 |
Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
|
|
Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
|
Base module from which any module should inherit. More...
#include <Module_base.hpp>
Public Member Functions | |
| virtual boost::program_options::options_description | add_options (void) |
| Virtual method for adding options to the module. | |
| virtual bool | check_options (std::string &message) const |
| Checks that the input options' values are coherent. | |
| virtual std::string | get_output_prefix (void) const |
| Returns a prefix that concatains the input line options used when running the module. | |
Static Public Member Functions | |
| static boost::program_options::options_description *& | get_options (void) |
| Access to the options' description of the module. | |
Base module from which any module should inherit.
Requirements are...
|
inlinevirtual |
Virtual method for adding options to the module.
Reimplemented in T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Biomolecule_representation_loader< Protein_representation, Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Biomolecule_representation_loader< Protein_representation_FIAT, Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Biomolecule_representation_loader< Protein_representation_FIT, Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Biomolecule_representation_loader< Protein_representation_HIAT, Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Biomolecule_representation_loader< Protein_representation_HIT, Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Conformation_loader< Conformation_builder_ >, T_Conformation_loader< Conformation >, T_Conformation_loader< Conformation_builder >, T_Conformation_loader< SBL::CSB::T_Conformation_builder_cartesian_default< Conformation > >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< Covalent_structure_builder >, T_Molecular_covalent_structure_loader< Default_molecular_covalent_structure_builder_martini >, T_Molecular_covalent_structure_loader< MCS_builder_biomols >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIT >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader_from_MOL< Covalent_structure >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Particle_traits::Molecular_system >, T_Molecular_system_loader< Traits::Particle_traits::Molecular_system >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< Traits::FT >, T_Numbers_file_loader< Traits::Point >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Primitive_labels_loader< Label_traits >, T_Primitive_labels_loader< Partner_label_traits, Mediator_label_traits, Extra_label_traits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Protein_representation_loader< Protein_representation >, T_Protein_representation_loader< Protein_representation, MCS_loader_biomols >, T_Protein_representation_loader< Protein_representation, Molecular_covalent_structure_loader >, T_Protein_representation_loader< Protein_representation_FIAT, MCS_loader_biomols_FIAT >, T_Protein_representation_loader< Protein_representation_FIT, MCS_loader_biomols_FIT >, T_Protein_representation_loader< Protein_representation_HIAT, MCS_loader_biomols_HIAT >, T_Protein_representation_loader< Protein_representation_HIT, MCS_loader_biomols_HIT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Traits::Graph, Traits::NT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Particle_annotator_collector< Name_and_radius_annotator, Dynamic_annotator >, T_Particle_annotator_collector< Name_annotator, Radius_annotator >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader< K::Point_d >, T_Points_d_file_loader< Traits::Point >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< typename Base::FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Spheres_3_file_loader< CGAL::Weighted_point_3< K >, K::Point_3 >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_sequences_module< Module_traits >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Module_traits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Traits, Alignment_engine >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< Module_traits >, T_Alpha_complex_of_molecular_model_module< Traits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< Module_traits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_without_label_module< Module_traits >, T_Cluster_engine_module< ModuleTraits >, T_Cluster_engine_module< Traits >, T_Earth_mover_distance_module< ModuleTraits >, T_Earth_mover_distance_module< Traits >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_interfaces_module< Module_traits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< Traits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, 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_vertex_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< Traits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_RMSD_comb_edge_weighted_module< Module_traits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< Traits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< Traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_3_module< Module_traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_patch_shelling_3_module< Module_traits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_mesh_3_module< Module_traits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, and T_Union_of_balls_surface_volume_3_module< Traits >.
|
inlinevirtual |
Checks that the input options' values are coherent.
Reimplemented in T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Biomolecule_representation_loader< Protein_representation, Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Biomolecule_representation_loader< Protein_representation_FIAT, Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Biomolecule_representation_loader< Protein_representation_FIT, Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Biomolecule_representation_loader< Protein_representation_HIAT, Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Biomolecule_representation_loader< Protein_representation_HIT, Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Conformation_loader< Conformation_builder_ >, T_Conformation_loader< Conformation >, T_Conformation_loader< Conformation_builder >, T_Conformation_loader< SBL::CSB::T_Conformation_builder_cartesian_default< Conformation > >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< Covalent_structure_builder >, T_Molecular_covalent_structure_loader< Default_molecular_covalent_structure_builder_martini >, T_Molecular_covalent_structure_loader< MCS_builder_biomols >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIT >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader_from_MOL< Covalent_structure >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Particle_traits::Molecular_system >, T_Molecular_system_loader< Traits::Particle_traits::Molecular_system >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< Traits::FT >, T_Numbers_file_loader< Traits::Point >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Primitive_labels_loader< Label_traits >, T_Primitive_labels_loader< Partner_label_traits, Mediator_label_traits, Extra_label_traits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Protein_representation_loader< Protein_representation >, T_Protein_representation_loader< Protein_representation, MCS_loader_biomols >, T_Protein_representation_loader< Protein_representation, Molecular_covalent_structure_loader >, T_Protein_representation_loader< Protein_representation_FIAT, MCS_loader_biomols_FIAT >, T_Protein_representation_loader< Protein_representation_FIT, MCS_loader_biomols_FIT >, T_Protein_representation_loader< Protein_representation_HIAT, MCS_loader_biomols_HIAT >, T_Protein_representation_loader< Protein_representation_HIT, MCS_loader_biomols_HIT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, No_particle_annotator, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Traits::Graph, Traits::NT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Particle_annotator_collector< Name_and_radius_annotator, Dynamic_annotator >, T_Particle_annotator_collector< Name_annotator, Radius_annotator >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader< K::Point_d >, T_Points_d_file_loader< Traits::Point >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< typename Base::FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Spheres_3_file_loader< CGAL::Weighted_point_3< K >, K::Point_3 >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_sequences_module< Module_traits >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Module_traits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Traits, Alignment_engine >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< Module_traits >, T_Alpha_complex_of_molecular_model_module< Traits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< Module_traits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_without_label_module< Module_traits >, T_Cluster_engine_module< ModuleTraits >, T_Cluster_engine_module< Traits >, T_Module_condition< Module, Predicate >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_interfaces_module< Module_traits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Molecular_structure_classifier_module< Module_traits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, 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_vertex_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< Traits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< Traits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< Traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_3_module< Module_traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_patch_shelling_3_module< Module_traits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_mesh_3_module< Module_traits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, and T_Union_of_balls_surface_volume_3_module< Traits >.
|
inlinestatic |
Access to the options' description of the module.
|
inlinevirtual |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented in T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Biomolecule_representation_loader< Protein_representation, Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Biomolecule_representation_loader< Protein_representation_FIAT, Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Biomolecule_representation_loader< Protein_representation_FIT, Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Biomolecule_representation_loader< Protein_representation_HIAT, Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Biomolecule_representation_loader< Protein_representation_HIT, Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Conformation_loader< Conformation_builder_ >, T_Conformation_loader< Conformation >, T_Conformation_loader< Conformation_builder >, T_Conformation_loader< SBL::CSB::T_Conformation_builder_cartesian_default< Conformation > >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< Covalent_structure_builder >, T_Molecular_covalent_structure_loader< Default_molecular_covalent_structure_builder_martini >, T_Molecular_covalent_structure_loader< MCS_builder_biomols >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIT >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader_from_MOL< Covalent_structure >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Particle_traits::Molecular_system >, T_Molecular_system_loader< Traits::Particle_traits::Molecular_system >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< Traits::FT >, T_Numbers_file_loader< Traits::Point >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Primitive_labels_loader< Label_traits >, T_Primitive_labels_loader< Partner_label_traits, Mediator_label_traits, Extra_label_traits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Protein_representation_loader< Protein_representation >, T_Protein_representation_loader< Protein_representation, MCS_loader_biomols >, T_Protein_representation_loader< Protein_representation, Molecular_covalent_structure_loader >, T_Protein_representation_loader< Protein_representation_FIAT, MCS_loader_biomols_FIAT >, T_Protein_representation_loader< Protein_representation_FIT, MCS_loader_biomols_FIT >, T_Protein_representation_loader< Protein_representation_HIAT, MCS_loader_biomols_HIAT >, T_Protein_representation_loader< Protein_representation_HIT, MCS_loader_biomols_HIT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, No_particle_annotator, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Traits::Graph, Traits::NT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Particle_annotator_collector< Name_and_radius_annotator, Dynamic_annotator >, T_Particle_annotator_collector< Name_annotator, Radius_annotator >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader< K::Point_d >, T_Points_d_file_loader< Traits::Point >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< typename Base::FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Spheres_3_file_loader< CGAL::Weighted_point_3< K >, K::Point_3 >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< Module_traits >, T_Alpha_complex_of_molecular_model_module< Traits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< Module_traits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_without_label_module< Module_traits >, T_Cluster_engine_module< ModuleTraits >, T_Cluster_engine_module< Traits >, T_Earth_mover_distance_module< ModuleTraits >, T_Earth_mover_distance_module< Traits >, T_Module_based_workflow< Dummy >, T_Module_based_workflow< Dummy >, T_Module_condition< Module, Predicate >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_interfaces_module< Module_traits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Molecular_structure_classifier_module< Module_traits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, 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_vertex_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< Traits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< Traits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< Traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_3_module< Module_traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_patch_shelling_3_module< Module_traits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_mesh_3_module< Module_traits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, and T_Union_of_balls_surface_volume_3_module< Traits >.
1.14.0