- s -

• s : core::optimization::lbfgs_iteration_data
• S_ : core::scoring::ResidualDipolarCoupling
• s_atomic_env_outside_arom_ring_to_types_map : core::chemical::gasteiger::PossibleAtomTypesForAtom
• s_element_bonds_in_arom_ring_to_types_map : core::chemical::gasteiger::PossibleAtomTypesForAtom
• s_mean : core::scoring::sc::_RESULTS
• s_median : core::scoring::sc::_RESULTS
• sa_inner_iterations_length_scale_ : core::pack::annealer::FASTERAnnealer
• sa_weights_ : core::scoring::packing::HolesParams
• safe_max_dis2 : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• safe_max_dis2_ : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::rna::RNA_LJ_BaseEnergy
• saltbridge_correction_ : core::scoring::FACTSPotential
• sample_five_prime_phosphate_ : core::pack::task::rna::RNA_ResidueLevelTask
• sample_level_ : core::pack::task::operation::RotamerExplosion
• sample_proton_chi_ : core::pack::task::ResidueLevelTask_
• sample_rna_chi_ : core::pack::task::rna::RNA_ResidueLevelTask
• sample_three_prime_phosphate_ : core::pack::task::rna::RNA_ResidueLevelTask
• samples_ : core::chemical::AddProtonChi , core::pack::rotamer_set::ContinuousRotamerSet
• samplingrot_offsets_ : core::pack::rotamer_set::ContinuousRotamerSet
• sasa : core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere
• sasa_ : core::pack::interaction_graph::RotamerDots , core::scoring::FACTSResidueInfo
• sasa_arrays_initialized_ : core::pack::interaction_graph::RotamerDots
• sasa_calc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• sasa_for_cc_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• sasa_is_current_ : core::pack::interaction_graph::RotamerDots
• sasaF2_ : core::scoring::FACTSResidueInfo
• satellite_suites : core::pose::rna::RNA_SuiteName
• saxs_score_variant_ : core::scoring::saxs::SAXSEnergy
• sBR_ : core::pack::interaction_graph::FASTERInteractionGraph
• sBR_limit_ : core::pack::annealer::FASTERAnnealer
• sBR_rotamers_ : core::pack::annealer::FASTERAnnealer
• sc : core::scoring::sc::_RESULTS
• sc_bounding_spheres_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• sc_scale_byres_ : core::scoring::electron_density::FastDensEnergy
• SC_scaling_ : core::scoring::electron_density::ElectronDensity
• scale_axis_stagger_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scale_dna_torsion_sd_ : core::scoring::dna::DNATorsionPotential
• scale_dna_torsion_tether_ : core::scoring::dna::DNATorsionPotential
• scale_factor_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::GenBornResidueInfo
• scale_rna_torsion_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• scale_rna_torsion_tether_ : core::scoring::rna::RNA_SugarCloseEnergy
• scaled_logodds_profile_ : core::scoring::methods::ProQ_Energy
• scCD_ : core::scoring::methods::ProClosureEnergy
• scheme_types_ : core::sequence::ScoringSchemeFactory
• scminmap_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• scNV_ : core::scoring::methods::ProClosureEnergy
• score : core::fragment::picking_old::vall::scores::VallFragmentScore , core::scoring::dna::DirectReadoutPotential , core::scoring::packing::HolesResult
• score1 : core::scoring::motif::MotifHit
• score2 : core::scoring::motif::MotifHit
• score_ : core::fragment::FragData , core::scoring::DimerPairing , core::scoring::rna::RNA_SuitePotential , core::scoring::TMscore , core::sequence::Cell , core::util::ChainbreakUtil
• score_bias_ : core::scoring::saxs::SAXSEnergy
• score_criteria_ : core::conformation::symmetry::SymSlideInfo
• score_function_ : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• score_function_info_ : core::scoring::ScoreFunction
• score_function_info_current_ : core::scoring::ScoreFunction
• score_fxn_ : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• score_multiply_ : core::conformation::symmetry::SymmetryInfo
• score_multiply_factor_ : core::conformation::symmetry::SymmetryInfo
• score_multiply_subunit_ : core::conformation::symmetry::SymmData
• score_name_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• score_patch : core::init::pre_talaris_2013_behavior_settings
• score_subunit_ : core::conformation::symmetry::SymmData
• score_type2name_ : core::scoring::ScoreTypeManager
• score_type_ : core::scoring::constraints::Constraint , core::scoring::constraints::DOF_Constraint , core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• score_type_2_active_ : core::scoring::EnergyGraph
• score_type_weights_ : core::scoring::methods::UnfoldedStateEnergy
• score_types_ : core::scoring::methods::EnergyMethod , core::scoring::PeptideBondedEnergyContainer , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator
• score_types_by_method_type_ : core::scoring::ScoreFunction
• score_types_to_ignore_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• score_upper_ : core::scoring::func::SOGFunc_Impl
• score_weights : core::init::pre_talaris_2013_behavior_settings
• score_window_context_ : core::scoring::electron_density::ElectronDensity
• scored_base_pair_list_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_base_stack_list_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scorefxn_info_ : core::scoring::Energies
• scorefxn_weights_ : core::scoring::Energies
• scoreline_prefix_ : core::io::silent::SilentStruct
• scoreRepacks : core::scoring::electron_density::PattersonCorrEnergy
• scores_ : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::scoring::motif::XformScore , core::sequence::SequenceAlignment
• scores_hist_ : core::scoring::custom_pair_distance::DistanceFunc
• scores_present_ : core::scoring::ScoreFunctionInfo
• scoreSymmComplex_ : core::scoring::electron_density::FastDensEnergy
• scoretypes_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• scoring_ : core::scoring::Energies
• scoring_mask_ : core::scoring::electron_density::ElectronDensity
• scoring_matrix_ : core::sequence::DP_Matrix , core::sequence::MatrixScoringScheme
• scoring_schemes_ : core::sequence::CompositeScoringScheme
• scoring_subunit_ : core::conformation::symmetry::SymmetryInfo
• scratch_pose_ : core::pose::copydofs::CopyDofs
• sd_ : core::scoring::constraints::BoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::MinMultiHarmonicFunc , core::scoring::methods::D2H_SA_Energy
• SD_ : core::scoring::ResidualDipolarCoupling
• sd_ang_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dih_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dis_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sdens : core::scoring::APBSConfig::R_PARAM
• sdev1_ : core::scoring::func::SoedingFunc
• sdev2_ : core::scoring::func::SoedingFunc
• sdev_ : core::chemical::AddChiRotamer , core::scoring::constraints::BigBinConstraint
• sdevs_ : core::scoring::func::SOGFunc_Impl
• sdf_type_ : core::chemical::sdf::MolFileIOBond
• sds_ : core::scoring::disulfides::Cb_Distance_Func
• second : core::fragment::FragID
• second_node_num_states_per_aatype_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• secondary_structure_potential_ : core::scoring::ScoringManager
• secstruct_ : core::conformation::Conformation , core::fragment::SecstructSRFD , core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::scoring::packing::PoseBalls
• secstructs_ : core::io::sequence_comparation::DesignContrast
• section_index_ : core::fragment::picking_old::vall::VallResidue
• segments_ : core::pose::datacache::SpecialSegmentsObserver
• selected_ : core::scoring::SelectedResPredicate
• selector_ : core::chemical::Patch , core::chemical::PatchCase , core::pack::task::residue_selector::NotResidueSelector
• selectors_ : core::chemical::ResidueSelector , core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::OrResidueSelector
• self_and_bg_dots_for_states_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• self_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• semirotameric_ncaa_rotlib_ : core::chemical::ResidueType
• send_to_stdout_ : core::optimization::NumericalDerivCheckResult
• sep : core::scoring::sc::MolecularSurfaceCalculator
• sep_aa1_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_aa2_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_aa_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_bfac_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_dist_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_dssp_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_hb_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_lj_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_nbrs_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_ss_ : core::scoring::motif::ResPairMotifMetaBinner , core::scoring::packing::HolesParams
• separate_scores_ : core::scoring::rna::data::RNA_DMS_Potential
• seq1_ : core::sequence::DerivedSequenceMapping
• seq2_ : core::sequence::DerivedSequenceMapping
• seq_ : core::import_pose::pose_stream::ExtendedPoseInputStream , core::sequence::Sequence
• seq_num : core::scoring::rna::chemical_shift::ChemicalShiftData
• seq_sep_ : core::scoring::hbonds::HBEvalTuple
• seq_sep_scale_ : core::scoring::SecondaryStructureWeights
• seq_sep_type2name_ : core::scoring::hbonds::HBondTypeManager
• seq_types_ : core::sequence::SequenceFactory
• seqid_ : core::environment::FoldTreeSketch::Node
• seqpos1_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• seqpos2_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• seqpos_ : core::conformation::Residue , core::io::PositionDdGInfo::PositionDdGInfo , core::io::rna::RDAT , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint
• seqs_ : core::sequence::CompositeSequence
• sequence_ : core::fragment::SingleResidueFragData , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::rna::RDAT , core::io::silent::SilentStruct , core::io::silent::SimpleSequenceData , core::pose::MiniPose
• sequence_profile_ : core::scoring::constraints::SequenceProfileConstraint
• sequences_ : core::io::rna::RDAT , core::sequence::SequenceAlignment
• serial : core::io::pdb::AtomInformation
• serialized_ : core::chemical::ResidueType
• set_of_rotamer_sets_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• set_up_metal_bonds_ : core::import_pose::ImportPoseOptions
• settings : core::scoring::sc::MolecularSurfaceCalculator
• sfd_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• sfd_req_1benmeths_ : core::scoring::MinimizationNode
• sfd_req_2benmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfs_req_1benmeths_ : core::scoring::MinimizationNode
• sfs_req_2benmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfxn_ : core::pack::interaction_graph::SimpleInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• sg_dist_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• sgsg_dihedral_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• ShanonEntropy_n_derivs_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• shared_silent_data_ : core::io::silent::SilentFileData
• shift_ : core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::SmoothScoreTermCoeffs
• short_name : update_ResidueType_enum_files.EnumInfo
• short_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• short_name_plural : update_ResidueType_enum_files.EnumInfo
• short_range_interactions_exist_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• shortest_paths_ : core::scoring::methods::LinearChainbreakEnergy
• sibling_ : core::scoring::trie::TrieNode< AT, CPDATA >
• sidechain_atom_id_ : core::scoring::constraints::BackboneStubConstraint
• sidechain_target_ : core::scoring::constraints::BackboneStubConstraint
• sig_centroid_ : core::scoring::fiber_diffraction::CentroidScatter
• sigma1_ : core::scoring::CSA
• sigma2_ : core::scoring::CSA
• sigma3_ : core::scoring::CSA
• sigma_ : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering
• sigma_charge_to_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• sigma_charge_to_lone_pair_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• sigmoid_coeffs_ : core::scoring::SmoothScoreTermCoeffs
• SIGMOID_SLOPE : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• sigmoidal_D0_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_D_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_die_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_S_ : core::scoring::etable::coulomb::Coulomb
• sign1_ : core::scoring::DimerPairing
• sign2_ : core::scoring::DimerPairing
• silent_ : core::optimization::MinimizerOptions
• silent_comments_ : core::io::silent::SilentStruct
• silent_energies_ : core::io::silent::SilentStruct
• silent_struct_type_ : core::io::silent::SilentFileData , core::io::silent::SilentFileOptions
• sim_type : core::scoring::APBSConfig::I_PARAM
• simple_fold_tree_ : core::kinematics::ShortestPathInFoldTree
• sin_x_over_x_ : core::scoring::saxs::SinXOverX
• since_last_sonm_update_ : core::scoring::TenANeighborNode
• singleton_ : core::scoring::saxs::FormFactorManager
• size2_ : core::id::SequenceMapping
• size_ : core::graph::Array0< T > , core::io::serialization::BUFFER , core::optimization::ParticleSwarmMinimizer , core::scoring::DenseEnergyContainer , core::scoring::Energies , core::scoring::motif::Xfrag , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• skip_chainbreak_torsions_ : core::scoring::rna::RNA_TorsionPotential
• skip_set_reasonable_fold_tree_ : core::import_pose::ImportPoseOptions
• slice_coords_ : core::scoring::packstat::LeeRichards
• slices_ : core::scoring::packstat::LeeRichards
• slide_info_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• slide_order_ : core::conformation::symmetry::SymSlideInfo
• slide_order_string_ : core::conformation::symmetry::SymmData
• slide_type_ : core::conformation::symmetry::SymSlideInfo
• SlideCriteriaVal_ : core::conformation::symmetry::SymSlideInfo
• slim_ : core::scoring::etable::Etable
• slim_etable_ : core::scoring::methods::LK_BallEnergy
• slope : core::scoring::etable::ExtraQuadraticRepulsion , core::util::Line
• slope_ : core::scoring::func::LinearPenaltyFunction , core::scoring::func::SigmoidFunc
• SMALL_BULGE_LIMIT : core::scoring::dssp::StrandPairing
• smooth_ : core::scoring::func::SOGFunc_Impl , core::scoring::hbonds::FadeInterval
• smooth_env_pair_potential_ : core::scoring::ScoringManager
• smooth_fa_elec : core::init::pre_talaris_2013_behavior_settings
• smooth_fa_elec_ : core::scoring::etable::coulomb::Coulomb , core::scoring::methods::EnergyMethodOptions
• smooth_hb_env_dep_ : core::scoring::hbonds::HBondOptions
• smooth_move_frac_ : core::scoring::MembranePotential
• smooth_nb_ : core::scoring::packing::PoseBalls
• smpbe_size : core::scoring::APBSConfig::R_PARAM
• smpbe_vol : core::scoring::APBSConfig::R_PARAM
• snn : core::scoring::fiber_diffraction::Hankel
• sog_cst_param_ : core::scoring::func::SOGFunc_Impl
• sol_weight_ : core::scoring::etable::EtableEvaluator
• solv1_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack
• solv2_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack
• solvation : core::scoring::etable::AtomPairEnergy
• solvF2BR_ : core::scoring::FACTSResidueInfo
• solvF2d_ : core::scoring::FACTSResidueInfo
• some_node_in_state_0_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• source_file : update_ResidueType_enum_files.EnumInfo
• sp2_BAH180_rise_ : core::scoring::hbonds::HBondOptions
• sp2_outer_width_ : core::scoring::hbonds::HBondOptions
• space : core::scoring::APBSConfig
• spacegroup_ : core::pose::CrystInfo
• span_ : core::scoring::MembraneTopology
• spanfile_ : core::scoring::MembraneTopology
• spanning_ : core::scoring::MembraneEmbed
• spanning_topology_ : core::conformation::membrane::MembraneInfo
• sparse_aa_neighbors_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• sparse_mat_info_for_state_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• sparse_matrix_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• specific_name : core::chemical::RingConformer
• sphere_ : core::scoring::packstat::CavityBall
• sphere_sasa : core::scoring::packstat::SasaResult
• spheres : core::scoring::packstat::PosePackData
• spline_interpolator_ : core::scoring::saxs::FormFactor
• sqr_num_aa_types_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• sqrt_HH_cutoff_ : core::scoring::NeighborList
• sqrt_XH_cutoff_ : core::scoring::NeighborList
• sqrt_XX_cutoff_ : core::scoring::NeighborList
• square_obs_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• sr_As_ : core::scoring::CenHBPotential
• sr_mus_ : core::scoring::CenHBPotential
• sr_sigmas_ : core::scoring::CenHBPotential
• srad : core::scoring::APBSConfig::R_PARAM
• srfm : core::scoring::APBSConfig::I_PARAM
• ss1_ : core::scoring::methods::ProQ_Energy , core::scoring::motif::ResPairMotif
• ss2_ : core::scoring::motif::ResPairMotif
• ss_ : core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::VallResidue , core::scoring::motif::Xfres
• ss_cutoff_ : core::scoring::SecondaryStructureWeights
• SS_dimer : core::scoring::Strands
• ss_lowstrand_ : core::scoring::SecondaryStructureWeights
• ss_penalty_ : core::fragment::picking_old::vall::eval::IdentityEval
• ss_pred_ : core::scoring::methods::ProQ_Energy
• SS_resnum : core::scoring::Strands
• SS_strand : core::scoring::Strands
• SS_strand_end : core::scoring::Strands
• ss_types_ : core::io::silent::SilentStructFactory
• ss_weights_ : core::scoring::methods::EnergyMethodOptions
• sscomp_ : core::scoring::motif::Xfrag
• ssdep_ : core::scoring::hbonds::SSWeightParameters
• ssdist_ : core::scoring::SecondaryStructurePotential
• st_atr_ : core::scoring::etable::EtableEvaluator
• st_rep_ : core::scoring::etable::EtableEvaluator
• st_sol_ : core::scoring::etable::EtableEvaluator
• stability_metric_ : core::chemical::gasteiger::GasteigerAtomTypeData
• stagger_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• stagger_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• stagger_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• standard_atomtype_to_carbon_donor_index_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• start : core::io::pdb::Field
• start_ : core::chemical::RigidDistanceVisitor , core::conformation::membrane::Span , core::fragment::Frame , core::io::serialization::BUFFER , core::kinematics::Edge , core::scoring::packstat::trace , core::scoring::ResRangePredicate , core::sequence::Sequence
• start_atom_ : core::kinematics::Edge
• start_index_ : core::chemical::RigidDistanceVisitor
• start_pos_ : core::chemical::RigidDistanceVisitor
• start_seq2_ : core::sequence::DerivedSequenceMapping
• start_with_current_ : core::pack::annealer::SimAnnealerBase
• starting_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• startpos_ : core::fragment::AnnotatedFragData
• state_assignments_ : core::pack::scmin::SidechainStateAssignment
• state_energies_in_current_context_ : core::pack::interaction_graph::FASTERNode
• state_energies_in_current_state_assignment_ : core::pack::interaction_graph::FASTERNode
• state_in_rh : core::pack::interaction_graph::history_queue_struct
• state_ind_for_this_aa_type_ : core::pack::interaction_graph::SparseMatrixIndex
• state_offset_for_aatype_ : core::pack::interaction_graph::OnTheFlyNode
• state_offset_for_restype_group_ : core::pack::interaction_graph::SymmOnTheFlyNode
• statistics_output_ : core::scoring::orbitals::OrbitalsStatistics
• std_devs_ : core::scoring::func::USOGFunc
• stddev_ : core::scoring::dna::DNA_BasePotential
• steepness_ : core::conformation::membrane::MembraneInfo , core::scoring::hbonds::HBondEnergy , core::scoring::Membrane_FAEmbed
• step_data_ : core::optimization::SimpleDerivCheckResult
• stepsize_ : core::scoring::func::EtableFunc
• stereochem_ : core::chemical::carbohydrates::CarbohydrateInfo
• stiffness_ : core::scoring::dna::DNA_BasePotential
• stop_ : core::kinematics::Edge
• stop_atom_ : core::kinematics::Edge
• store_ : core::indexed_structure_store::FragmentLookup
• store_argv_in_file_ : core::io::silent::SilentFileData
• store_rpes_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• stored_rpes_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• strand_fraction_ : core::fragment::SecondaryStructure
• strands_ : core::scoring::SS_Info
• stretch_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• strict_column_mode_ : core::io::silent::SilentFileData , core::io::silent::SilentStruct
• string_properties_ : core::chemical::ResidueProperties
• string_value_ : core::io::silent::SilentEnergy
• structure_ : core::io::rna::RDAT
• structure_is_outdated_ : core::pose::metrics::PoseMetricContainer , core::pose::metrics::StructureDependentCalculator
• structure_list_ : core::io::silent::SilentFileData
• structure_map_ : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• structure_moved_ : core::conformation::Conformation
• structure_score : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy
• structures_ : core::io::rna::RDAT
• stub1_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub2_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub3_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub_atom1_ : core::chemical::Adduct , core::chemical::AtomICoor
• stub_atom2_ : core::chemical::Adduct , core::chemical::AtomICoor
• stub_atom3_ : core::chemical::Adduct , core::chemical::AtomICoor
• sub_filters_ : core::pack::task::operation::ResFilterComposition
• subbin_cdf_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_cdf_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• subbin_ranges_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_ranges_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• subbin_type_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_type_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• subtree_intxn_sphere_radius_sqr_ : core::scoring::trie::TrieNode< AT, CPDATA >
• subunit_num_to_virt_id_ : core::conformation::symmetry::SymmData
• subunits_ : core::conformation::symmetry::SymmData
• sugar_edge_paired_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• suite_undefined : core::pose::rna::RNA_SuiteName
• suitename_ : core::scoring::rna::RNA_JR_SuiteEnergy
• suiteness : core::pose::rna::RNA_SuiteAssignment
• suiteness_bonus_ : core::scoring::rna::RNA_EnergyMethodOptions
• sulfur_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• sum_all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• sum_obs_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• sum_of_neighbors_masses_ : core::scoring::TenANeighborNode
• superenv_ : core::environment::EnvCore
• superposition_bonus_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• surf : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• surf_ : core::scoring::packing::PoseBalls
• surface : core::scoring::sc::_RESULTS
• surface_accessibility : core::scoring::packstat::CavityBallCluster
• surface_area : core::scoring::packstat::CavityBallCluster
• surface_area_ : core::scoring::packstat::LeeRichards
• surface_energy_weight_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_exposed_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• SURFACE_EXPOSED_CUTOFF : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• SURFACE_SCORE_BIN_SIZE : core::pack::interaction_graph::SurfacePotential
• surface_score_min_last_100_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_score_min_recent_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_score_weight_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• surrounding_sasa_smoothing_window : core::scoring::packstat::SasaOptions
• svm_model_ : core::scoring::ProQPotential
• swin : core::scoring::APBSConfig::R_PARAM
• symm_info_ : core::conformation::symmetry::SymmetricConformation , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symm_min_map_ : core::optimization::symmetry::SymAtomTreeMultifunc
• symm_ptrs : core::scoring::electron_density::ElectronDensity
• symm_transforms_ : core::conformation::symmetry::SymmData
• symmap : core::scoring::electron_density::ElectronDensity
• symmetric_transforms_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetry_name_ : core::conformation::symmetry::SymmData
• symmetry_status_ : core::pack::task::PackerTask_
• symmetry_type_ : core::conformation::symmetry::SymmData
• symminfo_ : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• symmOps : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• symmRotOps : core::scoring::electron_density::ElectronDensity
• syn_G_potential_bonus_ : core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::rna::RNA_TorsionPotential