Here is a list of all file members with links to the files they belong to:

- s -

• S2 : T17.anonymous.hpp
• S_ISDIR : file_sys_util.cc
• SAFELY_PASS_MUTEX : threadsafe_creation.hh
• SAFELY_PASS_THREADSAFETY_BOOL : threadsafe_creation.hh
• same_coordinates() : sweep_respair_energies.cc
• same_secondary_structure() : disulfides.hh
• sample_near_current_torsion() : turner_test_double_helix.cc
• sample_near_nucleoside_torsion() : turner_test_one_chain.cc
• sample_near_suite_torsion() : turner_test_one_chain.cc
• sample_new_base_in_two_base_pair_pose() : turner_rules_test.cc
• sample_rama_test() : stepwise_test.cc
• sample_rna_dofs_new() : capri15.cc
• sample_state_to_state() : turner_rules_test.cc
• sample_torsions() : test_carbohydrate_scoring.cc
• sample_trp_test() : stepwise_test.cc
• sample_trp_tyr_test() : stepwise_test.cc
• SampleTiltProtocolCOP : sample_tilt_protocol.cc
• SampleTiltProtocolOP : sample_tilt_protocol.cc
• SAN1() : sf4_hash.cc
• SAN2() : sf4_hash.cc
• SAN3() : sf4_hash.cc
• sasa_bunsats() : sasa_buns.cc
• sasa_cutoff : BuriedUnsatPolarsFinder2.cc
• sasa_separation() : sasa_buns.cc
• sasa_test() : test1.cc , rna_test.cc
• SASAfilter : UBQ_UBQ_E2.cc
• SasaOP : sasa.cc
• sat_allow : exposed_strand_finder.cc
• save_cluster_tree_lite() : test_cluster.cc
• save_contact_info() : get_info.cc
• save_feature() : rna_features.cc
• save_per_residue_scores() : score_aln2.cc , score_aln.cc
• save_ss_info() : get_info.cc
• save_torsion_M_v() : turner_rules_test.cc
• save_torsions() : turner_rules_test.cc
• saxs_energy() : call_saxs_score.cc
• SC : gen_env_dep_orient_draw.m
• sc_rmsd_AtomIDs() : rotamer_repack.cc
• scaffold_pdb : zinc1_homodimer_setup.cc
• scaffold_protein : HbondZinc.cc , HbondZinc_allpolar.cc , HbondZinc_ser.cc , HbondZincBackbone.cc , HbondZincHHHO.cc
• scan_energy() : test_mm.cc
• scan_Evalue() : rama_energy.cc
• scan_hbond_jumps() : hbscan.cc
• scan_neutral() : test_mm.cc
• scan_rotamer() : test_mm.cc
• schar : Svm.cc
• scheme_score() : scheme_v0_score.cc
• scmove_residue() : rotamer_repack.cc
• score() : gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , gen_env_dep_orient_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , cal_env.m , gen_env_dep_orient.m , draw_gen_env_dep_pair_decompose.m
• score0 : draw_gen_env_dep_orient_decompose.m
• score12_plot_test() : stepwise_test.cc
• score2bin() : turner_test_double_helix.cc , turner_test_one_chain.cc
• Score_ : performance_benchmark.cc
• score_alignment() : anneal_align.cc
• Score_analytic_etable_fa_atr_ : ScoreAnalyticEtable.bench.hh
• Score_analytic_etable_fa_intra_atr_ : ScoreAnalyticEtable.bench.hh
• Score_analytic_etable_fa_intra_rep_ : ScoreAnalyticEtable.bench.hh
• Score_analytic_etable_fa_intra_sol_ : ScoreAnalyticEtable.bench.hh
• Score_analytic_etable_fa_rep_ : ScoreAnalyticEtable.bench.hh
• Score_analytic_etable_fa_sol_ : ScoreAnalyticEtable.bench.hh
• score_and_minimize() : rna_assemble_test.cc
• Score_cart_bonded_ : ScoreEach.bench.hh
• Score_cbeta_ : ScoreEach.bench.hh
• Score_cbeta_smooth_ : ScoreEach.bench.hh
• Score_cen_env_smooth_ : ScoreEach.bench.hh
• Score_cen_pair_smooth_ : ScoreEach.bench.hh
• Score_cenpack_ : ScoreEach.bench.hh
• Score_cenpack_smooth_ : ScoreEach.bench.hh
• Score_ch_bond_ : ScoreEach.bench.hh
• Score_chainbreak_ : ScoreEach.bench.hh
• score_clustered_frags() : r_local_rdc.cc
• Score_co_ : ScoreEach.bench.hh
• Score_distance_chainbreak_ : ScoreEach.bench.hh
• Score_dslf_ca_dih_ : ScoreEach.bench.hh
• Score_dslf_cbs_ds_ : ScoreEach.bench.hh
• Score_dslf_cs_ang_ : ScoreEach.bench.hh
• Score_dslf_fa13_ : ScoreEach.bench.hh
• Score_dslf_ss_dih_ : ScoreEach.bench.hh
• Score_dslf_ss_dst_ : ScoreEach.bench.hh
• Score_e_pH_ : ScoreEach.bench.hh
• Score_env_ : ScoreEach.bench.hh
• Score_envsmooth_ : ScoreEach.bench.hh
• Score_fa_atr_ : ScoreEach.bench.hh
• Score_fa_cust_pair_dist_ : ScoreEach.bench.hh
• Score_fa_dun_ : ScoreEach.bench.hh
• Score_fa_dun_dev_ : ScoreEach.bench.hh
• Score_fa_dun_rot_ : ScoreEach.bench.hh
• Score_fa_dun_semi_ : ScoreEach.bench.hh
• Score_fa_elec_ : ScoreEach.bench.hh
• Score_fa_intra_atr_ : ScoreEach.bench.hh
• Score_fa_intra_rep_ : ScoreEach.bench.hh
• Score_fa_intra_sol_ : ScoreEach.bench.hh
• Score_fa_pair_ : ScoreEach.bench.hh
• Score_fa_pair_aro_aro_ : ScoreEach.bench.hh
• Score_fa_pair_aro_pol_ : ScoreEach.bench.hh
• Score_fa_pair_pol_pol_ : ScoreEach.bench.hh
• Score_fa_rep_ : ScoreEach.bench.hh
• Score_fa_sol_ : ScoreEach.bench.hh
• SCORE_FILE_DATA : cloud_demo.cc
• score_folded_residues() : rss_energy_calculator.cc
• Score_gauss_ : ScoreEach.bench.hh
• Score_gb_elec_ : ScoreEach.bench.hh
• Score_h2o_hbond_ : ScoreEach.bench.hh
• Score_hbond_bb_sc_ : ScoreEach.bench.hh
• Score_hbond_lr_bb_ : ScoreEach.bench.hh
• Score_hbond_lr_bb_sc_ : ScoreEach.bench.hh
• Score_hbond_sc_ : ScoreEach.bench.hh
• Score_hbond_sr_bb_ : ScoreEach.bench.hh
• Score_hbond_sr_bb_sc_ : ScoreEach.bench.hh
• Score_hs_pair_ : ScoreEach.bench.hh
• Score_linear_chainbreak_ : ScoreEach.bench.hh
• Score_lk_costheta_ : ScoreEach.bench.hh
• Score_lk_nonpolar_ : ScoreEach.bench.hh
• Score_lk_polar_ : ScoreEach.bench.hh
• score_loop() : unalignedEvaluate.cc
• score_loops() : unalignedEvaluate.cc
• Score_mm_bend_ : ScoreEach.bench.hh
• Score_mm_lj_intra_atr_ : ScoreEach.bench.hh
• Score_mm_lj_intra_rep_ : ScoreEach.bench.hh
• Score_mm_stretch_ : ScoreEach.bench.hh
• Score_mm_twist_ : ScoreEach.bench.hh
• Score_neigh_vect_ : ScoreEach.bench.hh
• Score_occ_sol_exact_ : ScoreEach.bench.hh
• Score_occ_sol_fitted_ : ScoreEach.bench.hh
• Score_occ_sol_fitted_onebody_ : ScoreEach.bench.hh
• Score_omega_ : ScoreEach.bench.hh
• Score_overlap_chainbreak_ : ScoreEach.bench.hh
• Score_p_aa_ : ScoreEach.bench.hh
• Score_p_aa_pp_ : ScoreEach.bench.hh
• Score_pack_stat_ : ScoreEach.bench.hh
• Score_pair_ : ScoreEach.bench.hh
• score_pdb() : score_pdbs.cc
• Score_pro_close_ : ScoreEach.bench.hh
• Score_rama2b_ : ScoreEach.bench.hh
• Score_rama_ : ScoreEach.bench.hh
• score_ref : cal_env.m
• Score_ref_ : ScoreEach.bench.hh
• Score_ref_nc_ : ScoreEach.bench.hh
• score_residue_pair() : sweep_respair_energies.cc
• Score_rg_ : ScoreEach.bench.hh
• score_rnp() : move_jump.cc , score_rnp.cc
• Score_rsigma_ : ScoreEach.bench.hh
• Score_sa_ : ScoreEach.bench.hh
• Score_sheet_ : ScoreEach.bench.hh
• Score_ss_pair_ : ScoreEach.bench.hh
• score_test() : simple_dna_regression_test.cc
• Score_unfolded_ : ScoreEach.bench.hh
• Score_vdw_ : ScoreEach.bench.hh
• score_w() : gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair_decompose.m
• score_w0 : draw_gen_env_dep_orient_decompose.m
• score_w2 : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• score_w3() : gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
• Score_yhh_planarity_ : ScoreEach.bench.hh
• scoreall() : design_cycpeptide_MPI.cc
• scorefilter : UBQ_UBQ_E2.cc
• ScoreFnType : Minimizer.bench.hh
• ScoreFunctionFingerprintMoverOP : version_scorefunction.cc , version_mpscorefxn.cc
• ScoreMoverCOP : r_score.cc
• ScoreMoverOP : r_score.cc
• scoring_test() : moves_test.cc
• screen_phosphates() : screen_phosphates.cc
• sd() : james_util.hh
• SD_M : gpu_homog_atom_coords.h , unique_atoms.h
• search_other_atoms() : polar_pdbstats.cc
• search_translations() : turner_rules_test_WORKS.cc , stepwise_helix_test.cc
• second_preminimized_namer() : erraser2.cc
• secstruct() : mp_parameters.cc
• seg_filters : MakeSegmentFile.cc
• seg_metrics : MakeSegmentFile.cc
• seg_script_opt : MakeSegmentFile.cc
• segment_path : MakeSegmentFile.cc
• select_loop_residues() : loop_minimize.cc , sidechain_min.cc
• select_residues_for_evaluation() : params_opt.cc
• select_string() : smhybrid.cc
• send_string_to_node() : pep_opt_parallel.cc
• separation() : buns.cc
• sequence_tolerance_main() : sequence_tolerance.cc
• sequence_tolerance_mf_main() : sequence_tolerance_mf.cc
• SequenceCoordsOP : mammoth_hack.cc
• sequences_from_cmd_line() : thread_fast.cc , score_aln.cc
• SER : gen_env_dep_orient.m , gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , cal_env.m , draw_matrix.m , load_pair_env_table.m
• SerializablePoseCOP : test_serialize.cc
• SerializablePoseOP : test_serialize.cc
• set() : gen_env_dep_pair_decompose.m , gen_vdw_radius_soft.m , gen_env_dep_orient_decompose.m , cal_env.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m
• set_achiral_spacegroups() : cryst_gen.cc
• set_all_loop_dihedrals_to_180() : graphics_demo.cc , long_loop.cc
• set_all_spacegroups() : cryst_gen.cc
• set_basic_dock_options() : dgdp.cc
• set_cb_pairs() : symdock_enum.cc , symdock_enum_3_1.cc , isct_test.cc
• set_chain_end_fold_tree() : phil.hh
• set_chival() : test_mm.cc
• set_disulf() : gen_trimer_disulf.cc
• set_dof() : plot_scoreterm.cc
• set_file_output() : helical_bundle_predict.cc
• set_fullatom_flag_test() : test1.cc
• set_helix_torsions() : OLD_TRIAL_protein_helix_assemble.cc
• set_ideal_geometry() : rna_test.cc
• set_inverso_conformation_main_chain() : make_retroinverso.cc
• set_inverso_conformation_side_chain() : make_retroinverso.cc
• set_loop_conformation() : design_truecycpeptide_fromstub.cc
• set_options() : sim_cryo.cc
• set_pattern() : count_cycpep_sequences.cc
• set_pep_cst() : pepspec_anchor_dock.cc , pep_prep.cc
• set_pep_csts() : pepspec.cc
• set_pose_conformation() : fit_helixparams.cc
• set_pose_occ_and_bfac() : byres_data.cc , rotamer_repack.cc
• set_sc_repacking() : design_truecycpeptide_fromstub.cc
• set_secstruct_from_psipred_ss2() : loop_minimize.cc , sidechain_min.cc
• set_stub_transform_test() : test1.cc
• set_temp_based_on_ens_diversity() : ensemble_generator.cc , ensemble_generator_score12_sidechain.cc
• set_throw_on_next_assertion_failure() : backtrace.cc , backtrace.hh
• set_to_state() : design_cycpeptide_MPI.cc
• set_torsion_and_align() : align_substructure.cc
• set_up_covalent_connections() : design_cycpeptide_MPI.cc
• set_up_engine() : test_cluster.cc
• set_up_pose() : design_truecycpeptide_fromstub.cc
• set_up_termini() : design_cycpeptide_MPI.cc
• setargs() : CL_args.hh
• SetSize : HbondZinc.cc , HbondZinc_allpolar.cc , HbondZinc_ser.cc , HbondZincBackbone.cc , HbondZincHHHO.cc
• setup_activity_table() : roc_optimizer.cc
• setup_align_atom_map() : drrafter_error_estimation.cc
• setup_alignment_map() : rna_thread.cc , easy_target_test.cc
• setup_atom_id_map() : entropy_test.cc
• setup_atom_number() : simple_dna_regression_test.cc , test1.cc , dna_spec_test.cc
• setup_backbone_atoms() : stepwise_helix_test.cc
• setup_bonded_protein_rna_pose() : capri15.cc
• setup_ca_constraints() : ensemble_generator.cc , ensemble_generator_score12_sidechain.cc , minimize_with_cst.cc , ensemble_generator_score12_sidechain_ver2.cc , minimize_with_cst.cc
• setup_CA_constraints() : easy_target_test.cc
• setup_capri_data() : capri15_scoring.hh
• setup_constraints() : easy_target_test.cc
• setup_coord_csts() : setup_coord_csts.cc
• setup_copy_DOF_input() : swa_rna_analytical_closure.cc
• setup_crazy_fold_tree() : rna_test.cc
• setup_design_res() : erraser_monte_carlo.cc
• setup_dinucleotide_pose() : turner_rules_test.cc
• setup_docking_ft_with_randomization() : test_carbohydrate_docking.cc
• setup_domain_list() : rna_test.cc
• setup_double_helix_pose() : turner_test_double_helix.cc
• setup_favor_native() : crossmatch.cc , crossmatch_d2.cc
• setup_for_folding() : SymmAbrelax.cc
• setup_fragment_mover() : flexibleLoopDesign.cc
• setup_frags_from_vall() : loop_model.hh
• setup_grids() : roc_optimizer.cc
• setup_heavy_atoms() : turner_rules_test_WORKS.cc
• setup_hotspot_filter() : r_build_hotspot_loops.cc
• setup_hydrophobic_cbetas() : stepwise_helix_test.cc
• setup_LHsampler() : test_LH.cc
• setup_loops_fragment_libraries_with_ss() : loop_model.hh
• setup_loops_from_mapping() : loop_model.hh
• setup_lowres_protocol() : roc_optimizer.cc
• setup_mask() : easy_target_test.cc , rna_thread.cc
• setup_movers() : ensemble_generator.cc , ensemble_generator_score12_sidechain_ver2.cc , ensemble_generator_score12_sidechain.cc
• setup_nnmake_style_quota() : diverse_fragments.cc
• setup_one_chain_pose() : turner_test_one_chain.cc
• setup_pdb_line() : johnk_parametrize_geometric_solvation.cc
• setup_pdbnames_next_round() : optE_test.cc
• setup_per_residue_rmsd_atom_map() : drrafter_error_estimation.cc
• setup_pert_foldtree() : a3b_hbs_creator.cc
• setup_pose() : turner_two_chain.cc , stepwise_centroid_test.cc
• setup_pose_input_stream() : stepwise_template_test.cc
• setup_pose_setup_class() : swa_rna_analytical_closure.cc
• setup_pose_with_loop() : loop_closure_test.cc
• setup_repeat_pose() : repeat_demo.cc
• setup_repeat_symminfo() : repeat_demo.cc
• setup_rhiju_fold_tree() : easy_target_test.cc
• setup_rmsd_atom_map() : drrafter_error_estimation.cc
• setup_rna_base_pair_constraints() : rna_test.cc
• setup_rna_chainbreak_constraints() : rna_test.cc
• setup_rna_minimizer() : cs_rosetta_rna.cc
• setup_rna_working_parameters() : swa_rna_analytical_closure.cc
• setup_roc_curve() : roc_optimizer.cc
• setup_sam_constraints() : capri15.cc
• setup_sam_constraints_for_t033() : capri15.cc
• setup_score_function() : rnp_ddg.cc
• setup_score_mover() : roc_optimizer.cc
• setup_secstruct() : easy_target_test.cc
• setup_secstruct_dssp() : domain_assemble.cc , david_find_surface_residues.cc , easy_target_test.cc
• setup_segment_insert() : ufv.cc , remodel.cc
• setup_slide_mover() : roc_optimizer.cc
• setup_start_coords() : roc_optimizer.cc
• setup_symmetric_dimer() : symtest.cc
• setup_t469_zn_tether() : easy_target_test.cc
• setup_tf() : mp_seqrecov.cc , sequence_recovery.cc , sequencerecovery.cc , bur_nodon_tyr.cc
• setup_transform_mover() : roc_optimizer.cc
• setup_two_base_pair_pose() : turner_rules_test.cc
• setup_two_base_pair_pose_with_chainbreak() : turner_rules_test.cc
• setup_VDW_rep_atom_map_list() : parin_test.cc
• setup_zf_pose() : zf_relax.cc
• sf2multivec() : params_opt.cc
• sfd : genP23.cc , heterodock.cc , hczndimer.cc , gentetra_from_trimer.cc , gentetra_bpy_from_znhis.cc , gentetra.cc , gensym_3bpy_from_dimer.cc , pentcb_design.cc , genmatch_3bpy.cc , hubabinitio.cc , hubdenovo.cc , hubfragdesign.cc , pentcb.cc , pentcb_test.cc , rescore_i213.cc , sicdock.cc , test_ikrs.cc , test_ikrs2.cc , dock_asym.cc , genI213_gensym.cc , cxdesign.cc , cxdock.cc , crossmatch.cc , crossmatch_3e.cc , crossmatch_d2.cc , CXdock.cc , cxdock_sheet.cc , CXdock_TMP.cc , d3_bpy_linker.cc , dxdock.cc , dxdock_movie.cc , gen3bpy.cc , gen_xtal_dimer_from_trimer.cc , genI213.cc , genI213_2comp.cc , genI213_2dsf.cc , genI213_nocontacts.cc , design_DL.cc
• SFOP : coiled_coil.cc , coiled_coil_zn.cc
• SFT_dfpmin : Minimizer.bench.hh
• SFT_dfpmin_armijo : Minimizer.bench.hh
• SFT_dfpmin_armijo_nonmonotone : Minimizer.bench.hh
• SG_C : gpu_homog_atom_coords.h , unique_atoms.h
• shear_moves_test() : moves_test.cc
• ShearMover_ : performance_benchmark.cc
• sheet_start : homodimer_maker.cc
• sheet_stop : homodimer_maker.cc
• sheffler_voids() : for_dkim.cc
• shell : gen_vdw_radius.m , gen_vdw_radius_soft.m
• shift : gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• shift_angles() : pep_prep.cc , pepspec_anchor_dock.cc
• shift_center_and_PCA() : bettercluster.cc
• ship_coordinates_to_gpu() : BundlePairRmsdCalculatorGPU.cc , SmotifPairRmsdCalculatorGPU.CC
• show() : windowed_rmsd.cc , spanfile_from_pdb.cc , TracerTest.cc , mp_span_from_pdb.cc
• show_accuracy_report() : erraser2.cc
• show_allowed_residue_types() : dna_spec_test.cc
• show_clashes() : dna_spec_test.cc , simple_dna_regression_test.cc
• show_cluster_assignment() : test_cluster.cc
• show_dna_geometry() : simple_dna_regression_test.cc
• show_intrachain_energies() : test1.cc
• show_pairing_info() : dna_spec_test.cc , simple_dna_regression_test.cc
• show_protein_DNA_interactions() : dna_spec_test.cc , simple_dna_regression_test.cc
• show_rasmol_hbonds() : test1.cc , simple_dna_regression_test.cc , dna_spec_test.cc
• show_residue_hbonds() : hbond_connect.cc , dna_spec_test.cc , simple_dna_regression_test.cc
• show_residue_residue_clashes() : dna_spec_test.cc , simple_dna_regression_test.cc
• sic_fast_x() : sic_fast_x.hh
• sicdock_max_threads() : make_motif_tables.cc , motif_hash_util.cc , motif_denovo_hb.cc
• sicdock_num_threads() : motif_denovo_hb.cc , motif_hash_util.cc , make_motif_tables.cc
• sicdock_thread_num() : motif_denovo_hb.cc , motif_hash_util.cc , make_motif_tables.cc
• sicfast() : genI213_nocontacts.cc , genP23.cc , isct_test.cc , pentcb.cc , pentcb_test.cc , sic_fast_x_BROKEN.cpp , tmp.cpp , symdock_enum_3_1.cc , genI213_gensym.cc , genI213_nocontacts.cc , symdock_enum.cc , symdock_enum_3_1.cc , symdock_enum.cc , CXdock_TMP.cc , genI213_2comp.cc , genI213_gensym.cc
• sidechain_fastrelax() : design_tight_clusters.cc , detect_tight_clusters.cc
• sidechain_sample() : entropy_test.cc
• sidechain_sasa() : will_mutalyze.cc , rescore_i213.cc , matdes_mutalyze.cc , matdes_design_2comp.cc , matdes_design.cc , design_symm_110330_good.cc , design_symm.cc , design_symm.bak.110314.cc , des_pos_ddG.cc , char_native.cc , design_symm_no_hack_elec.cc
• SIGMOID : Svm.hh
• sigmoid() : symdock_enum_3_1.cc
• sigmoid_predict() : Svm.cc
• sigmoid_train() : Svm.cc
• sigmoidish_neighbor() : genI213_nocontacts.cc , genmatch.cc , genmatch_3bpy.cc , genmatch_m8.cc , gensym_3bpy_from_dimer.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , pentcb.cc , pentcb_test.cc , genP23.cc , genI213_2dsf.cc , genI213_gensym.cc , gen_d2.cc , gen_d2_3his_ooc.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , gen_disulf_homodimer.cc , gen3bpy.cc , gen_homo_hc.cc , genI213_2comp.cc , gen_xtal_dimer_from_trimer.cc , genI213.cc
• sign() : cryst_gen.cc , cryst_design.cc
• sign_t : format.h
• simple_benchmark() : test1.cc
• simple_centroid_test() : test1.cc
• simple_copy_test() : test1.cc
• simple_dna_test() : test1.cc
• simple_frag_test() : test1.cc
• simple_hbond_test() : test1.cc
• simple_loop_modeling_test() : test1.cc
• simple_loop_modeling_test_wrapper() : test1.cc
• simple_minimization() : rnp_ddg.cc
• simple_opte_test() : optE_test.cc , optE_simple.cc
• simple_packing() : rnp_ddg.cc
• simple_relax() : simple_relax.cc
• simple_rotamer_recovery() : simple_rotamer_recovery.cc
• simple_rotamer_test() : test1.cc
• SimpleBBMoverOP : rblinker2.cc , rblinker2_overlay_bound.cc , rblinker2_test.cc
• simulate_ERMS() : SID_ERMS_prediction.cc
• SIN_C_N_CA : gpu_refold_test_cpu.hh
• SIN_CA_C_N : gpu_refold_test_cpu.hh
• SIN_N_CA_C : gpu_refold_test_cpu.hh
• single_position_motif_scan() : motif_scan.cc
• single_res_task() : rotamer_repack.cc
• single_sasa_calc() : cryst_reporters.hh
• six_coords_to_real6() : loodo.cc
• Size : score_hotspot_cst.cc , lowresdock_patchdock_hotspot_cst.cc , hotspot_stub_constraint_test.cc , sasa.cc , rama.cc , make_frag_ssdep.cc , make_blueprint.cc , local_rmsd.cc , frag2profile.cc , ShapeScoring.cc , pick_lowestscore_pose.cc
• SizePairVec : align_substructure.cc
• Sizes : gen_d2_3his_ooc.cc , FunGroupTK.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , gen_homo_hc.cc , genmatch_d6_bpy.cc , hubdenovo.cc , IKFGDB.cc , mkresfile_i213.cc , rescore_i213.cc , test_ikrs.cc , test_ikrs2.cc , test_ikrs_flymake.cc , will_mutalyze.cc , willmatch_2d6_bhe.cc , willmatch_chorismate.cc , willmatch_d6_bpy.cc
• sizes : test_kc.cc
• Sizes : FunGroupTK_test.cc , cryst_reporters.hh , calc_ddG.cc , char_native.cc , coiled_coil_search.cc , des_pos_ddG.cc , design_symm.bak.110314.cc , design_symm.cc , design_symm_110330_good.cc , design_symm_no_hack_elec.cc , matdes_design.cc , matdes_design_2comp.cc , matdes_mutalyze.cc , relax_building_block.cc , phil.hh , disulf_stat.cc , gen_d2.cc
• SizeSet : supercharge.cc
• skip() : diffbinder.cpp
• skip_hd_docking : homodimer_design.cc
• skip_relax : SID_rescore.cc
• skipping_relax() : helix_from_sequence.cc
• slice_ellipsoid_envelope() : swa_rna_util.cc
• slice_pdb() : stepwise_centroid_test.cc
• slice_sample_res_and_surrounding() : swa_rna_util.cc
• slice_sequence() : stepwise_centroid_test.cc
• slidearound() : bettercluster.cc
• SlideTaskCOP : d3_bpy_linker.cc
• SlideTaskOP : d3_bpy_linker.cc
• slow_clash() : xyzStripeHash_test.cc
• slow_nbcount() : xyzStripeHash_test.cc
• slow_nbget() : xyzStripeHash_test.cc
• slow_nbset() : xyzStripeHash_test.cc
• sm : gen_vdw_radius_soft.m
• SMALL : kinematic_closure_helpers.cc
• SMALL_ENOUGH : sturm.hh
• small_min_test() : test1.cc
• small_moves_test() : moves_test.cc
• SmallMover_ : performance_benchmark.cc
• smooth_motif_column() : motif_scan.cc
• smoothed : smooth_2D.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair_decompose.m
• smoothed_ref : cal_env.m
• smoothen_values() : avrg_silent.cc
• SmoothFragRepackMoverOP : cenrot_jd2.cc
• soft_overlap_score() : overlap_score.hh
• soft_pack() : gcc185_test.cc
• soften_clash_check() : clash_score.hh
• solve_c_svc() : Svm.cc
• solve_epsilon_svr() : Svm.cc
• solve_nu_svc() : Svm.cc
• solve_nu_svr() : Svm.cc
• solve_one_class() : Svm.cc
• SonCOP : SharedPtrDemo.cc
• SonCSP : SharedPtrDemo.cc
• SonOP : SharedPtrDemo.cc
• SonSP : SharedPtrDemo.cc
• sort_min() : design_tight_clusters.cc , detect_tight_clusters.cc
• sort_mine() : turner_test_one_chain.cc
• sort_numerically_ascending() : score_ddgs.cc
• sortclusterlist() : bettercluster.cc
• source_interface : david_pocket_align_and_save.cc
• SpacegroupSetting : spacegroup.hh
• spanfile_for_each_chain() : spanfile_from_pdb.cc , mp_span_from_pdb.cc
• spanfile_from_pdb() : spanfile_from_pdb.cc , mp_span_from_pdb.cc
• spanning() : mp_parameters.cc
• SpartaSuperDeviationMoverOP : sparta_superdev.cc
• spec_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• sphere_cen_nc_calculator() : per_residue_solvent_exposure.cc
• sphere_coverage() : tcdock.cc
• sphere_FA_nc_anyatom_calculator() : per_residue_solvent_exposure.cc
• sphere_FA_nc_calculator() : per_residue_solvent_exposure.cc
• SphereGrinder() : spheregrinder.cc
• spinner_test() : stepwise_helix_test.cc
• spirit_namespace : json_spirit_reader_template.h
• split_chains() : InterfaceMutMaker.cc
• split_fa_dun() : byres_data.cc , rotamer_repack.cc
• split_pdb_into_ss_chunks() : challenge.cc
• split_segments_longer_than_6mers() : homolog_finder_farna.cc
• split_silent_file_data() : turner_rules_test.cc
• split_string() : batchrelax_mpi.cc
• sprintf() : printf.h
• sq() : coiled_coil.cc , coiled_coil_zn.cc
• sqr() : genI213_gensym.cc , genI213_nocontacts.cc , genmatch.cc , genmatch_3bpy.cc , genmatch_m8.cc , genP23.cc , gensym_3bpy_from_dimer.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , gpu_mat_vec.hh , hczndimer.cc , IKFGDB.cc , pentcb.cc , pentcb_test.cc , matdes_design_2comp.cc , symdock_enum_3_1.cc , make_motif_tables.cc , genI213_2comp.cc , genI213_2dsf.cc
• SQR : lmmin.cc
• sqr() : RDCTest.cc , r_count_neighbours.cc , r_frag_quality.cc , FunGroupTK.cc , FunGroupTK_test.cc , gen3bpy.cc , gen_d2.cc , gen_d2_3his_ooc.cc , gen_d2_4his.cc , gen_d2_hhhc.cc , gen_disulf_homodimer.cc , gen_homo_hc.cc , gen_xtal_dimer_from_trimer.cc , genI213.cc
• squeeze() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• squote : Tag.cc
• sr_core_core : gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
• sr_core_surf : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• sr_surf_core() : gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
• SS : gen_env_dep_orient_draw.m
• ss_ds_ts_assign_test() : rna_design.cc
• SS_Map : capri15.cc
• SS_Prediction : density_grid.cc
• SS_PredictionOP : density_grid.cc
• SS_Quotas : loop_model.hh
• ss_test() : test1.cc
• ssize_t : types.hh
• SSTR : batchrelax_mpi.cc
• star_main() : star_abinitio.cc
• start_file_test() : test1.cc
• start_index : exposed_strand_finder.cc
• start_sig : r_count_neighbours.cc
• start_sig2 : r_count_neighbours.cc
• stat_output() : calc_stress_tensor.cc
• statistics() : design_contrast_and_statistic.cc
• std_clash_check() : clash_score.hh
• steepness : SID_ERMS_prediction.cc
• stepwise_lores_test() : stepwise_lores_test.cc
• stepwise_monte_carlo() : stepwise.cc
• stepwise_monte_carlo_legacy() : stepwise.cc
• stepwise_template_test() : stepwise_template_test.cc
• storage_tensor : calc_stress_tensor.cc
• store_backbone() : design_cycpeptide_MPI.cc
• store_energies() : monomer_ddg.cc , ddg_benchmark.cc
• store_hb_counts() : lig_polar_sat.cc
• storeposedata() : bettercluster.cc
• str() : motif_denovo_hb.cc
• strand_span : exposed_strand_finder.cc
• strategy : calibur.cc
• strerror_r() : format-inl.h
• strerror_s() : format-inl.h
• strict_dssp_changes : segment_file_generator.cc
• String : pick_bab.cc , remodel.cc , ufv.cc , helical_param.cc , build_repeats.cc , score_delete_segments.cc , sasa.cc , rama.cc , pick_lowestscore_pose.cc , foldptn.cc , frag2profile.cc , local_rmsd.cc , make_frag_ssdep.cc , make_blueprint.cc , pair_distance.cc
• string_to_pose() : test_serialize.cc
• string_view : core.h
• STRINGIFY : crash_report.cc
• STRINGIFY_IMPL : crash_report.cc
• strings : phil.hh
• Strings : score_pdbs.cc , motif_denovo_hb.cc , hubdenovo.cc , PDBTest.cc , dock_test.cc
• strip_comment_and_whitespace() : diffbinder.cpp
• strip_terminal_glycines() : design_cycpeptide_MPI.cc
• strip_termini() : coiled_coil_search.cc , symdock_hybrid.cc , symdock_hybrid_cc3.cc
• struct_file : exposed_strand_finder.cc , homodimer_maker.cc
• stub() : gpu_mat_vec.hh
• stubc() : gpu_mat_vec.hh
• stubcrev() : gpu_mat_vec.hh
• stubIdentityFile : dumpstubinteractions.cc
• stubrev() : gpu_mat_vec.hh
• stubstubEnergyFile : dumpstubinteractions.cc
• stubtargetEnergyFile : dumpstubinteractions.cc
• subplot() : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_decompose.m , draw_matrix.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m
• subvv() : gpu_mat_vec.hh
• SUCCESS() : phosphorylation.cc , design_glycans.cc , test_coenzymes.cc , test_CarbohydrateInfo.cc , test_carbohydrate_scoring.cc , test_carbohydrate_docking.cc , N-terminal_acetylation.cc , glycosyltransfer.cc , DNA_methylation.cc , dock_glycans.cc , mucintypeglycosylation.cc , design_glycans.cc , test_glycan_linkages.cc , glycomutagenesis.cc
• sugar_frag_RNA_test() : rna_test.cc
• sugar_geometry_RNA_test() : rna_test.cc
• sulphur_dist_cutoff : BuriedUnsatPolarsFinder2.cc
• sum() : monomer_ddg.cc , ddg_benchmark.cc
• sum_a1_r : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• sum_a2_r : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• sum_a_a_r : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
• sum_ij : calc_Pij.m
• sum_r : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• sum_r_aa : calc_Pi_ang.m , calc_Pi_sc.m , calc_NtoP.m , calc_Pi.m
• sum_r_aa_core : gen_env_dep_pair.m , draw_gen_env_dep_pair.m
• Sum_r_core_core : gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
• Sum_r_core_surf : gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
• Sum_r_surf_core : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• Sum_r_surf_surf : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• sumr : pre_fill_dfire_2D.m
• SuperDeviationMoverOP : superdev.cc , super.cc , casp9_superdev.cc
• superimpose() : ensemble_analysis.cc
• superimpose_A_to_all() : repeat_dock.cc
• superimpose_pdb() : rna_graft.cc
• superimpose_pose() : challenge.cc
• superimpose_pose_transform() : challenge.cc
• superimpose_pose_using_aln() : tj_util.hh
• superimpose_smotifs() : SmotifHasher.cc
• superimpose_tmalign() : multimodel_gdt.cc
• superimpose_via_alignment() : hybrid.cc
• superimposebb() : design_truecycpeptide_fromstub.cc
• surf_core() : draw_gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m
• surf_core_close : draw_matrix.m
• surf_core_dat_r_ang : gen_env_dep_orient_draw.m
• surf_core_p_r_ang : gen_env_dep_orient_draw.m
• surf_core_sum_r : gen_env_dep_orient_draw.m
• surf_core_th1 : gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• surf_core_th2 : gen_env_dep_orient.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• surf_surf() : gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_pair_decompose.m
• surf_surf_dat_r_ang : gen_env_dep_orient_draw.m
• surf_surf_p_r_ang : gen_env_dep_orient_draw.m
• surf_surf_sum_r : gen_env_dep_orient_draw.m
• surf_surf_th1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
• surf_surf_th2() : gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• surface : david_extract_domain.cc , david_extract_dinucleotide_musashi_reference.cc , david_find_surface_residues.cc , david_fill_gaps.cc
• SURFACE_EXPOSED_CUTOFF : hydrophobic_patch_stats_calculator.cc
• svm_binary_svc_probability() : Svm.cc
• svm_check_parameter() : Svm.cc , Svm.hh
• svm_check_probability_model() : Svm.cc , Svm.hh
• svm_cross_validation() : Svm.cc , Svm.hh
• svm_destroy_param() : Svm.cc , Svm.hh
• svm_free_and_destroy_model() : Svm.cc , Svm.hh
• svm_free_model_content() : Svm.cc , Svm.hh
• svm_get_labels() : Svm.cc , Svm.hh
• svm_get_nr_class() : Svm.cc , Svm.hh
• svm_get_nr_sv() : Svm.cc , Svm.hh
• svm_get_sv_indices() : Svm.cc , Svm.hh
• svm_get_svm_type() : Svm.cc , Svm.hh
• svm_get_svr_probability() : Svm.cc , Svm.hh
• svm_group_classes() : Svm.cc
• svm_load_model() : Svm.cc , Svm.hh
• svm_predict() : Svm.cc , Svm.hh
• svm_predict_probability() : Svm.cc , Svm.hh
• svm_predict_values() : Svm.cc , Svm.hh
• svm_print_string : Svm.cc
• svm_save_model() : Svm.cc , Svm.hh
• svm_set_print_string_function() : Svm.cc , Svm.hh
• svm_svr_probability() : Svm.cc
• svm_train() : Svm.cc , Svm.hh
• svm_train_one() : Svm.cc
• svm_type_table : Svm.cc
• swa_rna_cluster() : swa_rna_main.cc
• swa_rna_sample() : add_delete_monte_carlo.cc , swa_rna_main.cc
• swap() : pca_simple.hh , Svm.cc , pca_simplie.hh
• swap_poses() : util.hh
• swapalignmentvector() : bettercluster.cc
• swapchains() : bettercluster.cc
• swapvector() : bettercluster.cc
• sweep_params_from_match_constraint_file() : sweep_respair_energies.cc
• switch_to_cen() : spiro.cc , dubois.cc , bpy.cc
• switch_to_fa() : bpy.cc , dubois.cc , spiro.cc
• sym_Chi : hczndimer.cc
• sym_Clo : hczndimer.cc
• SymDock_main_local() : r_SymDock_viewer.cc
• SYMICS : tcdock.cc
• symm : smooth_2D.m
• symm_self_rep() : smhybrid.cc
• SymmAbRelaxTest() : SymmAbrelax.cc
• SymmDataTest() : SymmDataTest.cc
• symmetrize_map() : symmetrize_3d_ramamap.cc , symmetrize_new_ramamap.cc , symmetrize_old_ramamap.cc
• symmfile_octa : symfiles.hh
• symmfile_tetra : symfiles.hh
• SymmSilentFileTest() : SymmSilentFile.cc
• SYMOCT : tcdock.cc
• SYMTET : tcdock.cc