- s -

sa_faraggi_max() : protocols::frag_picker
safe_secstruct() : protocols::jumping
safe_set_conf() : protocols::environment
safe_set_extended_torsions_and_idealize_loops() : protocols::loops
sample_all_rotations_at_jump() : protocols::toolbox::sample_around
saved_reference_pose() : protocols::rosetta_scripts
score_cst() : protocols::abinitio::abscript
SCORE_FRAG_STORE() : protocols::loops::loop_closure::ccd
score_sort_criterion() : protocols::stepwise::modeler::rna
score_type_filter_tracer() : protocols::simple_filters
scorefxn_update_from_options() : protocols::enzdes::enzutil
section() : protocols::sparta
see_edge_or_core_or_loop_or_short_edge() : protocols::features::strand_assembly
see_whether_sheet_is_antiparallel() : protocols::features::strand_assembly
see_whether_sheets_can_be_combined() : protocols::features::strand_assembly
see_whether_this_sw_has_SS_bond() : protocols::features::strand_assembly
select_best_poses() : protocols::ligand_docking
select_epitope_residues() : protocols::antibody
select_interface_residues() : protocols::interface
select_loop_frags() : protocols::loops
select_loop_residues() : protocols::loops
select_RBsegments() : protocols::rbsegment_relax
seq_num_sort_criterion() : protocols::stepwise::modeler::rna
seq_pdb_str() : protocols::dna
seq_to_str() : protocols::dna
sequencealign() : protocols::frag_picker::scores
SerializableState_get() : protocols::moves
SerializableState_set() : protocols::moves
serialize_ids() : protocols::features
serialize_residue_xyz_coords() : protocols::features
set_base_segment_chainbreak_constraints() : protocols::dna
set_bg_color() : protocols::viewer
set_CCD_torsions_to_zero() : protocols::stepwise::modeler::rna
set_constraints() : protocols::rbsegment_relax
set_difference() : protocols::stepwise::modeler::rna
set_extended_torsions() : protocols::loops
set_extended_torsions_and_idealize_loops() : protocols::loops
set_jumps() : protocols::ligand_docking
set_local_movemap() : protocols::vip
set_loop_cutpoint_in_pose_fold_tree() : protocols::loops
set_loop_pose() : protocols::generalized_kinematic_closure
set_move_map_for_centroid_loop() : protocols::loops
set_native_in_mover() : protocols::jd2
set_nucleotide_to_A_form() : protocols::stepwise::legacy::modeler::rna
set_output_res_num() : protocols::farna
set_pose_and_scorefxn_for_edens_scoring() : protocols::electron_density
set_protocol_and_batch_id() : protocols::features
set_rb_constraints() : protocols::rbsegment_relax
set_repulsive_bb_cores() : protocols::ligand_docking
set_rna_secstruct() : protocols::farna
set_scorefxn_from_tag() : protocols::loop_modeling::utilities
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_task_factory_from_tag() : protocols::loop_modeling::utilities
set_to_origin() : protocols::toolbox::rigid_body
set_union() : protocols::stepwise::modeler::rna
set_xyz_coord() : protocols::fibril
setup_A_LH_foldtree() : protocols::antibody
setup_atom_pair_constraints() : protocols::medal
setup_base_pair_constraints() : protocols::farna
setup_bulge_jump_point() : protocols::stepwise::legacy::modeler::rna
setup_centroid_constraints() : protocols::hybridization
setup_chain_break_jump_point() : protocols::stepwise::legacy::modeler::rna
setup_chain_break_variants() : protocols::stepwise::modeler::rna
setup_coarse_chainbreak_constraints() : protocols::farna
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_copy_DOF_input() : protocols::stepwise::legacy::modeler::rna
setup_disconnected() : protocols::rbsegment_relax
setup_dme_point_graph() : protocols::simple_moves
setup_faraggi_map() : protocols::frag_picker
setup_fold_trees() : protocols::stepwise::setup
setup_foldtree() : protocols::docking
setup_for_dna() : protocols::relax
setup_fullatom_constraints() : protocols::hybridization
setup_interface_atompair_constraints() : protocols::hybridization
setup_interface_coordinate_constraints() : protocols::hybridization
setup_jumps() : protocols::stepwise::setup
setup_LH_A_foldtree() : protocols::antibody
setup_membrane_topology() : protocols::relax
setup_name2type() : protocols::frag_picker
setup_packer() : protocols::mpi_refinement
setup_packer_task() : protocols::antibody
setup_pose_from_rbsegs() : protocols::rbsegment_relax
setup_pose_input_stream() : protocols::stepwise::modeler::protein
setup_pose_rbsegs_keep_loops() : protocols::rbsegment_relax
setup_pose_setup_class() : protocols::stepwise::legacy::modeler::rna
setup_pose_with_moving_residue_alternative_list() : protocols::stepwise::modeler::rna::rigid_body
setup_protein_backbone_atom_id_map() : protocols::stepwise::modeler::protein
setup_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
setup_sampler() : protocols::stepwise::sampler::rna
setup_score() : protocols::abinitio::abscript , protocols::star
setup_simple_fold_tree() : protocols::stepwise::legacy::modeler::rna
setup_simple_full_length_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
setup_single_loop_double_arm_remodeling_foldtree() : protocols::grafting
setup_single_loop_single_arm_remodeling_foldtree() : protocols::grafting
setup_star_topology() : protocols::rbsegment_relax
setup_suite_atom_id_map() : protocols::stepwise::modeler::rna
setup_three_prime_phosphate_based_on_next_residue() : protocols::stepwise::modeler::rna::phosphate
setup_type2name() : protocols::frag_picker
setup_user_coordinate_constraints() : protocols::hybridization
setup_user_defined_jumps() : protocols::stepwise::setup
setup_vall_cheating_fragments() : protocols::frags
setup_vall_fragments() : protocols::frags
setup_vary_polar_hydrogen_geometry() : protocols::simple_moves
setup_vary_rna_bond_geometry() : protocols::simple_moves
setup_working_parameters_explicit() : protocols::stepwise::modeler::working_parameters
setup_working_parameters_for_swa() : protocols::stepwise::modeler::working_parameters
shift_jumps() : protocols::forge::methods
ShortToRealAngle() : protocols::loophash
show_scorefxn_weight_lines() : protocols::stepwise::modeler::rna
sidechain_rmsd_filter_tracer() : protocols::simple_filters
sigmoid() : protocols::noesy_assign
simple_fold_tree() : protocols::antibody , protocols::antibody_legacy , protocols::star
simple_one_loop_fold_tree() : protocols::antibody , protocols::antibody_legacy
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
sleep() : protocols::stepwise::modeler::rna
slice() : protocols::stepwise::modeler
slice_out_pose() : protocols::stepwise::modeler
slide_into_contact_and_score() : protocols::sic_dock
slide_into_contact_and_score_DEPRICATED() : protocols::sic_dock
slide_together_tracer() : protocols::ligand_docking
smallmer_from_largemer() : protocols::forge::methods
sort_by_length() : protocols::fldsgn::topology
sort_copy_dofs() : protocols::stepwise::modeler::rna
sort_function() : protocols::frag_picker
sort_numerically_ascending() : protocols::ddg
sort_pair_list() : protocols::stepwise::legacy::modeler::rna
sort_PoseWithScore() : protocols::abinitio
sort_scores() : protocols::frag_picker::scores
sort_seq_num_list() : protocols::stepwise::modeler::rna
sp_parse_taskdef() : protocols::elscripts
spherical() : protocols::fldsgn::potentials::sspot
split() : protocols::sparta
split_by_ca_ca_dist() : protocols::loops
split_by_resSeq() : protocols::loops
split_pose() : protocols::stepwise::modeler
split_topology_by_jump() : protocols::membrane::geometry
split_up_remark_line() : protocols::toolbox::match_enzdes_util
split_WhiteSpace() : protocols::sparta
sqr() : protocols::cartesian , protocols::kinmatch , protocols::loophash , protocols::sic_dock
square() : protocols::rbsegment_relax
ss_index() : protocols::frag_picker::quota
ss_length_check() : protocols::frags
star_fold_tree() : protocols::protein_interface_design
StarAbinitio_main() : protocols::star
START_BLOCK() : protocols::jd2
start_from_tracer() : protocols::ligand_docking
steal_ligands() : protocols::comparative_modeling
store_distance_snapshot() : protocols::noesy_assign
store_distmap_with_namedatoms() : protocols::noesy_assign
store_RDC_segments_in_pose() : protocols::scoring
str() : protocols::kinmatch
string_join() : protocols::dna
string_to_int() : protocols::stepwise::modeler::rna
string_to_real() : protocols::stepwise::modeler::rna
struct_ids_from_tag() : protocols::features
stub_from_points() : protocols::hotspot_hashing
stub_tgt_angle() : protocols::hotspot_hashing
stub_to_points() : protocols::hotspot_hashing
substitute_residue() : protocols::dna
suite_rmsd() : protocols::stepwise::modeler::rna
suite_square_deviation() : protocols::stepwise::modeler::rna
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_overhangs_heavy() : protocols::grafting
superimpose_pose_legacy() : protocols::stepwise::modeler::align
superimpose_pose_on_subset_bb() : protocols::fibril
superimpose_pose_on_subset_CA() : protocols::toolbox::pose_manipulation
superimpose_with_stepwise_aligner() : protocols::stepwise::modeler::align
superposition_transform() : protocols::seeded_abinitio , protocols::toolbox
switch_focus_among_poses_randomly() : protocols::stepwise::modeler
switch_focus_to_other_pose() : protocols::stepwise::modeler
SymDock_main() : protocols::symmetric_docking
symmetrize_spans() : protocols::membrane::symmetry
symmetrizeBfactors() : protocols::electron_density