- s -

• s : app::pyrosetta_toolkit::modules::SQLPDB , app::pyrosetta_toolkit::window_modules::interactive_terminal::interactive_terminal
• SA : amino_acids
• scaffold_loop : basic::options::OptionKeys::AnchoredPDBCreator
• scaffold_pdb : basic::options::OptionKeys::AnchoredPDBCreator
• score : test::G100_Functions_Input , test::G205_Module_RegionalScoring , test::Workshop4test , test::Workshop8test
• score2 : test::Workshop4test
• score3 : test::Workshop4test
• score_analysis : test::G204_Module_ScoreAnalysis
• score_high : app::surface_docking::surface_docking
• score_pack : app::surface_docking::surface_docking
• score_types : test::T200_Scoring
• ScoredPDBList : app::pyrosetta_toolkit::modules::ScoreAnalysis
• scorefxn : PyMOL_demo , test::G101_Functions_Output , test::G205_Module_RegionalScoring , test::T010_LoadPDB , test::T150_PyMOL_Integration , test::T200_Scoring , test::T250_Constraints , test::T400_Refinement , test::T500_Packing , test::T660_LoopBuilding , test::T800_ClassicRelax , test::T880_Other , test::Workshop3test , test::Workshop5test , test::Workshop6test , test::Workshop7test
• scorefxn2 : test::Workshop3test
• scorefxn_high : demo::D060_Folding , docking , loops , loops_kic , test::T650_LoopsKIC , test::Workshop7test
• scorefxn_high_min : docking
• scorefxn_low : demo::D060_Folding , docking , loops , loops_kic , test::T650_LoopsKIC , test::Workshop7test
• scores : demo::D060_Folding
• ScoreTypesRegistry : src
• script_root_dir : BuildPackagedBindings
• se_cutoff : sequence_recovery
• seq : PyMOL_demo , test::T850_SubClassing
• seq_mover : test::Workshop5test
• seq_recov_filename : sequence_recovery
• sequence : demo::D060_Folding
• sequence_match_position : usec
• sequence_match_sequence : usec
• sf : app::delta_score_per_mutation , test::Workshop9test
• sf_new : test::T850_SubClassing , test::T860_SubClassing_EnergyMethods , test::T870_SubClassing_EnergyMethods2
• sfxn : test::T220_AtomAtomPairEnergies
• shear_mover : test::Workshop5test
• shearmover : test::T400_Refinement
• shearmoves : demo::D070_Refinement
• shit_stat_altpos : clean_pdb_keep_ligand
• shit_stat_insres : clean_pdb_keep_ligand
• shit_stat_misdns : clean_pdb_keep_ligand
• shit_stat_modres : clean_pdb_keep_ligand
• short_frag_filename : demo::D060_Folding
• short_frag_length : demo::D060_Folding
• short_inserts : demo::D060_Folding
• short_to_long : amino_acids
• show_time_on_cerr : basic
• SHRINK_FACTOR : basic
• silent : basic::options
• size : amino_acids
• skip_sitegraft_repack : local
• skipl : numeric::kinematic_closure
• slid : test::Workshop7test
• slide : test::Workshop7test
• slide_criteria_type : make_symmdef_file_denovo
• slide_criteria_val : make_symmdef_file_denovo
• slide_into_contact : docking , test::T600_Docking
• slide_order : make_symmdef_file_denovo
• slide_type : make_symmdef_file_denovo
• small_mover : test::Workshop5test
• smallmover : test::T400_Refinement
• smallmoves : demo::D070_Refinement
• smartfilter : calccontacts
• sol : extract_scores_and_constraints
• sol_cycles : app::surface_docking::surface_docking
• sol_inner_cycles : app::surface_docking::surface_docking
• sol_outer_cycles : app::surface_docking::surface_docking
• sol_pdb : extract_scores_and_constraints
• sol_pose : app::surface_docking::surface_docking
• some_storage : test::T860_SubClassing_EnergyMethods
• spin : docking , test::T600_Docking
• sql : test::G203_Module_SQLPDB
• square : test::Workshop9test
• standard : basic::options
• star : ObjexxFCL
• start : test::Workshop5test
• start_clock : basic
• start_pose : app::surface_docking::surface_docking
• starting_p : docking , loops , loops_kic , test::T600_Docking , test::T650_LoopsKIC
• starting_p_centroid : docking , loops , loops_kic , test::T650_LoopsKIC
• starting_pose : test::Workshop7test
• state : extract_scores_and_constraints
• std_scorefxn : app::surface_docking::surface_docking
• sub_matrix_filename : sequence_recovery
• subsystem_size : make_symmdef_file_denovo
• subunits : make_symmdef_file_denovo
• success : loops_kic , test::T650_LoopsKIC
• superimpose_to_native : score_app
• surf_coor : PDBInfo
• surface : PDBInfo
• surface_atom_cutoff : local
• surface_residue_cutoff : local
• sw_high : test::Workshop8test
• sw_low : test::Workshop8test
• switch : test::Workshop4test
• switch2 : test::Workshop4test
• switch_high : app::surface_docking::surface_docking
• switch_low : app::surface_docking::surface_docking , test::Workshop7test
• symm_type_name : make_symmdef_file_denovo