- s -

S : core::chemical::element
S_p_sp3 : core::chemical::orbitals
S_PEPTOID : core::chemical
sa : core::scoring
SACCHARIDE : core::enzymes
SAMPLE : core::pose::full_model_info
SAMPLE_APPLIER : protocols::stepwise::screener
SAMPLE_APPLIER_WITH_RESIDUE_LIST : protocols::stepwise::screener
sample_cis_peptide_bond : protocols::generalized_kinematic_closure::perturber
SAMPLED_ROSETTA : protocols::cluster::calibur
sasa_lr : core::scoring::methods
SasaMethodType_total : core::scoring::sasa
SasaRadii_total : core::scoring::sasa
saxs_cen_score : core::scoring
saxs_fa_score : core::scoring
saxs_score : core::scoring
Sb : core::chemical::element
Sc : core::chemical::element
SC_BB : core::scoring::motif
SC_BRANCH_POINT : core::chemical
SC_FRAGMENT : core::chemical
SC_ORBITALS : core::chemical
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
SCALE1 : core::io::pdb
SCALE2 : core::io::pdb
SCALE3 : core::io::pdb
SCORER : protocols::stepwise::screener
SCPA_cterm_isopeptide_lariat : protocols::cyclic_peptide_predict
SCPA_invalid_type : protocols::cyclic_peptide_predict
SCPA_n_to_c_amide_bond : protocols::cyclic_peptide_predict
SCPA_nterm_isopeptide_lariat : protocols::cyclic_peptide_predict
SCPA_number_of_types : protocols::cyclic_peptide_predict
SCPA_sidechain_isopeptide : protocols::cyclic_peptide_predict
SCPA_terminal_disulfide : protocols::cyclic_peptide_predict
SCREENING_FILE : protocols::jd2::JobInputterInputSource
Se : core::chemical::element
SEPTANOSE : core::chemical
seq_design_basic : protocols::antibody::design
seq_design_conservative : protocols::antibody::design
seq_design_none : protocols::antibody::design
seq_design_profile_sets : protocols::antibody::design
seq_design_profile_sets_combined : protocols::antibody::design
seq_design_profiles : protocols::antibody::design
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
SEQADV : core::io::pdb
seqdep_ref : core::scoring
SeqDesignStrategyEnum_total : protocols::antibody::design
SEQRES : core::io::pdb
SEQUENTIAL : core::conformation::symmetry
SERIALIZED_POSE_FILE : protocols::jd2::JobInputterInputSource
set_backbone_bin : protocols::generalized_kinematic_closure::perturber
set_bondangle : protocols::generalized_kinematic_closure::perturber
set_bondlength : protocols::generalized_kinematic_closure::perturber
set_dihedral : protocols::generalized_kinematic_closure::perturber
SFHEADER_SCORE_LINE : core::io::silent
SFHEADER_SCORE_TYPE_LINE : core::io::silent
SFHEADER_SEQUENCE_LINE : core::io::silent
Sg : core::chemical::element
SG_CONNECT : core::chemical
SHAPE_1M7 : core::pose::rna
SHEET : core::io::pdb
sheet : core::scoring
SHOVE_BB : core::chemical
SHOW_ALL_TRIALS : protocols::viewer::graphics_states_param
SHOW_BACKBONE : protocols::viewer::graphics_states_param
SHOW_BBSPHERES : protocols::viewer::graphics_states_param
SHOW_BEST : protocols::viewer::graphics_states_param
SHOW_CARTOON : protocols::viewer::graphics_states_param
SHOW_H : protocols::viewer::graphics_states_param
SHOW_LOW : protocols::viewer::graphics_states_param
SHOW_MC_TRIALS : protocols::viewer::graphics_states_param
SHOW_NO_H : protocols::viewer::graphics_states_param
SHOW_NOBB : protocols::viewer::graphics_states_param
SHOW_NOSC : protocols::viewer::graphics_states_param
SHOW_SCSPHERES : protocols::viewer::graphics_states_param
SHOW_STICK : protocols::viewer::graphics_states_param
SHOW_WIREFRAME : protocols::viewer::graphics_states_param
Si : core::chemical::element
SIALIC_ACID : core::chemical
side1 : protocols::analysis
side2 : protocols::analysis
SIDECHAIN : protocols::noesy_assign
SIDECHAIN_AMINE : core::chemical
SIDECHAIN_CONJUGATION : core::chemical
sidechain_neighbors : core::scoring
SIDECHAIN_THIOL : core::chemical
SIGMA : core::scoring::nmr
SIGMA_ATOM : core::chemical
SILENT_FILE : protocols::cluster::calibur , protocols::jd2::JobInputterInputSource
SIMPLE_POSE_SELECTION : protocols::stepwise::screener
SIMPLE_RMSD : protocols::stepwise::screener
simplesequencedata : core::io::silent
SINGLE_GLYCAN : protocols::viewer::graphics_states_param
SingleBond : core::chemical
SingleBondOrder : core::chemical
SITE : core::io::pdb
site_constraint : core::scoring
SIZED : protocols::toolbox
SIZED_ANY : protocols::toolbox
SIZED_COMB : protocols::toolbox
skip_rate : protocols::loops
Sm : core::chemical::element
SMALL_OVERLAP : core::scoring::motif
SMM_BASE_NAME : core::simple_metrics::metrics
SMM_END_OF_LIST : core::simple_metrics::metrics
SMM_FULL_NAME : core::simple_metrics::metrics
SMM_INVALID_MODE : core::simple_metrics::metrics
SMM_ONELETTER_CODE : core::simple_metrics::metrics
SMM_THREELETTER_CODE : core::simple_metrics::metrics
Sn : core::chemical::element
SnugDock : protocols::docking
SOLID_STATE_NMR : core::io::rcsb
SOLUTION_NMR : core::io::rcsb
SOLUTION_SCATTERING : core::io::rcsb
SOLUTION_SCATTERING_THEORETICAL_MODEL : core::io::rcsb
SOLVENT : core::chemical
SORT_BY_CIS_PEPTIDE_BONDS : protocols::cyclic_peptide_predict
SORT_BY_ENERGIES : protocols::cyclic_peptide_predict
SORT_BY_HBONDS : protocols::cyclic_peptide_predict
SORT_BY_RMSD : protocols::cyclic_peptide_predict
SOURCE : core::io::pdb
SOUTH : core::chemical::rna
SP2_HYBRID : core::chemical
SP3_HYBRID : core::chemical
span_ins : core::scoring
SPECIAL_ROT : core::chemical
special_rot : core::scoring
SPECIAL_SEGMENTS_OBSERVER : core::pose::datacache
SPHERE_MODE_BB : protocols::viewer
SPHERE_MODE_LIGAND : protocols::viewer
SPHERE_MODE_SC : protocols::viewer
spin_down : protocols::pack_daemon
SPINLABEL : core::chemical
SPLIT : core::io::pdb
split_unfolded_two_body : core::scoring
SPRSDE : core::io::pdb
square_planar_metal : protocols::cyclic_peptide
square_pyramidal_metal : protocols::cyclic_peptide
Sr : core::chemical::element
SRI : core::chemical
SRLZ_file : core::import_pose
ss_contact_worst : core::scoring
ss_pair : core::scoring
SSBOND : core::io::pdb
stack_elec : core::scoring
stack_elec_base_base : core::scoring
stack_elec_base_bb : core::scoring
STACK_ELEC_NBLIST : core::scoring::EnergiesCacheableDataType
STAGE_1 : protocols::abinitio
STAGE_2 : protocols::abinitio
STAGE_3 : protocols::abinitio
STAGE_3a : protocols::abinitio
STAGE_3b : protocols::abinitio
STAGE_4 : protocols::abinitio
start : protocols::loops
start_cdr_loop : protocols::antibody
stop : protocols::loops
strand : protocols::loops::loop_closure::ccd
STRICT_WC_STACKED_PAIR : core::scoring::rna
string_string_pair_msg : protocols::jd3::deallocation
STRIP_VIRTUAL_SIDE_CHAIN : core::pack::palette
STRIPEHASH : core::conformation
STRUCTUREDATA_OBSERVER : core::pose::datacache
STUB_APPLIER : protocols::stepwise::screener
STUB_DISTANCE : protocols::stepwise::screener
SUBMOTIF : protocols::stepwise::monte_carlo::mover
SUBTRACT : protocols::calc_taskop_filters
Success : protocols::loops::loop_mover
success_message : protocols::pack_daemon
suck : core::scoring
suga : core::scoring::rna::chemical_shift
SUGAR : core::chemical::rna
sugar_bb : core::scoring
SUGAR_INSTANTIATOR : protocols::stepwise::screener
suiteness_bonus : core::scoring
SULFATED_SUGAR : core::chemical
SULFATION : core::chemical
SULFOAMINO_SUGAR : core::chemical
SULPH : protocols::match
SUM : core::scoring::nmr
sum : core::simple_metrics::metrics
SUM : protocols::calc_taskop_filters
summary_type_total : core::simple_metrics::metrics
SURFACE : core::chemical
surface : core::scoring
SWITCH_EDGE : protocols::legacy_sewing
SWITCH_TO_FULLATOM : protocols::abinitio
sym_bonus_lr : core::scoring::methods
sym_lig : core::scoring
symE_bonus : core::scoring
SYN : core::chemical::rna , core::fragment::rna