Here is a list of all documented functions with links to the class documentation for each member:

- s -

• save() : Genetrank_gene_radar, T_Bicolor_interface_oserialization< BicolorInterface >, T_Mediated_interface_oserialization< MediatedInterface >, T_Molecular_interface_connected_component_oserialization< MolecularInterface >, T_Molecular_interface_oserialization< MolecularInterface >, T_Tricolor_interface_oserialization< TricolorInterface >, T_Bicolor_interface_oserialization< MolecularInterfaceBuilder >, T_Mediated_interface_oserialization< MolecularInterfaceBuilder >, T_Tricolor_interface_oserialization< MolecularInterfaceBuilder >
• save_alignment_graph_to_dot() : KpaxAlignmentGraph
• save_conformations() : T_Conformation_loader< Conformation_builder_ >
• save_connected_components_to_files() : KpaxAlignmentGraph
• save_override() : T_Multiple_archives_serialization_xml_oarchive< DataType, OutputArchive, IsLessData >
• second_residue_chain() : Molecular_SS_bond< System >
• second_residue_id() : Molecular_SS_bond< System >
• second_residue_inscode() : Molecular_SS_bond< System >
• second_residue_name() : Molecular_SS_bond< System >
• serialize() : T_Particle_vertex_base< ParticleTraits, GT, Vb >, T_RMSD_comb_edge_weighted_module< ModuleTraits >
• SET_AND_GET() : T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_system_loader< Molecular_system_ >
• set_annotated_contact() : MCI_specification
• set_blosum_30() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_blosum_45() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_blosum_62() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_blosum_80() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_chain_type() : T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >
• set_circle_resolution() : T_PyMOL_viewer< Dummy >
• set_cloning() : T_PyMOL_viewer< Dummy >
• set_color() : T_PyMOL_viewer< Dummy >
• set_coordinates_n() : Molecular_coordinates_utilities
• set_current_set_of_labels_index() : T_Domain_label_traits< Dummy >
• set_dataset() : BM_Batch
• set_dot_graph_vertex_label() : T_Directed_acyclic_graph_with_layers< VertexProperty, EdgeProperty >
• set_edge_radius() : T_PyMOL_viewer< Dummy >
• set_end_module() : T_Module_based_workflow< Dummy >
• set_epsilon() : T_Union_of_balls_mesh_3_module< ModuleTraits >
• set_executable_path() : BM_Run_specification_tuple
• set_graphics_color() : T_PyMOL_viewer< Dummy >
• set_graphics_transparent() : T_PyMOL_viewer< Dummy >
• set_infinite_factor() : T_PyMOL_viewer< Dummy >
• set_lo() : problem< graph, dp_mat, lambda_mat, parameter >
• set_module_instance_name() : Module_base
• set_Morse_function() : T_Morse_Smale_Witten_chain_complex< MorseFunction, StableManifoldTraits >
• set_output_directory() : BM_Batch
• set_output_directory_prefix() : BM_Batch
• set_pam_120() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_pam_200() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_pam_250() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_pam_40() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_particle() : T_Particle_vertex_base< ParticleTraits, GT, Vb >
• set_report_mode() : Module_base
• set_representation() : T_PyMOL_viewer< Dummy >
• set_sampling_viewer() : T_Union_of_balls_mesh_3_module< ModuleTraits >
• set_standard_substitution_matrix() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_start_module() : T_Module_based_workflow< Dummy >
• set_substitution_matrix() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_system_label() : T_Particle_with_system_label< ParticleBase, PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits, IsSerializedLabel >
• set_top_molecule() : T_PyMOL_viewer< Dummy >
• set_transparent() : T_PyMOL_viewer< Dummy >
• set_up() : problem< graph, dp_mat, lambda_mat, parameter >
• set_vertex_radius() : T_PyMOL_viewer< Dummy >
• set_vertex_resolution() : T_PyMOL_viewer< Dummy >
• set_visible() : T_PyMOL_viewer< Dummy >
• set_vtml_200() : T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
• set_weights() : T_Point_cloud_rigid_registration_3< FT >
• sheet_current_strand_atom_name() : Molecular_secondary_structure_element< System >
• sheet_current_strand_chain_identifier() : Molecular_secondary_structure_element< System >
• sheet_current_strand_residue_insertion_code() : Molecular_secondary_structure_element< System >
• sheet_current_strand_residue_name() : Molecular_secondary_structure_element< System >
• sheet_current_strand_residue_sequence_number() : Molecular_secondary_structure_element< System >
• sheet_num_strands() : Molecular_secondary_structure_element< System >
• sheet_previous_strand_atom_name() : Molecular_secondary_structure_element< System >
• sheet_previous_strand_chain_identifier() : Molecular_secondary_structure_element< System >
• sheet_previous_strand_residue_insertion_code() : Molecular_secondary_structure_element< System >
• sheet_previous_strand_residue_name() : Molecular_secondary_structure_element< System >
• sheet_previous_strand_residue_sequence_number() : Molecular_secondary_structure_element< System >
• sheet_sense() : Molecular_secondary_structure_element< System >
• sheet_strand() : Molecular_secondary_structure_element< System >
• show() : Genetrank_gene_radar
• side_of_oriented_sphere_3_object() : T_Delaunay_triangulation_spherical_traits_3_base< Kernel, BasicKernel, SphereRep >
• sign() : Molecular_coordinates_utilities
• simplify() : T_Morse_theory_based_analyzer< MorseSmaleWittenChainComplex >
• solve() : branch_and_bound< problem >, dp_mat_apurva< graph, lambda_matrix >
• sort_databases() : PALSE_xml_DB
• spearman() : PALSE_statistic_handle
• split() : problem< graph, dp_mat, lambda_mat, parameter >
• split_per_IFO() : BM_Batch
• split_per_NFO() : BM_Batch
• split_per_selected_IFO_option() : BM_Batch
• split_per_selected_NFO_option() : BM_Batch
• split_per_selected_option() : BM_Batch
• split_per_selected_options() : BM_Batch
• start() : T_Module_based_workflow< Dummy >
• statistics() : T_Nucleic_acid_representation< PolynucleotideChain >, T_Protein_representation< PolypeptideChain >, T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Conformation_loader< Conformation_builder_ >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_system_loader< Molecular_system_ >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Numbers_file_loader< FT, Tag >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Graph_loader< GraphType, FT >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader_generic< PointD, PointD_filler >, Module_base, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Module_based_workflow< Dummy >, T_Module_condition< Module, Predicate >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >
• store_cost_components() : MCI_set_of_contacts
• store_data() : T_Multiple_archives_serialization_xml_oarchive< DataType, OutputArchive, IsLessData >
• store_solution_score() : MCI_set_of_contacts
• store_solutions_to_file_as_dict() : MCI_solutions
• strip_variant() : Genetrank_GeneProteinTranslator
• sub_node_col() : lambda_matrix< graph >
• sub_node_row() : lambda_matrix< graph >
• successful_ambiguous_failed_split() : Genetrank_Translations
• summary() : Genetrank_Translations, Genetrank_network_statistical_analysis
• T_Score_computer_K() : T_Score_computer_K< CanonizedResidue >
• T_Seeder_basic() : T_Seeder_basic< StructureType >
• T_Seeder_DP_score() : T_Seeder_DP_score< StructureType, ScoreComputer >
• T_Spanning_tree_solver() : T_Spanning_tree_solver< IntersectionGraph, StopCondition, SpanningTreeGenerator, Algorithm >