Here is a list of all namespace members with links to the namespace documentation for each member:

- s -

• S : core::chemical::element
• S_p_sp3 : core::chemical::orbitals
• sa : core::scoring
• SA_EnergyCreator_registrator : core::init
• safe_read() : core::chemical::gasteiger
• safe_write() : core::chemical::gasteiger
• SAMPLE : core::pose::full_model_info
• sample_layer_lines_from_bins() : core::scoring::fiber_diffraction
• SasaCalcCOP : core::scoring::sasa
• SasaCalcOP : core::scoring::sasa
• SasaMethodCOP : core::scoring::sasa
• SasaMethodEnum : core::scoring::sasa
• SasaMethodOP : core::scoring::sasa
• SasaMethodType_total : core::scoring::sasa
• SasaOptionsOP : core::scoring::packstat
• SasaRadii : core::scoring::sasa
• SasaRadii_total : core::scoring::sasa
• SasaResultOP : core::scoring::packstat
• saxs_cen_score : core::scoring
• saxs_fa_score : core::scoring
• saxs_score : core::scoring
• SAXSEnergyCreator_registrator : core::init
• SAXSEnergyCreatorCEN_registrator : core::init
• SAXSEnergyCreatorFA_registrator : core::init
• Sb : core::chemical::element
• Sc : core::chemical::element
• SC_BB : core::scoring::motif
• SC_PH : core::scoring::motif
• SC_PO : core::scoring::motif
• sc_sc : core::pack::interaction_graph
• SC_SC : core::scoring::motif
• sc_whole : core::pack::interaction_graph
• ScalarWeightedFuncCOP : core::scoring::func
• ScalarWeightedFuncOP : core::scoring::func
• SCMinMinimizerMapCOP : core::pack::scmin
• SCMinMinimizerMapOP : core::pack::scmin
• SCMinMultifuncCOP : core::pack::scmin
• SCMinMultifuncOP : core::pack::scmin
• Score : core::scoring
• SCORE12_PATCH : core::scoring
• SCORE13 : core::scoring
• score_atom_centrally() : core::scoring::mm
• score_mapping() : core::io::pdb
• score_type_for_orb_params() : core::scoring::orbitals
• score_type_from_name() : core::scoring
• ScoreFileSilentStructCreator_registrator : core::init
• ScoreFunctionCOP : core::scoring
• ScoreFunctionInfoCOP : core::scoring
• ScoreFunctionInfoOP : core::scoring
• ScoreFunctionOP : core::scoring
• ScoreFunctionSP : core::scoring
• scorefxn_is_symmetric() : core::pose::symmetry
• ScoreJumpFileSilentStructCreator_registrator : core::init
• ScorePair : core::import_pose::atom_tree_diffs
• Scores : core::import_pose::atom_tree_diffs
• ScoresPair : core::import_pose::atom_tree_diffs
• ScoresPairList : core::import_pose::atom_tree_diffs
• ScoreStructOP : core::io::raw_data
• ScoreType : core::scoring
• ScoreTypes : core::scoring
• ScoringSchemeOP : core::sequence
• Se : core::chemical::element
• sealed_symmetric_fold_tree() : core::pose::symmetry
• search_x() : core::scoring::packstat
• secant() : core::scoring::fiber_diffraction
• SecondaryStructureCOP : core::fragment
• SecondaryStructureEnergyCreator_registrator : core::init
• SecondaryStructureOP : core::fragment
• SecondaryStructurePotentialCOP : core::scoring
• SecondaryStructurePotentialOP : core::scoring
• SecStructGenAP : core::fragment::picking_old::vall::gen
• SecStructGenCAP : core::fragment::picking_old::vall::gen
• SecStructGenCOP : core::fragment::picking_old::vall::gen
• SecStructGenOP : core::fragment::picking_old::vall::gen
• select_cav_balls() : core::scoring::packstat
• select_coord_for_residue() : core::pack::task::operation::util
• separate_definitions_from_comments() : update_ResidueType_enum_files
• seq_sep_M2 : core::scoring::hbonds
• seq_sep_M3 : core::scoring::hbonds
• seq_sep_M4 : core::scoring::hbonds
• seq_sep_MAX : core::scoring::hbonds
• seq_sep_other : core::scoring::hbonds
• seq_sep_P2 : core::scoring::hbonds
• seq_sep_P3 : core::scoring::hbonds
• seq_sep_P4 : core::scoring::hbonds
• seq_sep_PM1 : core::scoring::hbonds
• seqdep_ref : core::scoring
• seqpos_is_base_step_anchor() : core::scoring::dna
• seqs_from_cmd_lines() : core::sequence
• sequence_map_from_pdbinfo() : core::pose
• SequenceAlignmentCOP : core::sequence
• SequenceAlignmentOP : core::sequence
• SequenceAnnotationCOP : core::environment
• SequenceAnnotationOP : core::environment
• SequenceCOP : core::sequence
• SequenceCouplingCOP : core::sequence
• SequenceCouplingCreator_registrator : core::init
• SequenceCouplingOP : core::sequence
• SequenceCreatorCOP : core::sequence
• SequenceCreatorOP : core::sequence
• SequenceDependentRefEnergyCOP : core::scoring::methods
• SequenceDependentRefEnergyOP : core::scoring::methods
• SequenceFactoryOP : core::io::silent
• SequenceMappingCOP : core::id
• SequenceMappingOP : core::id
• SequenceOP : core::sequence
• SequenceProfileConstraintCOP : core::scoring::constraints
• SequenceProfileConstraintCreator_registrator : core::init
• SequenceProfileConstraintOP : core::scoring::constraints
• SequenceProfileCOP : core::sequence
• SequenceProfileCreator_registrator : core::init
• SequenceProfileOP : core::sequence
• SEQUENTIAL : core::conformation::symmetry
• set_asymm_unit_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• set_base_partner() : core::scoring::dna
• set_chi_according_to_coordinates() : core::conformation
• set_fold_tree_from_symm_data() : core::conformation::symmetry
• set_full_model_info() : core::pose::full_model_info
• set_glycosidic_torsion() : core::pose::carbohydrates
• set_r_array() : core::scoring::fiber_diffraction
• set_r_inv_array() : core::scoring::fiber_diffraction
• set_reasonable_fold_tree() : core::import_pose
• set_residue_pair_xform() : core::scoring::motif
• set_ss_from_phipsi() : core::pose
• set_svn_version_and_url() : core
• setPoseExtraScore() : core::pose
• SetRotamerCouplingsCreator_registrator : core::init
• SetRotamerCouplingsOP : core::pack::task::operation
• SetRotamerLinksCreator_registrator : core::init
• SetRotamerLinksOP : core::pack::task::operation
• setup_aa2name() : core::chemical
• setup_aa2oneletter() : core::chemical
• setup_atom_id_map() : core::pose::copydofs
• setup_atom_id_map_match_atom_names() : core::pose::copydofs
• setup_atom_links() : core::conformation
• setup_atom_type_reassignments_from_commandline() : core::chemical
• setup_backrub_atom_tree() : core::kinematics
• setup_bgres_cops() : core::pack
• setup_centroid_scatter() : core::scoring::fiber_diffraction
• setup_cloned_atom() : core::kinematics
• setup_corresponding_atoms() : core::conformation
• setup_cylindrical_coords() : core::scoring::fiber_diffraction
• setup_dof_mask_from_move_map() : core::pose
• setup_dof_to_torsion_map() : core::pose
• setup_element2name() : core::chemical::element
• setup_form_factors() : core::scoring::fiber_diffraction
• setup_icoor_reassignments_from_commandline() : core::chemical
• setup_IG_res_res_weights() : core::pack
• setup_links() : core::conformation
• setup_links_simple() : core::conformation
• setup_matching_atoms_with_given_names() : core::scoring
• setup_matching_CA_atoms() : core::scoring
• setup_matching_heavy_atoms() : core::scoring
• setup_matching_protein_backbone_heavy_atoms() : core::scoring
• setup_name2aa() : core::chemical
• setup_name2element() : core::chemical::element
• setup_oneletter2aa() : core::chemical
• setup_symmetric_conformation() : core::conformation::symmetry
• setup_water_builders_for_residue_type() : core::scoring::methods
• Sg : core::chemical::element
• SG_Dist_FuncOP : core::scoring::disulfides
• sgn() : core::io::pdb
• SGSG_Dihedral_FuncOP : core::scoring::disulfides
• SHAPE_1M7 : core::scoring::rna::data
• ShapeComplementarityCalculatorCOP : core::scoring::sc
• ShapeComplementarityCalculatorOP : core::scoring::sc
• SharedSilentDataOP : core::io::silent
• SharedSilentDataType : core::io::silent
• sheet : core::scoring
• shift_jump_numbers_in_dofs() : core::conformation::symmetry
• ShortestPathInFoldTreeAP : core::kinematics
• ShortestPathInFoldTreeCOP : core::kinematics
• ShortestPathInFoldTreeOP : core::kinematics
• ShortRangeTwoBodyEnergyCOP : core::scoring::methods
• ShortRangeTwoBodyEnergyOP : core::scoring::methods
• ShortSize : core
• show_atom_tree() : core::conformation
• show_base_pair_params() : core::scoring::dna
• show_base_pair_params_with_z_scores() : core::scoring::dna
• show_base_step_params() : core::scoring::dna
• show_detail() : core::scoring
• show_dna_geometry() : core::scoring::dna
• show_foldtree() : core::conformation::symmetry
• show_new_base_step_params() : core::scoring::dna
• Si : core::chemical::element
• SidechainStateAssignmentCOP : core::pack::scmin
• SidechainStateAssignmentOP : core::pack::scmin
• sigmoidish_neighbor() : core::scoring::packing
• sigmoidish_neighbor_deriv() : core::scoring::packing
• SigmoidWeightedCenListRealOP : core::scoring
• SigmoidWeightedCenListVectorOP : core::scoring
• SilentEnergy_sort_by_name() : core::io::silent
• SilentFileDataOP : core::io::silent
• SilentFileLoaderCOP : core::io::silent
• SilentFileLoaderCreator_registrator : core::init
• SilentFileLoaderOP : core::io::silent
• SilentFileOptionsCOP : core::io::silent
• SilentFileOptionsCreator_registrator : core::init
• SilentFileOptionsOP : core::io::silent
• SilentFilePoseInputStreamOP : core::import_pose::pose_stream
• SilentStructCOP : core::io::silent
• SilentStructCreatorCOP : core::io::silent
• SilentStructCreatorOP : core::io::silent
• SilentStructFactoryOP : core::io::silent
• SilentStructOP : core::io::silent
• SilentStructOPs : core::io::silent
• SimAnnealerBaseOP : core::pack::annealer
• simple_mapping_from_file() : core::sequence
• simple_numeric_deriv_check() : core::optimization
• simple_visualize_fold_tree() : core::kinematics
• simple_visualize_fold_tree_and_movemap() : core::kinematics
• simple_visualize_fold_tree_and_movemap_bb_chi() : core::kinematics
• SimpleDerivCheckResultCOP : core::optimization
• SimpleDerivCheckResultOP : core::optimization
• SimpleInteractionGraphCOP : core::pack::interaction_graph
• SimpleInteractionGraphOP : core::pack::interaction_graph
• SimpleSequenceCreator_registrator : core::init
• simplesequencedata : core::io::silent
• SimpleSequenceDataOP : core::io::silent
• SingleBond : core::chemical
• SingleBondOrder : core::chemical
• SingleLigandRotamerLibraryAP : core::pack::dunbrack
• SingleLigandRotamerLibraryCAP : core::pack::dunbrack
• SingleLigandRotamerLibraryCOP : core::pack::dunbrack
• SingleLigandRotamerLibraryOP : core::pack::dunbrack
• SingleResidueCenrotLibraryAP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCAP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCOP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryOP : core::pack::dunbrack::cenrot
• SingleResidueDunbrackLibraryAP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCAP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCOP : core::pack::dunbrack
• SingleResidueDunbrackLibraryOP : core::pack::dunbrack
• SingleResidueFragDataCOP : core::fragment
• SingleResidueFragDataOP : core::fragment
• SingleResiduePeptoidLibraryAP : core::pack::dunbrack
• SingleResiduePeptoidLibraryCAP : core::pack::dunbrack
• SingleResiduePeptoidLibraryCOP : core::pack::dunbrack
• SingleResiduePeptoidLibraryOP : core::pack::dunbrack
• SingleResidueRotamerLibraryAP : core::pack::dunbrack
• SingleResidueRotamerLibraryCAP : core::pack::dunbrack
• SingleResidueRotamerLibraryCOP : core::pack::dunbrack
• SingleResidueRotamerLibraryOP : core::pack::dunbrack
• site_constraint : core::scoring
• SiteConstraintCOP : core::scoring::constraints
• SiteConstraintCreator_registrator : core::init
• SiteConstraintOP : core::scoring::constraints
• SiteConstraintResiduesCOP : core::scoring::constraints
• SiteConstraintResiduesCreator_registrator : core::init
• SiteConstraintResiduesOP : core::scoring::constraints
• size() : core::io::serialization
• Size : core
• Size4 : core::pack::dunbrack
• Size5 : core::pack::dunbrack
• SizeCR : core::pose::motif
• Sizes : core::scoring::motif
• SKIP_HBONDER_CUT : core::scoring::geometric_solvation
• skip_redundant_constraints() : core::scoring::constraints
• SliceIter : core::scoring::packstat
• Slices : core::scoring::packstat
• SlideCriteriaType : core::conformation::symmetry
• SlideType : core::conformation::symmetry
• Sm : core::chemical::element
• SMALL_OVERLAP : core::scoring::motif
• SmoothCenPairEnergyCreator_registrator : core::init
• SmoothEnvEnergyCreator_registrator : core::init
• SmoothEnvPairPotentialCOP : core::scoring
• SmoothEnvPairPotentialOP : core::scoring
• Sn : core::chemical::element
• SoedingFuncOP : core::scoring::func
• SOFT_REP_DESIGN_WTS : core::scoring
• SOFT_REP_WTS() : core::scoring
• SOGFunc_ImplOP : core::scoring::func
• SOGFuncOP : core::scoring::func
• sort_pose_by_score() : core::pose
• SOUTH : core::chemical::rna
• SP2_HYBRID : core::chemical
• SP3_HYBRID : core::chemical
• SpanCOP : core::conformation::membrane
• spanfile_name() : core::conformation::membrane
• spanfile_names() : core::conformation::membrane
• SpanningTopologyCOP : core::conformation::membrane
• SpanningTopologyOP : core::conformation::membrane
• SpanOP : core::conformation::membrane
• SPAtomCIter : core::scoring::packstat
• SPAtomIter : core::scoring::packstat
• SPAtoms : core::scoring::packstat
• special_rot : core::scoring
• SpecialSegmentsObserverCOP : core::pose::datacache
• SpecialSegmentsObserverOP : core::pose::datacache
• SphereCIter : core::scoring::packstat
• SphereIter : core::scoring::packstat
• Spheres : core::scoring::packstat
• spline_coeffs() : core::scoring::electron_density
• SplineFuncCOP : core::scoring::func
• SplineFuncOP : core::scoring::func
• split() : core::io::pdb
• SQ() : core::scoring::electron_density
• sqr() : core::scoring::membrane , core::scoring::methods , core::scoring::motif , core::scoring::packing , core::scoring
• square() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::fiber_diffraction
• SquareWell2FuncCOP : core::scoring::func
• SquareWell2FuncOP : core::scoring::func
• SquareWellFuncCOP : core::scoring::func
• SquareWellFuncOP : core::scoring::func
• Sr : core::chemical::element
• SRPL_TR() : core::pack::dunbrack
• SS_InfoCOP : core::scoring
• SS_InfoOP : core::scoring
• SS_Killhairpins_InfoCOP : core::scoring
• SS_Killhairpins_InfoOP : core::scoring
• ss_pair : core::scoring
• SSize : core
• stack_elec : core::scoring
• stack_elec_base_base : core::scoring
• stack_elec_base_bb : core::scoring
• STACK_ELEC_NBLIST : core::scoring::EnergiesCacheableDataType
• StackElecEnergyCreator_registrator : core::init
• start_sig : core::scoring::membrane , core::scoring::methods
• start_sig2 : core::scoring::membrane , core::scoring::methods
• steal_alignment() : core::sequence
• steal_constant_length_frag_set_from_pose() : core::fragment
• steal_frag_set_from_pose() : core::fragment
• store_CSA_in_pose() : core::scoring
• store_DC_in_pose() : core::scoring
• store_RDC_in_pose() : core::scoring
• store_RDC_ROHL_in_pose() : core::scoring
• strand_orientation_vector() : core::scoring::dna
• StrandPairingCOP : core::scoring::dssp
• StrandPairingOP : core::scoring::dssp
• StrandPairingSetCOP : core::scoring::dssp
• StrandPairingSetOP : core::scoring::dssp
• Strategy : core::conformation
• streams_from_cmd_line() : core::import_pose::pose_stream
• string : core::import_pose::pose_stream
• String : core::import_pose , core::io::pdb , core::pose
• string_to_int() : core::scoring::rna::chemical_shift
• string_to_real() : core::scoring::rna::chemical_shift
• strip_whitespace() : core::chemical::orbitals , core::chemical , core::scoring::packing
• STRIPEHASH : core::conformation
• StrStrMap : core::chemical::sdf
• Structure_Map : core::io::silent
• StructureMap : core::io::raw_data
• stub_id_to_named_stub_id() : core::conformation , core::pose
• sub_to_full() : core::pose::full_model_info
• subtract_chi_angles() : core::pack::dunbrack::peptoid , core::pack::dunbrack
• suck : core::scoring
• SuckerEnergyCreator_registrator : core::init
• suga : core::scoring::rna::chemical_shift
• SUGAR : core::chemical::rna
• sugar_atoms : core::chemical::rna
• sugar_bb : core::scoring
• SugarBackboneEnergyCOP : core::scoring::methods::carbohydrates
• SugarBackboneEnergyCreator_registrator : core::init
• SugarBackboneEnergyOP : core::scoring::methods::carbohydrates
• suiteness_bonus : core::scoring
• sum_water_weights_iterator : core::scoring::geometric_solvation
• SumFuncOP : core::scoring::func
• superimpose_pose() : core::scoring
• surface : core::scoring
• SurfaceEnergiesCOP : core::scoring::solid_surface
• SurfaceEnergiesOP : core::scoring::solid_surface
• SurfaceEnergyCreator_registrator : core::init
• SurfEnergyCreator_registrator : core::init
• SurfVolEnergyCreator_registrator : core::init
• surrogate_atom_for_orbital() : core::scoring::orbitals
• SWAlignerCOP : core::sequence
• SWAlignerOP : core::sequence
• swap() : core::id
• swap4_aligned() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• swap_bytes() : core::io::serialization
• swap_seqpos() : core::scoring::methods
• swap_transform() : core::pose
• switch_to_residue_type_set() : core::util
• sym_bonus_lr : core::scoring::methods
• sym_dof_jump_num() : core::pose::symmetry
• sym_dof_names() : core::pose::symmetry
• sym_lig : core::scoring
• sym_rmsd_with_super_subset() : core::scoring
• SymAtomTreeMinimizerCOP : core::optimization::symmetry
• SymAtomTreeMinimizerOP : core::optimization::symmetry
• SymDofCOP : core::conformation::symmetry
• SymDofOP : core::conformation::symmetry
• symE_bonus : core::scoring
• symECreator_registrator : core::init
• SymmDataCOP : core::conformation::symmetry
• SymmDataLoaderCOP : core::conformation::symmetry
• SymmDataLoaderCreator_registrator : core::init
• SymmDataLoaderOP : core::conformation::symmetry
• SymmDataOP : core::conformation::symmetry
• SymmDataOptionsCOP : core::conformation::symmetry
• SymmDataOptionsCreator_registrator : core::init
• SymmDataOptionsOP : core::conformation::symmetry
• symmetric_components() : core::pose::symmetry
• symmetric_pack_rotamers() : core::pack
• symmetric_pack_rotamers_run() : core::pack
• symmetric_pack_rotamers_setup() : core::pack
• symmetric_repackable_residues() : core::pack
• symmetric_rotamer_trials() : core::pack
• SymmetricConformation : core::pack
• SymmetricConformationCOP : core::conformation::symmetry
• SymmetricConformationOP : core::conformation::symmetry
• SymmetricEnergiesCOP : core::scoring::symmetry
• SymmetricEnergiesOP : core::scoring::symmetry
• SymmetricLigandEnergyCreator_registrator : core::init
• SymmetricRotamerSetFactoryOP : core::pack::rotamer_set::symmetry
• SymmetricRotamerSetsCOP : core::pack::rotamer_set::symmetry
• SymmetricRotamerSetsOP : core::pack::rotamer_set::symmetry
• SymmetricScoreFunctionCOP : core::scoring::symmetry
• SymmetricScoreFunctionOP : core::scoring::symmetry
• symmetrize_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• symmetrize_scorefunction() : core::scoring::symmetry
• symmetry_info() : core::pose::symmetry
• SymmetryInfo : core::pack
• SymmetryInfoCOP : core::conformation::symmetry
• SymmetryInfoOP : core::conformation::symmetry
• SymMinimizerMapCOP : core::optimization::symmetry
• SymMinimizerMapOP : core::optimization::symmetry
• SymmLinearMemoryInteractionGraphCOP : core::pack::interaction_graph
• SymmLinearMemoryInteractionGraphOP : core::pack::interaction_graph
• SymmMinimalistInteractionGraphCOP : core::pack::interaction_graph
• SymmMinimalistInteractionGraphOP : core::pack::interaction_graph
• SymmOnTheFlyInteractionGraphCOP : core::pack::interaction_graph
• SymmOnTheFlyInteractionGraphOP : core::pack::interaction_graph
• SymSlideInfoCOP : core::conformation::symmetry
• SymSlideInfoOP : core::conformation::symmetry
• SYN : core::chemical::rna