- s -

• safe_read() : core::chemical::gasteiger
• safe_write() : core::chemical::gasteiger
• SC_ORBITALS() : core::chemical
• SCORE12_PATCH() : core::scoring
• SCORE13() : core::scoring
• score_atom_centrally() : core::scoring::mm
• score_type_for_orb_params() : core::scoring::orbitals
• score_type_from_name() : core::scoring
• scorefxn_is_symmetric() : core::pose::symmetry
• sealed_symmetric_fold_tree() : core::pose::symmetry
• search_x() : core::scoring::packstat
• select_cav_balls() : core::scoring::packstat
• select_coord_for_residue() : core::pack::task::operation::util
• seqpos_is_base_step_anchor() : core::scoring::dna
• seqs_from_cmd_lines() : core::sequence
• sequence_map_from_pdbinfo() : core::pose
• 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_reasonable_fold_tree() : core::import_pose
• set_ss_from_phipsi() : core::pose
• set_svn_version_and_url() : core
• setPoseExtraScores() : core::pose
• setup_aa2name() : core::chemical
• setup_aa2oneletter() : core::chemical
• setup_atom_id_map() : core::pose
• setup_atom_id_map_match_atom_names() : core::pose
• setup_atom_links() : core::conformation
• setup_backrub_atom_tree() : core::kinematics
• setup_bgres_cops() : core::pack
• setup_cloned_atom() : core::kinematics
• setup_corresponding_atoms() : core::conformation
• setup_dof_mask_from_move_map() : core::pose
• setup_dof_to_torsion_map() : core::pose
• 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_oneletter2aa() : core::chemical
• setup_symmetric_conformation() : core::conformation::symmetry
• setup_water_builders_for_residue_type() : core::scoring::methods
• sgn() : core::io::pdb
• shift_jump_numbers_in_dofs() : core::conformation::symmetry
• 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
• SIDECHAIN_CONJUGATION() : core::chemical
• sigmoidish_neighbor() : core::scoring::packing
• sigmoidish_neighbor_deriv() : core::scoring::packing
• SilentEnergy_sort_by_name() : core::io::silent
• 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
• size() : core::io::serialization
• skip_redundant_constraints() : core::scoring::constraints
• SOFT_REP_DESIGN_WTS() : core::scoring
• SOFT_REP_WTS() : core::scoring
• sort_pose_by_score() : core::pose
• SPECIAL_ROT() : core::chemical
• spline_coeffs() : core::scoring::electron_density
• split() : core::io::pdb
• SQ() : core::scoring::electron_density
• sqr() : core::scoring::methods , core::scoring::packing , core::scoring
• square() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• 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
• streams_from_cmd_line() : core::import_pose::pose_stream
• 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
• stub_id_to_named_stub_id() : core::conformation , core::pose
• sub_to_full() : core::pose::full_model_info
• subtract_chi_angles() : core::pack::dunbrack
• SULFATION() : core::chemical
• superimpose_pose() : core::scoring
• surrogate_atom_for_orbital() : core::scoring::orbitals
• 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_dof_jump_num() : core::pose::symmetry
• sym_dof_names() : core::pose::symmetry
• sym_rmsd_with_super_subset() : core::scoring
• 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
• symmetrize_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• symmetrize_scorefunction() : core::scoring::symmetry
• symmetry_info() : core::pose::symmetry