comparator_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Sample_selector_module< ModuleTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_RST_MST_D_Family_matching_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, T_Archive_file_loader< InputArchive, SerializedData >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Domain_annotator_for_particles< Annotations >, T_Graph_loader< GraphType, FT >, T_Module_condition< Module, Predicate >, T_Sequences_loader< FT >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Weights_file_loader< FT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Numbers_file_loader< FT, Tag >, T_Clustering_loader< Graph, Clustering >, T_Weighted_points_d_loader< PointD, WeightType >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, No_particle_annotator, T_Force_field_atomic_traits< TForceFieldFunctionTraits >::Potential_energy_parameters_loader, Conformations_loader, and Space_filling_model_loader.
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inlinestaticinherited |
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Return the name of the class itself.
Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Exploration_parameters_default< NumberType, Distance >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< GraphType, FT >, T_Sequences_loader< FT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Points_d_file_loader< PointD >, T_Weights_file_loader< FT >, T_Numbers_file_loader< FT, Tag >, T_Weighted_points_d_loader< PointD, WeightType >, T_Clustering_loader< Graph, Clustering >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, No_particle_annotator, Conformations_loader, and Space_filling_model_loader.
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inlinestaticinherited |
Access to the options' description of the module.
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inlinevirtualinherited |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Molecular_interfaces_module< ModuleTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< ModuleTraits::Nearest_neighbors_graph, ModuleTraits::Morse_function, ModuleTraits::Distance_graph_function >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Exploration_parameters_update_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Earth_mover_distance_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Module_condition< void, Predicate >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Sample_selector_module< ModuleTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Cluster_engine_module< ModuleTraits >, T_Archive_file_loader< InputArchive, SerializedData >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Domain_annotator_for_particles< Annotations >, T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< GraphType, FT >, T_Sequences_loader< FT >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Weights_file_loader< FT >, T_Points_d_file_loader< PointD >, T_Module_condition< Module, Predicate >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Weighted_points_d_loader< PointD, WeightType >, T_Numbers_file_loader< FT, Tag >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Clustering_loader< Graph, Clustering >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, No_particle_annotator, Conformations_loader, and Space_filling_model_loader.
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inlinestaticinherited |
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inlinestaticinherited |
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inlinevirtual |
Loads the data.
Reimplemented in T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Weights_file_loader< FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Points_d_file_loader< PointD >, T_Numbers_file_loader< FT, Tag >, T_Domain_annotator_for_particles< Annotations >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Exploration_parameters_default< NumberType, Distance >, T_Weighted_points_d_loader< PointD, WeightType >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Clustering_loader< Graph, Clustering >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, No_particle_annotator, T_Force_field_atomic_traits< TForceFieldFunctionTraits >::Potential_energy_parameters_loader, Conformations_loader, and Space_filling_model_loader.
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