- s -

sasa_cutoff : BuriedUnsatPolarsFinder2.cc
SASAfilter : UBQ_UBQ_E2.cc
sat_allow : exposed_strand_finder.cc
SC : gen_env_dep_orient_draw.m
scaffold_pdb : zinc1_homodimer_setup.cc
scaffold_protein : HbondZinc.cc , HbondZincHHHO.cc , HbondZincBackbone.cc , HbondZinc_ser.cc , HbondZinc_allpolar.cc
score : draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , cal_env.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m
score0 : draw_gen_env_dep_orient_decompose.m
Score_ : performance_benchmark.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_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_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_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_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_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_rg_ : ScoreEach.bench.hh
Score_rsigma_ : ScoreEach.bench.hh
Score_sa_ : ScoreEach.bench.hh
Score_sheet_ : ScoreEach.bench.hh
Score_ss_pair_ : ScoreEach.bench.hh
Score_unfolded_ : ScoreEach.bench.hh
Score_vdw_ : ScoreEach.bench.hh
score_w : gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_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
score_w3 : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
Score_yhh_planarity_ : ScoreEach.bench.hh
scorefilter : UBQ_UBQ_E2.cc
seg_filters : MakeSegmentFile.cc
seg_metrics : MakeSegmentFile.cc
seg_script_opt : MakeSegmentFile.cc
segment_path : MakeSegmentFile.cc
SER : gen_env_dep_pair.m , gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.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 , draw_matrix.m , cal_env.m , load_pair_env_table.m , gen_env_dep_orient.m
sfd : genmatch_3bpy.cc , genP23.cc , gensym_3bpy_from_dimer.cc , gentetra.cc , gentetra_bpy_from_znhis.cc , gentetra_from_trimer.cc , hczndimer.cc , heterodock.cc , dock_asym.cc , hubabinitio.cc , hubdenovo.cc , hubfragdesign.cc , pentcb.cc , pentcb_design.cc , pentcb_test.cc , rescore_i213.cc , sicdock.cc , test_ikrs.cc , test_ikrs2.cc , genI213_gensym.cc , genI213_nocontacts.cc , cxdesign.cc , cxdock.cc , crossmatch.cc , crossmatch_3e.cc , crossmatch_d2.cc , CXdock.cc , cxdock_sheet.cc , CXdock_TMP.cc , design_DL.cc , dxdock.cc , dxdock_movie.cc , gen3bpy.cc , gen_xtal_dimer_from_trimer.cc , genI213.cc , genI213_2comp.cc , genI213_2dsf.cc , d3_bpy_linker.cc
ShearMover_ : performance_benchmark.cc
sheet_start : homodimer_maker.cc
sheet_stop : homodimer_maker.cc
shell : gen_vdw_radius_soft.m , gen_vdw_radius.m
shift : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
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
skip_hd_docking : homodimer_design.cc
skip_relax : SID_rescore.cc
sm : gen_vdw_radius_soft.m
SmallMover_ : performance_benchmark.cc
smoothed : smooth_2D.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m
smoothed_ref : cal_env.m
source_interface : david_pocket_align_and_save.cc
squote : Tag.cc
sr_core_core : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
sr_core_surf : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
sr_surf_core : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
SS : gen_env_dep_orient_draw.m
start_sig : r_count_neighbours.cc
start_sig2 : r_count_neighbours.cc
steepness : SID_ERMS_prediction.cc
storage_tensor : calc_stress_tensor.cc
strand_span : exposed_strand_finder.cc
strategy : calibur.cc
strict_dssp_changes : segment_file_generator.cc
struct_file : exposed_strand_finder.cc , homodimer_maker.cc
stubIdentityFile : dumpstubinteractions.cc
stubstubEnergyFile : dumpstubinteractions.cc
stubtargetEnergyFile : dumpstubinteractions.cc
sulphur_dist_cutoff : BuriedUnsatPolarsFinder2.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 : gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
sum_a_a_r : gen_env_dep_orient.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.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_NtoP.m , calc_Pi.m , calc_Pi_ang.m , calc_Pi_sc.m
sum_r_aa_core : draw_gen_env_dep_pair.m , gen_env_dep_pair.m
Sum_r_core_core : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
Sum_r_core_surf : draw_gen_env_dep_pair_decompose.m , 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
surf_core : draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_matrix.m , gen_env_dep_orient_draw.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.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 , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m
surf_core_th2 : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
surf_surf : draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_matrix.m , gen_env_dep_orient_draw.m , 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 : gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
surf_surf_th2 : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
surface : david_extract_dinucleotide_musashi_reference.cc , david_extract_domain.cc , david_fill_gaps.cc , david_find_surface_residues.cc
SURFACE_EXPOSED_CUTOFF : hydrophobic_patch_stats_calculator.cc
svm_print_string : Svm.cc
svm_type_table : Svm.cc
SYMICS : tcdock.cc
symm : smooth_2D.m
symmfile_octa : symfiles.hh
symmfile_tetra : symfiles.hh
SYMOCT : tcdock.cc
SYMTET : tcdock.cc