- s -

• sa_faraggi_max() : protocols::frag_picker
• safe_secstruct() : protocols::jumping
• safe_set_extended_torsions_and_idealize_loops() : protocols::loops
• sample_user_specified_virtual_riboses() : protocols::swa::rna
• sample_virtual_ribose_and_bulge_and_close_chain() : protocols::swa::rna
• saved_reference_pose() : protocols::rosetta_scripts
• SC_ORBITALS() : core::chemical
• SCORE12_PATCH() : core::scoring
• SCORE13() : core::scoring
• score_atom_centrally() : core::scoring::mm
• SCORE_FRAG_STORE() : protocols::loops::loop_closure::ccd
• score_sort_citeria() : protocols::swa::rna
• score_type_filter_tracer() : protocols::simple_filters
• score_type_from_name() : core::scoring
• scorefxn_is_symmetric() : core::pose::symmetry
• scorefxn_update_from_options() : protocols::enzdes::enzutil
• SDFParserTracer() : core::chemical::sdf
• sealed_symmetric_fold_tree() : core::pose::symmetry
• search_x() : core::scoring::packstat
• section() : protocols::sparta
• select_best_poses() : protocols::ligand_docking
• select_cav_balls() : core::scoring::packstat
• select_coord_for_residue() : core::pack::task::operation::util
• select_loop_frags() : protocols::loops
• select_loop_residues() : protocols::loops
• select_RBsegments() : protocols::rbsegment_relax
• seq_num_sort_citeria() : protocols::swa::rna
• seq_pdb_str() : protocols::dna
• seq_to_str() : protocols::dna
• seqpos_is_base_step_anchor() : core::scoring::dna
• seqs_from_cmd_lines() : core::sequence
• sequence_map_from_pdbinfo() : core::pose
• SerializableState_get() : protocols::moves
• SerializableState_set() : protocols::moves
• serialize_ids() : protocols::features
• set_asymm_unit_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• set_base_coordinate_frame() : protocols::swa::rna
• set_base_partner() : core::scoring::dna
• set_base_segment_chainbreak_constraints() : protocols::dna
• set_bg_color() : protocols::viewer
• set_CCD_torsions_to_zero() : protocols::swa::rna
• set_chi_according_to_coordinates() : core::conformation
• set_constraints() : protocols::rbsegment_relax
• Set_Difference() : protocols::swa::rna
• set_extended_torsions() : protocols::loops
• set_extended_torsions_and_idealize_loops() : protocols::loops
• set_fold_tree_from_symm_data() : core::conformation::symmetry
• set_jumps() : protocols::ligand_docking
• set_local_movemap() : protocols::vip
• set_loop_cutpoint_in_pose_fold_tree() : protocols::loops
• set_move_map_for_centroid_loop() : protocols::loops
• set_native_in_mover() : protocols::jd2
• set_nucleotide_to_A_form() : protocols::swa::rna
• set_pose_and_scorefxn_for_edens_scoring() : protocols::electron_density
• set_rb_constraints() : protocols::rbsegment_relax
• set_reasonable_fold_tree() : core::import_pose
• set_repulsive_bb_cores() : protocols::ligand_docking
• set_rna_secstruct() : protocols::rna
• set_secstruct_from_dssp() : protocols::loops
• set_secstruct_from_psipred_ss2() : protocols::loops
• set_single_loop_fold_tree() : protocols::forge::methods , protocols::loops
• set_sphere() : protocols::ligand_docking
• set_ss_from_phipsi() : core::pose
• set_to_origin() : protocols::swa::rna
• Set_Union() : protocols::swa::rna
• set_xyz_coord() : protocols::fibril
• 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_atom_pair_constraints() : protocols::medal
• setup_backrub_atom_tree() : core::kinematics
• setup_base_pair_constraints() : protocols::rna
• setup_bgres_cops() : core::pack
• setup_bulge_jump_point() : protocols::swa::rna
• setup_centroid_constraints() : protocols::hybridization
• setup_chain_break_jump_point() : protocols::swa::rna
• setup_cloned_atom() : core::kinematics
• setup_coarse_chainbreak_constraints() : protocols::rna
• setup_conformer_map() : protocols::motifs
• setup_constraints() : protocols::medal , protocols::star
• setup_convergence_checks_from_cmdline() : protocols::canonical_sampling::mc_convergence_checks
• setup_coordinate_constraints() : protocols::medal
• setup_corresponding_atoms() : core::conformation
• setup_dme_point_graph() : protocols::simple_moves
• setup_dof_mask_from_move_map() : core::pose
• setup_dof_to_torsion_map() : core::pose
• setup_faraggi_map() : protocols::frag_picker
• setup_FB_CC_JP_list() : protocols::swa::rna
• setup_foldtree() : protocols::docking
• setup_fullatom_constraints() : protocols::hybridization
• 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_membrane_topology() : protocols::relax
• setup_name2aa() : core::chemical
• setup_name2type() : protocols::frag_picker
• setup_oneletter2aa() : core::chemical
• setup_packer_task() : protocols::antibody2
• setup_pose_from_rbsegs() : protocols::rbsegment_relax
• setup_pose_input_stream() : protocols::swa
• setup_pose_rbsegs_keep_loops() : protocols::rbsegment_relax
• setup_protein_backbone_atom_id_map() : protocols::swa::protein
• setup_protein_CA_atom_id_map() : protocols::swa::protein
• setup_residue_at_origin_list() : protocols::swa::rna
• setup_score() : protocols::star
• setup_simple_fold_tree() : protocols::swa::rna
• setup_suite_atom_id_map() : protocols::swa::rna
• setup_symmetric_conformation() : core::conformation::symmetry
• setup_type2name() : protocols::frag_picker
• setup_water_builders_for_residue_type() : core::scoring::methods
• shift_jump_numbers_in_dofs() : core::conformation::symmetry
• shift_jumps() : protocols::forge::methods
• ShortToRealAngle() : protocols::loophash
• 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
• show_scorefxn_weight_lines() : protocols::swa::rna
• SIDECHAIN_CONJUGATION() : core::chemical
• sidechain_rmsd_filter_tracer() : protocols::simple_filters
• sigmoid() : protocols::noesy_assign
• sigmoidish_neighbor() : core::scoring::packing
• sigmoidish_neighbor_deriv() : core::scoring::packing
• SilentEnergy_sort_by_name() : core::io::silent
• simple_fold_tree() : protocols::antibody , protocols::antibody2 , protocols::star
• simple_mapping_from_file() : core::sequence
• simple_numeric_deriv_check() : core::optimization
• simple_one_loop_fold_tree() : protocols::antibody , protocols::antibody2
• simple_visualize_fold_tree() : core::kinematics
• simple_visualize_fold_tree_and_movemap() : core::kinematics
• simple_visualize_fold_tree_and_movemap_bb_chi() : core::kinematics
• simplifyWhiteSpace() : protocols::sparta
• single_ligand_motif_from_stream() : protocols::motifs
• single_motif_from_filename() : protocols::motifs
• single_motif_from_stream() : protocols::motifs
• single_residue_from_stream() : protocols::motifs
• size() : core::io::serialization
• skip_redundant_constraints() : core::scoring::constraints
• sleep() : protocols::swa::rna
• slide_into_contact_and_score() : protocols::sic_dock
• slide_together_tracer() : protocols::ligand_docking
• smallmer_from_largemer() : protocols::forge::methods
• SOFT_REP_DESIGN_WTS() : core::scoring
• SOFT_REP_WTS() : core::scoring
• sort_by_length() : protocols::fldsgn::topology
• sort_criteria() : protocols::swa::rna
• sort_criteria2() : protocols::swa::rna
• sort_function() : protocols::frag_picker
• sort_numerically_ascending() : protocols::ddg
• Sort_pair_list() : protocols::swa::rna
• sort_pose_data_by_score() : protocols::swa::rna
• sort_PoseWithScore() : protocols::abinitio
• sort_residue_list() : protocols::swa::rna
• sort_scores() : protocols::frag_picker::scores
• sort_seq_num_list() : protocols::swa::rna
• sp_parse_taskdef() : protocols::elscripts
• SPECIAL_ROT() : core::chemical
• spherical() : protocols::fldsgn::potentials::sspot
• spline_coeffs() : core::scoring::electron_density
• split() : core::io::pdb , protocols::sparta
• split_by_ca_ca_dist() : protocols::loops
• split_by_resSeq() : protocols::loops
• split_up_remark_line() : protocols::toolbox::match_enzdes_util
• split_WhiteSpace() : protocols::sparta
• SQ() : core::scoring::electron_density
• sqr() : protocols::loophash , protocols::sic_dock , protocols::cartesian , core::scoring::methods , core::scoring , protocols::kinmatch , core::scoring::packing
• square() : protocols::rbsegment_relax , core::scoring::electron_density , core::scoring::electron_density_atomwise
• SRDL_TR() : core::pack::dunbrack
• ss_index() : protocols::frag_picker::quota
• ss_weights_RG() : core::scoring
• STANDARD_WTS() : core::scoring
• star_fold_tree() : protocols::protein_interface_design
• StarAbinitio_main() : protocols::star
• START_BLOCK() : protocols::jd2
• start_from_tracer() : protocols::ligand_docking
• steal_alignment() : core::sequence
• steal_constant_length_frag_set_from_pose() : core::fragment
• steal_frag_set_from_pose() : core::fragment
• steal_ligands() : protocols::comparative_modeling
• stochastic_pack() : core::pack
• store_CSA_in_pose() : core::scoring
• store_DC_in_pose() : core::scoring
• store_distance_snapshot() : protocols::noesy_assign
• store_distmap_with_namedatoms() : protocols::noesy_assign
• store_RDC_in_pose() : core::scoring
• store_RDC_ROHL_in_pose() : core::scoring
• store_RDC_segments_in_pose() : protocols::scoring
• str() : protocols::kinmatch
• strand_orientation_vector() : core::scoring::dna
• streams_from_cmd_line() : core::import_pose::pose_stream
• string_find() : protocols::rna
• string_join() : protocols::dna
• string_to_int() : protocols::swa::rna , core::scoring::rna::chemical_shift
• string_to_real() : protocols::swa::rna , core::scoring::rna::chemical_shift
• strip_whitespace() : core::chemical , core::scoring::packing , core::chemical::orbitals
• stub_from_points() : protocols::hotspot_hashing
• stub_id_to_named_stub_id() : core::pose , core::conformation
• stub_tgt_angle() : protocols::hotspot_hashing
• stub_to_points() : protocols::hotspot_hashing
• substitute_residue() : protocols::dna
• subtract_chi_angles() : core::pack::dunbrack
• suite_assign() : protocols::rna
• suite_rmsd() : protocols::swa::rna
• suite_square_deviation() : protocols::swa::rna
• SULFATION() : core::chemical
• sum_constraint_scoreterms() : protocols::enzdes::enzutil
• sum_IntraNOE() : protocols::noesy_assign
• sum_peak_volumes() : protocols::noesy_assign
• sum_total_residue_energy() : protocols::protein_interface_design
• superimpose() : protocols::toolbox
• superimpose_pose() : core::scoring
• superimpose_pose_on_subset_bb() : protocols::fibril
• superimpose_pose_on_subset_CA() : protocols::toolbox::pose_manipulation
• 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
• SymDock_main() : protocols::symmetric_docking
• 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::pose::symmetry , core::conformation::symmetry
• symmetry_info() : core::pose::symmetry