- s -

• s() : core::scoring::fiber_diffraction::OneGaussianScattering
• s1_end() : core::scoring::Hairpin
• s1_start() : core::scoring::Hairpin
• S2() : core::scoring::electron_density::ElectronDensity
• s2_end() : core::scoring::Hairpin
• s2_start() : core::scoring::Hairpin
• s_MaxElectronsInOrbital() : core::chemical::ElectronConfiguration
• SA_Energy() : core::scoring::methods::SA_Energy
• sa_weight() : core::scoring::packing::HolesParams
• safely_append_polymer_residue_after_seqpos() : core::conformation::Conformation
• safely_prepend_polymer_residue_before_seqpos() : core::conformation::Conformation
• same_edge() : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• same_type_as_me() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::scoring::Energies , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies
• sample_five_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• sample_level() : core::pack::task::operation::RotamerExplosion
• sample_proton_chi() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• sample_res() : core::pose::full_model_info::FullModelInfo
• sample_rna_chi() : core::pack::task::rna::RNA_ResidueLevelTask
• sample_three_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• sampling_id_for_current_rotamer() : core::pack::rotamer_set::ContinuousRotamerSet
• sanity_check() : core::conformation::symmetry::SymmData , core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• sasa() : core::scoring::FACTSResidueInfo
• SasaCalc() : core::scoring::sasa::SasaCalc
• SasaCalculator2() : core::pose::metrics::simple_calculators::SasaCalculator2
• SasaCalculatorLegacy() : core::pose::metrics::simple_calculators::SasaCalculatorLegacy
• sasaF2() : core::scoring::FACTSResidueInfo
• SasaMethod() : core::scoring::sasa::SasaMethod
• SasaOptions() : core::scoring::packstat::SasaOptions
• SasaResult() : core::scoring::packstat::SasaResult
• save_data() : core::io::rna::RDAT
• save_data_with_idx() : core::io::rna::RDAT
• save_energy() : core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborIterator
• save_momento() : core::pack::scmin::ResidueAtomTreeCollection
• SAXSEnergy() : core::scoring::saxs::SAXSEnergy
• SAXSEnergyCEN() : core::scoring::saxs::SAXSEnergyCEN
• SAXSEnergyCreator() : core::scoring::saxs::SAXSEnergyCreator
• SAXSEnergyCreatorCEN() : core::scoring::saxs::SAXSEnergyCreatorCEN
• SAXSEnergyCreatorFA() : core::scoring::saxs::SAXSEnergyCreatorFA
• SAXSEnergyFA() : core::scoring::saxs::SAXSEnergyFA
• sBR() : core::pack::annealer::FASTERAnnealer
• sc_bb_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• SC_BB_EnergyInvoker() : core::scoring::etable::SC_BB_EnergyInvoker< Evaluator >
• sc_bounding_sphere() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• sc_H_orbital() : core::scoring::orbitals::OrbitalsStatistics
• sc_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• SC_SC_EnergyInvoker() : core::scoring::etable::SC_SC_EnergyInvoker< Evaluator >
• SC_Whole_EnergyInvoker() : core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator >
• ScalarWeightedFunc() : core::scoring::func::ScalarWeightedFunc
• scale() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• scale_axis_stagger() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scale_factor() : core::scoring::GenBornResidueInfo
• scale_inneriterations() : core::pack::annealer::SimAnnealerBase
• scale_outeriterations() : core::pack::annealer::SimAnnealerBase
• scaleIntensities() : core::scoring::electron_density::ElectronDensity
• scfxn_rules_for_energy() : core::scoring::orbitals::OrbitalsScore
• scfxn_rules_for_weight() : core::scoring::orbitals::OrbitalsScore
• scmin_numerical_derivative_check() : core::pack::scmin::SCMinMultifunc
• SCMinMinimizerMap() : core::pack::scmin::SCMinMinimizerMap
• SCMinMultifunc() : core::pack::scmin::SCMinMultifunc
• score() : core::fragment::FragData , core::optimization::Particle , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::DimerPairing , core::scoring::mm::MMBondAngleScore , core::scoring::mm::MMBondLengthScore , core::scoring::mm::MMLJEnergyTable , core::scoring::mm::MMLJScore , core::scoring::mm::MMTorsionScore , core::scoring::motif::ResPairMotif , core::scoring::packstat::PackingScore , core::scoring::ProQPotential , core::scoring::ScoreFunction , core::scoring::SecondaryStructurePotential , core::sequence::Cell , core::sequence::ChemicalShiftScoringScheme , core::sequence::CompassScoringScheme , core::sequence::CompositeScoringScheme , core::sequence::DPScoringScheme , core::sequence::L1ScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ProfSimScoringScheme , core::sequence::ScoringScheme , core::sequence::SequenceAlignment , core::sequence::SimpleScoringScheme
• score_all_particles() : core::optimization::ParticleSwarmMinimizer
• score_atom_centrally() : core::scoring::methods::MMBondAngleEnergy
• score_atom_pair() : core::scoring::elec::FA_ElecEnergy
• score_by_scoretype() : core::scoring::ScoreFunction
• score_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential , core::scoring::disulfides::DisulfideMatchingPotential
• score_filter() : core::io::silent::SilentFileData
• score_fun() : core::scoring::TMscore
• score_function() : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• score_multiply() : core::conformation::symmetry::SymmetryInfo
• score_multiply_factor() : core::conformation::symmetry::SymmetryInfo
• score_normal_center() : core::scoring::MembranePotential
• score_of_bin() : core::scoring::motif::XformScore
• score_of_bin_normalized() : core::scoring::motif::XformScore
• score_this_disulfide() : core::scoring::disulfides::FullatomDisulfidePotential
• score_this_disulfide_old() : core::scoring::disulfides::FullatomDisulfidePotential
• score_type() : core::scoring::constraints::Constraint , core::scoring::constraints::DOF_Constraint
• score_type_2_active() : core::scoring::EnergyGraph
• score_type_from_name() : core::scoring::ScoreTypeManager
• score_types() : core::scoring::methods::EnergyMethod
• score_types_by_method_type() : core::scoring::ScoreFunction
• score_types_for_method() : core::pack::dunbrack::cenrot::CenRotDunEnergyCreator , core::pack::dunbrack::DunbrackEnergyCreator , core::pack::interaction_graph::HPatchEnergyCreator , core::pack::interaction_graph::SurfaceEnergyCreator , core::scoring::carbon_hbonds::CarbonHBondEnergyCreator , core::scoring::constraints::ConstraintsEnergyCreator , core::scoring::cryst::XtalMLEnergyCreator , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator , core::scoring::disulfides::CentroidDisulfideEnergyCreator , core::scoring::disulfides::DisulfideMatchingEnergyCreator , core::scoring::disulfides::FullatomDisulfideEnergyCreator , core::scoring::dna::DNAChiEnergyCreator , core::scoring::dna::DNATorsionEnergyCreator , core::scoring::elec::FA_ElecEnergyAroAllCreator , core::scoring::elec::FA_ElecEnergyAroAroCreator , core::scoring::elec::FA_ElecEnergyCreator , core::scoring::elec::FA_GrpElecEnergyCreator , core::scoring::elec::RNA_FA_ElecEnergyCreator , core::scoring::electron_density::ElecDensAllAtomCenEnergyCreator , core::scoring::electron_density::ElecDensCenEnergyCreator , core::scoring::electron_density::ElecDensEnergyCreator , core::scoring::electron_density::FastDensEnergyCreator , core::scoring::electron_density::PattersonCorrEnergyCreator , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator , core::scoring::etable::EtableClassicIntraEnergyCreator , core::scoring::etable::EtableEnergyCreator , core::scoring::fiber_diffraction::FiberDiffractionEnergyCreator , core::scoring::fiber_diffraction::FiberDiffractionEnergyDensCreator , core::scoring::fiber_diffraction::FiberDiffractionEnergyGpuCreator , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator , core::scoring::hackaro::HackAroEnergyCreator , core::scoring::hbonds::HBondEnergyCreator , core::scoring::interface_::DDPscoreCreator , core::scoring::loop_graph::LoopCloseEnergyCreator , core::scoring::membrane::FaMPEnvEnergyCreator , core::scoring::membrane::FaMPEnvSmoothEnergyCreator , core::scoring::membrane::FaMPSolvEnergyCreator , core::scoring::membrane::MPCbetaEnergyCreator , core::scoring::membrane::MPEnvEnergyCreator , core::scoring::membrane::MPLipoEnergyCreator , core::scoring::membrane::MPNonHelixPenaltyCreator , core::scoring::membrane::MPPairEnergyCreator , core::scoring::membrane::MPTerminiPenaltyCreator , core::scoring::membrane::MPTMProjPenaltyCreator , core::scoring::methods::BurialEnergyCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::CenRotEnvEnergyCreator , core::scoring::methods::CenRotPairEnergyCreator , core::scoring::methods::ChainbreakEnergyCreator , core::scoring::methods::ChemicalShiftAnisotropyEnergyCreator , core::scoring::methods::ContactOrderEnergyCreator , core::scoring::methods::CustomAtomPairEnergyCreator , core::scoring::methods::D2H_SA_EnergyCreator , core::scoring::methods::dfire::DFIRE_EnergyCreator , core::scoring::methods::DipolarCouplingEnergyCreator , core::scoring::methods::DirectReadoutEnergyCreator , core::scoring::methods::DistanceChainbreakEnergyCreator , core::scoring::methods::DNA_BaseEnergyCreator , core::scoring::methods::EnergyMethodCreator , core::scoring::methods::EnvEnergyCreator , core::scoring::methods::EnvSmoothEnergyCreator , core::scoring::methods::Fa_MbenvEnergyCreator , core::scoring::methods::Fa_MbsolvEnergyCreator , core::scoring::methods::FACTSEnergyCreator , core::scoring::methods::FreeDOF_EnergyCreator , core::scoring::methods::GaussianOverlapEnergyCreator , core::scoring::methods::GenBornEnergyCreator , core::scoring::methods::GoapEnergyCreator , core::scoring::methods::HybridVDW_EnergyCreator , core::scoring::methods::IntermolEnergyCreator , core::scoring::methods::LinearChainbreakEnergyCreator , core::scoring::methods::LK_BallEnergyCreator , core::scoring::methods::LK_hackCreator , core::scoring::methods::LK_PolarNonPolarEnergyCreator , core::scoring::methods::MembraneCbetaEnergyCreator , core::scoring::methods::MembraneCenPairEnergyCreator , core::scoring::methods::MembraneEnvEnergyCreator , core::scoring::methods::MembraneEnvPenaltiesCreator , core::scoring::methods::MembraneEnvSmoothEnergyCreator , core::scoring::methods::MembraneLipoCreator , core::scoring::methods::MissingEnergyCreator , core::scoring::methods::MMBondAngleEnergyCreator , core::scoring::methods::MMBondLengthEnergyCreator , core::scoring::methods::MMLJEnergyInterCreator , core::scoring::methods::MMLJEnergyIntraCreator , core::scoring::methods::MMTorsionEnergyCreator , core::scoring::methods::NMerPSSMEnergyCreator , core::scoring::methods::NMerRefEnergyCreator , core::scoring::methods::NMerSVMEnergyCreator , core::scoring::methods::OmegaTetherEnergyCreator , core::scoring::methods::OtherPoseEnergyCreator , core::scoring::methods::P_AA_EnergyCreator , core::scoring::methods::P_AA_pp_EnergyCreator , core::scoring::methods::PackStatEnergyCreator , core::scoring::methods::PairEnergyCreator , core::scoring::methods::PeptideBondEnergyCreator , core::scoring::methods::pHEnergyCreator , core::scoring::methods::PoissonBoltzmannEnergyCreator , core::scoring::methods::ProClosureEnergyCreator , core::scoring::methods::ProQ_EnergyCreator , core::scoring::methods::Rama2BOffsetEnergyCreator , core::scoring::methods::RamachandranEnergy2BCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::ReferenceEnergyCreator , core::scoring::methods::ReferenceEnergyNoncanonicalCreator , core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator , core::scoring::methods::ResidualDipolarCouplingEnergyCreator , core::scoring::methods::RG_Energy_FastCreator , core::scoring::methods::RG_LocalEnergyCreator , core::scoring::methods::RMS_EnergyCreator , core::scoring::methods::SA_EnergyCreator , core::scoring::methods::SecondaryStructureEnergyCreator , core::scoring::methods::SequenceDependentRefEnergyCreator , core::scoring::methods::SmoothCenPairEnergyCreator , core::scoring::methods::SmoothEnvEnergyCreator , core::scoring::methods::SuckerEnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::WaterAdductHBondEnergyCreator , core::scoring::methods::WaterAdductIntraEnergyCreator , core::scoring::methods::YHHPlanarityEnergyCreator , core::scoring::nv::NVscoreCreator , core::scoring::orbitals::OrbitalsScoreCreator , core::scoring::packing::HolesEnergyCreator , core::scoring::packing::SurfEnergyCreator , core::scoring::packing::SurfVolEnergyCreator , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator , core::scoring::rna::data::RNA_ChemicalMappingEnergyCreator , core::scoring::rna::data::RNA_DataBackboneEnergyCreator , core::scoring::rna::RG_Energy_RNACreator , core::scoring::rna::RNA_BulgeEnergyCreator , core::scoring::rna::RNA_FullAtomStackingEnergyCreator , core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator , core::scoring::rna::RNA_JR_SuiteEnergyCreator , core::scoring::rna::RNA_LJ_BaseEnergyCreator , core::scoring::rna::RNA_Mg_EnergyCreator , core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator , core::scoring::rna::RNA_SugarCloseEnergyCreator , core::scoring::rna::RNA_SuiteEnergyCreator , core::scoring::rna::RNA_TorsionEnergyCreator , core::scoring::rna::RNA_VDW_EnergyCreator , core::scoring::rna::StackElecEnergyCreator , core::scoring::saxs::FastSAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symECreator , core::scoring::vdwaals::VDW_EnergyCreator
• scored_base_pair_list() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_base_stack_list() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_frag_ids() : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreFileData() : core::io::raw_data::ScoreFileData
• ScoreFileSilentStruct() : core::io::silent::ScoreFileSilentStruct
• ScoreFileSilentStructCreator() : core::io::silent::ScoreFileSilentStructCreator
• scorefunction() : core::pack::interaction_graph::SimpleInteractionGraph
• ScoreFunction() : core::scoring::ScoreFunction
• ScoreFunctionInfo() : core::scoring::ScoreFunctionInfo
• ScoreJumpFileSilentStruct() : core::io::silent::ScoreJumpFileSilentStruct
• ScoreJumpFileSilentStructCreator() : core::io::silent::ScoreJumpFileSilentStructCreator
• ScoreLessThanComparator() : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• scoreline_prefix() : core::io::silent::SilentStruct
• scores() : core::fragment::picking_old::vall::VallLibrarian , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::sequence::SequenceAlignment
• scores_present() : core::scoring::ScoreFunctionInfo
• scores_to_probs_() : core::sequence::SequenceProfile
• ScoreStructJSON() : core::io::raw_data::ScoreStructJSON
• ScoreStructText() : core::io::raw_data::ScoreStructText
• scoring() : core::scoring::Energies
• scoring_begin() : core::pose::Pose , core::scoring::Energies
• scoring_end() : core::pose::Pose , core::scoring::Energies
• scoring_matrix() : core::sequence::MatrixScoringScheme
• scoring_schemes() : core::sequence::CompositeScoringScheme
• ScoringManager() : core::scoring::ScoringManager
• ScoringScheme() : core::sequence::ScoringScheme
• ScoringSchemeFactory() : core::sequence::ScoringSchemeFactory
• sd() : core::scoring::constraints::BoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::HarmonicFunc , core::scoring::func::MinMultiHarmonicFunc
• sd_ang() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dih() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dis() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sdev() : core::scoring::constraints::BigBinConstraint
• sdf_type() : core::chemical::sdf::MolFileIOBond
• SDFParser() : core::chemical::sdf::SDFParser
• search_memb_center() : core::scoring::MembranePotential
• search_memb_normal() : core::scoring::MembranePotential
• secant_interpolation() : core::optimization::LineMinimizationAlgorithm
• secondary_structure_weights() : core::scoring::methods::EnergyMethodOptions
• SecondaryStructure() : core::fragment::SecondaryStructure
• SecondaryStructureEnergy() : core::scoring::methods::SecondaryStructureEnergy
• SecondaryStructurePotential() : core::scoring::SecondaryStructurePotential
• SecondaryStructureWeights() : core::scoring::SecondaryStructureWeights
• SecondLoop() : core::scoring::sc::MolecularSurfaceCalculator
• secstruct() : core::conformation::Conformation , core::fragment::FragData , core::fragment::SecondaryStructure , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pose::Pose , core::scoring::packing::PoseBalls
• SecStructGen() : core::fragment::picking_old::vall::gen::SecStructGen
• SecstructSRFD() : core::fragment::SecstructSRFD
• section_index() : core::fragment::picking_old::vall::VallResidue
• sections() : core::fragment::picking_old::vall::VallLibrary
• segments() : core::pose::datacache::SpecialSegmentsObserver
• select() : core::chemical::ResidueSelector
• select_chain_by_index() : core::pack::task::residue_selector::ChainSelector
• select_chain_by_pdb_chain_char() : core::pack::task::residue_selector::ChainSelector
• select_orient_atoms() : core::chemical::ResidueType , core::conformation::Residue
• select_residues() : core::chemical::ResidueTypeSet
• SelectedResPredicate() : core::scoring::SelectedResPredicate
• selector() : core::chemical::PatchCase , core::pack::task::operation::OperateOnResidueSubset
• Selector_AA() : core::chemical::Selector_AA
• Selector_CMDFLAG() : core::chemical::Selector_CMDFLAG
• Selector_MATCH_VARIANTS() : core::chemical::Selector_MATCH_VARIANTS
• Selector_NAME1() : core::chemical::Selector_NAME1
• Selector_NAME3() : core::chemical::Selector_NAME3
• Selector_NO_VARIANTS() : core::chemical::Selector_NO_VARIANTS
• Selector_PROPERTY() : core::chemical::Selector_PROPERTY
• Selector_UPPER_POSITION() : core::chemical::Selector_UPPER_POSITION
• Selector_VARIANT_TYPE() : core::chemical::Selector_VARIANT_TYPE
• selfmerge() : core::scoring::dssp::StrandPairingSet
• SemiRotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• send_to_stdout() : core::optimization::NumericalDerivCheckResult
• sep_ss() : core::scoring::packing::HolesParams
• seq() : core::sequence::CompositeSequence
• seq1() : core::sequence::DerivedSequenceMapping
• seq2() : core::sequence::DerivedSequenceMapping
• seq_from_file() : core::sequence::SequenceFactory
• seq_sep_type_from_name() : core::scoring::hbonds::HBondTypeManager
• seqid() : core::environment::FoldTreeSketch::Node
• seqpos() : core::conformation::Residue , core::fragment::Frame , core::fragment::NonContinuousFrame , core::io::PositionDdGInfo::PositionDdGInfo , core::io::rna::RDAT , core::pack::interaction_graph::RotamerDots , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::SequenceProfileConstraint
• seqs() : core::sequence::CompositeSequence
• sequence() : core::fragment::FragData , 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 , core::pose::Pose , core::sequence::Sequence
• Sequence() : core::sequence::Sequence
• sequence() : core::sequence::SequenceAlignment
• sequence_indices() : core::sequence::SequenceAlignment
• sequence_mapping() : core::sequence::SequenceAlignment
• sequence_matches() : core::conformation::Conformation
• sequence_profile() : core::scoring::constraints::SequenceProfileConstraint
• sequence_sep() : core::scoring::hbonds::HBEvalTuple
• SequenceAlignment() : core::sequence::SequenceAlignment
• SequenceAnnotation() : core::environment::SequenceAnnotation
• SequenceCoupling() : core::sequence::SequenceCoupling
• SequenceCouplingCreator() : core::sequence::SequenceCouplingCreator
• SequenceCreator() : core::sequence::SequenceCreator
• SequenceDependentRefEnergy() : core::scoring::methods::SequenceDependentRefEnergy
• SequenceFactory() : core::sequence::SequenceFactory
• SequenceMapping() : core::id::SequenceMapping
• SequenceProfile() : core::sequence::SequenceProfile
• SequenceProfileConstraint() : core::scoring::constraints::SequenceProfileConstraint
• SequenceProfileConstraintCreator() : core::scoring::constraints::SequenceProfileConstraintCreator
• SequenceProfileCreator() : core::sequence::SequenceProfileCreator
• SequenceRegistrator() : core::sequence::SequenceRegistrator< T >
• sequences() : core::io::rna::RDAT
• sequences_are_in_frame() : core::sequence::SequenceAlignment
• serialize() : core::grid::CartGrid< T >
• serialize_weights() : core::scoring::ScoreFunction
• set() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::MoveMap , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pose::datacache::ObserverCache , core::scoring::electron_density::ElectronDensity , core::scoring::EMapVector
• set_aa() : core::chemical::ResidueSelector
• set_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• set_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• set_active_restype_index() : core::pack::scmin::ResidueAtomTreeCollection
• set_adduct_flag() : core::chemical::ResidueType
• set_adp_strategy() : core::scoring::cryst::PhenixInterface
• set_all_chi() : core::conformation::Residue
• set_all_extra_parameters() : core::chemical::AtomType
• set_allocated() : core::graph::NegSpaceElement< T >
• set_allow_dof() : core::conformation::symmetry::SymDof
• set_allow_phosphate_virtualization() : core::pack::task::rna::RNA_ResidueLevelTask
• set_allow_scoring() : core::scoring::MembraneTopology
• set_allow_tmh_scoring() : core::scoring::MembraneTopology
• set_alpha() : core::pose::Pose
• set_alt_aa_offsets_from_edge() : core::pack::interaction_graph::PDNode
• set_alternate() : core::pack::interaction_graph::SimpleNode
• set_alternate_no_E_update() : core::pack::interaction_graph::SimpleNode
• set_alternate_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• set_amino_acid_types() : core::pack::interaction_graph::PDNode
• set_anchor_residue() : core::conformation::symmetry::SymmData
• set_angle() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_angle_atom() : core::scoring::methods::GoapRsdType
• set_annotations() : core::io::rna::RDAT
• set_antiparallel_weight() : core::scoring::SecondaryStructureWeights
• set_array() : core::graph::NegSpaceElement< T >
• set_array_size() : core::graph::ArrayPool< T >
• set_assign_state_to_all_nodes_immediately() : core::pack::annealer::RotamerAssigningAnnealer
• set_atmid() : core::scoring::methods::GoapRsdType
• set_atom_base() : core::chemical::ResidueType
• set_atom_type() : core::chemical::ResidueType
• set_auto_update() : core::scoring::NeighborList
• set_backbone_backbone_acceptor() : core::scoring::hbonds::HBondSet
• set_backbone_backbone_donor() : core::scoring::hbonds::HBondSet
• set_backbone_burial() : core::scoring::rna::data::RNA_DataInfo
• set_backbone_exposed() : core::scoring::rna::data::RNA_DataInfo
• set_backbone_heavyatom() : core::chemical::ResidueType
• set_background_residue_rotamer_dots() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• set_bb() : core::kinematics::MoveMap
• set_bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• set_bb_bbE() : core::pack::interaction_graph::SimpleEdge
• set_bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• set_bb_don_avail() : core::scoring::hbonds::HBondResidueMinData
• set_bb_true_range() : core::kinematics::MoveMap
• set_beta() : core::pose::Pose
• set_binname_i() : core::scoring::bin_transitions::BinTransitionData
• set_binname_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_binrange_i() : core::scoring::bin_transitions::BinTransitionData
• set_binrange_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_block_size() : core::graph::ArrayPool< T >
• set_bond_angle() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_bond_length() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_branch_atom() : core::scoring::methods::GoapRsdType
• set_bump_check() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• set_bump_overlap_factor() : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• set_c_repeat() : core::scoring::fiber_diffraction::FiberDiffractionOptions
• set_calculated() : core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo
• set_calculation_method() : core::scoring::sasa::SasaCalc
• set_careful_base_pair_classifier() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• set_cartesian() : core::pack::RTMin
• set_cartesian_bonded_linear() : core::scoring::methods::EnergyMethodOptions
• set_cartesian_bonded_parameters() : core::scoring::methods::EnergyMethodOptions
• set_center() : core::scoring::MembraneEmbed
• set_centroid() : core::import_pose::ImportPoseOptions
• set_chain_strings() : core::pack::task::residue_selector::ChainSelector
• set_chains() : core::io::silent::SilentStruct , core::pose::PDBInfo
• set_chains_whose_residues_are_separate_chemical_entities() : core::io::pdb::FileDataOptions
• set_changed() : core::scoring::FACTSResidueInfo
• set_charged_residues_map() : core::scoring::methods::PBLifetimeCache
• set_check_if_residues_are_Ctermini() : core::io::pdb::FileDataOptions
• set_check_if_residues_are_Ntermini() : core::io::pdb::FileDataOptions
• set_chi() : core::conformation::Residue , core::kinematics::MoveMap , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose
• set_chi_mean() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_chi_sd() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_chi_torsions() : core::io::silent::RNA_SilentStruct
• set_chi_true_range() : core::kinematics::MoveMap
• set_ciBR_only() : core::pack::annealer::FASTERAnnealer
• set_cif_files() : core::scoring::cryst::PhenixInterface
• set_comments() : core::io::rna::RDAT
• set_conformational_data() : core::scoring::methods::PBLifetimeCache
• set_conserved() : core::pose::datacache::PositionConservedResiduesStore
• set_constraints() : core::scoring::constraints::CstMinimizationData
• set_conventional_chains() : core::pose::full_model_info::FullModelParameters
• set_conventional_numbering() : core::pose::full_model_info::FullModelParameters
• set_coordinates() : core::fragment::BBTorsionSRFD
• set_coords() : core::io::silent::RNA_SilentStruct
• set_couplings() : core::pack::task::operation::SetRotamerCouplings
• set_crossover() : core::scoring::etable::count_pair::CountPairGeneric
• set_crystinfo() : core::pose::PDBInfo
• set_current() : core::pack::interaction_graph::SimpleNode
• set_current_distance() : core::scoring::loop_graph::LoopScoreInfo
• set_current_no_E_update() : core::pack::interaction_graph::SimpleNode
• set_cutoff_lr() : core::scoring::CenHBPotential
• set_cutoff_sr() : core::scoring::CenHBPotential
• set_d() : core::conformation::Residue , core::pack::scmin::ResidueAtomTreeCollection
• set_data() : core::scoring::electron_density::ElectronDensity , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• set_data_annotations() : core::io::rna::RDAT
• set_decoy_tag() : core::io::silent::SilentStruct
• set_default() : core::scoring::FACTSPotential , core::scoring::methods::GoapEnergy , core::scoring::TMscore
• set_defaults() : core::scoring::func::SOGFunc_Impl , core::scoring::sasa::SasaCalc
• set_delta() : core::pose::Pose
• set_density_sc_scale_byres() : core::scoring::methods::EnergyMethodOptions
• set_deriv_check_result() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• set_derivative_graph() : core::scoring::symmetry::SymmetricEnergies
• set_dihedral() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_disallow_quench() : core::pack::annealer::SimAnnealerBase
• set_dist_to_connect_point() : core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::GenericResidueConnectionData
• set_distance() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::task::residue_selector::NeighborhoodResidueSelector
• set_dof() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pose::Pose
• set_dof_moved() : core::conformation::Conformation
• set_dofs() : core::conformation::symmetry::SymmetryInfo
• set_edge() : core::scoring::rna::data::RNA_Datum
• set_edge_index() : core::pack::interaction_graph::DoubleLazyEdge
• set_edge_weight() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• set_effective_sequence_separation() : core::scoring::constraints::MultiConstraint
• set_elec_sigmoidal_die_params() : core::scoring::methods::EnergyMethodOptions
• set_energy_method_options() : core::scoring::ScoreFunction
• set_energy_state() : core::scoring::methods::PBLifetimeCache
• set_enumeration_shell() : core::scoring::FACTSResidueInfo
• set_epsilon() : core::pose::Pose
• set_equiv() : core::pack::rotamer_set::RotamerLinks
• set_errorfull_deltaE_threshold() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• set_etable() : core::scoring::ScoreFunction
• set_exclude_polar_atoms_by_charge() : core::scoring::sasa::SasaCalc
• set_exit_if_missing_heavy_atoms() : core::io::pdb::FileDataOptions
• set_explicit_hydrogen_included_radii_set() : core::scoring::sasa::SasaCalc
• set_extra_parameter() : core::chemical::AtomType
• set_extra_samples() : core::pack::rotamer_set::RotamerSet_
• set_farray_from_sso() : core::pose::datacache::SpecialSegmentsObserver
• set_fcen10() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• set_fcen12() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• set_fcen6() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• set_filename() : core::io::silent::SilentFileData
• set_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• set_first() : core::scoring::packstat::trace
• set_fixed_energies() : core::scoring::MinimizationGraph
• set_fixed_stub() : core::scoring::constraints::LocalCoordinateConstraint
• set_flat_score_multiply() : core::conformation::symmetry::SymmetryInfo
• set_focus() : core::pack::task::residue_selector::NeighborhoodResidueSelector
• set_focus_selector() : core::pack::task::residue_selector::NeighborhoodResidueSelector
• set_fold_tree() : core::io::silent::RNA_SilentStruct
• set_fold_tree_io() : core::import_pose::ImportPoseOptions
• set_force_bitflip() : core::io::silent::SilentStruct
• set_force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• set_fractions() : core::fragment::SecondaryStructure
• set_from_extra_data() : core::chemical::sdf::MolFileIOMolecule
• set_from_residue_list_string() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• set_from_residue_selector() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• set_full_model_parameters() : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• set_func() : core::scoring::loop_graph::LoopScoreInfo
• set_gamma() : core::pose::Pose
• set_gasteiger_atom_type() : core::chemical::ResidueType
• set_gasteiger_typeset() : core::chemical::ResidueType
• set_grid_spacing() : core::scoring::electron_density::ElectronDensityOptions
• set_half_width() : core::scoring::func::LinearPenaltyFunction
• set_handedness_score_flag() : core::scoring::SecondaryStructureWeights
• set_hbond_options() : core::scoring::hbonds::HBondSet
• set_hightemp() : core::pack::annealer::SimAnnealerBase
• set_icodes() : core::pose::PDBInfo
• set_icoor() : core::chemical::ResidueType
• set_id() : core::optimization::DOF_Node
• set_ideal_xyz() : core::chemical::ResidueType
• set_IGEdgeReweights() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• set_ignore_unrecognized_res() : core::io::pdb::FileDataOptions
• set_ignore_waters() : core::io::pdb::FileDataOptions
• set_ignore_zero_occupancy() : core::io::pdb::FileDataOptions
• set_implicit_hydrogen_included_radii_set() : core::scoring::sasa::SasaCalc
• set_in_range() : core::scoring::bin_transitions::BinTransitionData
• set_include_carbon_sulfer_only_in_hydrophobic_calc() : core::scoring::sasa::SasaCalc
• set_include_hydrogens_explicitly() : core::scoring::sasa::SasaCalc
• set_include_probe_radius_in_atom_radii() : core::scoring::sasa::SasaCalc
• set_include_probe_radius_in_calc() : core::scoring::sasa::SasaMethod
• set_index() : core::pack::task::residue_selector::ResidueIndexSelector
• set_index_and_owner() : core::graph::UEVertex< V, E >
• set_interfaces() : core::conformation::symmetry::SymmData
• set_job_data() : core::chemical::sdf::MolWriter
• set_jump() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::DownJumpSRFD , core::kinematics::AtomTree , core::kinematics::MoveMap , core::pack::task::residue_selector::JumpDownstreamSelector , core::pack::task::residue_selector::JumpUpstreamSelector , core::pose::Pose
• set_jump_atom_stub_id() : core::conformation::Conformation , core::kinematics::AtomTree
• set_jump_atoms() : core::kinematics::FoldTree
• set_jump_name() : core::conformation::symmetry::SymmetryInfo
• set_jump_now() : core::kinematics::AtomTree
• set_keep_input_protonation_state() : core::io::pdb::FileDataOptions
• set_landing_atom() : core::scoring::loop_graph::LoopScoreInfo
• set_landing_domain() : core::scoring::loop_graph::Loop
• set_landing_pos() : core::scoring::loop_graph::Loop
• set_length() : core::scoring::loop_graph::LoopScoreInfo
• set_line_continuation() : core::io::pdb::HeaderInformation
• set_links() : core::pack::task::operation::SetRotamerLinks
• set_localstrandpair_penalty() : core::scoring::SecondaryStructureWeights
• set_long_range_container() : core::scoring::Energies
• set_lower_connect_atom() : core::chemical::ResidueType
• set_lowtemp() : core::pack::annealer::SimAnnealerBase
• set_mainchain_atoms() : core::chemical::ResidueType
• set_mainchain_torsions() : core::io::silent::RNA_SilentStruct
• set_map_type() : core::scoring::cryst::PhenixInterface
• set_mapreso() : core::scoring::electron_density::ElectronDensityOptions
• set_matrix_entry() : core::scoring::bin_transitions::BinTransitionData
• set_max_context_neighbor_cutoff() : core::scoring::Energies
• set_max_frag_length() : core::fragment::FragSet
• set_max_pos() : core::fragment::FragSet
• set_max_rot_bumpenergy() : core::pack::rotamer_set::BumpSelector
• set_max_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_max_surface_deltaE() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• set_mean_and_stddev() : core::scoring::dna::DNA_BasePotential
• set_membrane() : core::import_pose::ImportPoseOptions
• set_membrane_info() : core::conformation::Conformation
• set_membrane_jump() : core::conformation::membrane::MembraneInfo
• set_memory_max_for_rpes() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• set_metal_bond_angle_constraint_multiplier() : core::import_pose::ImportPoseOptions
• set_metal_bond_dist_constraint_multiplier() : core::import_pose::ImportPoseOptions
• set_metal_bond_LJ_multiplier() : core::import_pose::ImportPoseOptions
• set_method_weights() : core::scoring::methods::EnergyMethodOptions , core::scoring::ScoreFunction
• set_mg_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• set_min_pos() : core::fragment::FragSet
• set_minimization_graph() : core::scoring::Energies
• set_missing_dens_as_jump() : core::io::pdb::FileDataOptions
• set_mm_atom_type() : core::chemical::ResidueType
• set_multicomponent_info() : core::conformation::symmetry::SymmetryInfo
• set_n_bins() : core::scoring::bin_transitions::BinTransitionData
• set_n_chi_bins() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• set_n_mainchain_torsions_i() : core::scoring::bin_transitions::BinTransitionData
• set_n_mainchain_torsions_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_name() : core::grid::CartGrid< T > , core::io::rna::RDAT
• set_name1() : core::chemical::ResidueSelector
• set_native_task() : core::pack::task::operation::ReplicateTask
• set_natoms() : core::scoring::hbonds::HBondResidueMinData
• set_natoms_for_residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• set_nblist() : core::scoring::Energies
• set_nbrs() : core::scoring::hbonds::HBondSet
• set_ncaa_rotlib_n_bin_per_rot() : core::chemical::ResidueType
• set_ncaa_rotlib_n_rotameric_bins() : core::chemical::ResidueType
• set_ncaa_rotlib_path() : core::chemical::ResidueType
• set_nchi() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_ncopies() : core::fragment::FragmentIO
• set_network_state() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• set_new_chain_order() : core::io::pdb::PDB_DReaderOptions
• set_new_conformation() : core::pose::Pose
• set_new_energies_object() : core::pose::Pose
• set_new_topology() : core::kinematics::AtomTree
• set_next() : core::graph::NegSpaceElement< T >
• set_nneighbors() : core::scoring::hbonds::HBondResidueMinData
• set_no_longer_perturbed() : core::pack::interaction_graph::FASTERNode
• set_no_optH() : core::import_pose::ImportPoseOptions
• set_non_main_chain_sugar_coords() : core::io::silent::RNA_SilentStruct
• set_noncanonical_connection() : core::conformation::Conformation
• set_nonideal() : core::pack::RTMin , core::pack::scmin::SCMinMinimizerMap
• set_nonrotameric_chi_bbdep_scoring_step_size() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• set_nonrotameric_chi_bbind_scoring_step_size() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• set_nonrotameric_chi_start_angle() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• set_normal() : core::scoring::MembraneEmbed
• set_not_to_quench() : core::pack::annealer::SimAnnealerBase
• set_nrchi_lower_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_periodicity() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• set_nrchi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_sample() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_start_angle() : core::chemical::ResidueType
• set_nrchi_symmetric() : core::chemical::ResidueType
• set_nrchi_upper_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nres() : core::scoring::electron_density::ElectronDensity
• set_nres_mono() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy
• set_nseq() : core::scoring::TMscoreStore
• set_nu() : core::kinematics::MoveMap
• set_nu_true_range() : core::kinematics::MoveMap
• set_num_background_nodes() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• set_num_background_residues() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_num_neighbors_counting_self_static() : core::graph::Node
• set_num_nodes() : core::graph::Graph , core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• set_num_residues_in_protein() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_num_sa_trajectories() : core::pack::annealer::FASTERAnnealer
• set_num_states_for_node() : core::pack::interaction_graph::InteractionGraphBase
• set_num_vertices() : core::graph::UpperEdgeGraph< V, E >
• set_number_of_energy_sum_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• set_numbering() : core::pose::PDBInfo
• set_nus() : core::kinematics::MoveMap
• set_obey_ENDMDL() : core::io::pdb::PDB_DReaderOptions
• set_observed_sufficient_boolean_true() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• set_offset() : core::id::SequenceMapping , core::io::rna::RDAT
• set_omega() : core::pose::Pose
• set_one_body_energy() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• set_one_body_energy_for_node_state() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• set_orbital_icoor_id() : core::chemical::ResidueType
• set_orbital_type_and_bond() : core::chemical::orbitals::AssignOrbitals
• set_orbital_xyz() : core::conformation::Residue
• set_order_by_energy() : core::import_pose::pose_stream::SilentFilePoseInputStream
• set_other_pose_list() : core::pose::full_model_info::FullModelInfo
• set_owner() : core::scoring::Energies
• set_pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• set_packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::task::residue_selector::ClashBasedRepackShellSelector
• set_pair_and_func_map() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• set_parallel_weight() : core::scoring::SecondaryStructureWeights
• set_parameter() : core::chemical::AtomType , core::chemical::MMAtomType , core::chemical::orbitals::OrbitalType , core::pose::full_model_info::FullModelParameters
• set_parameter_as_res_list() : core::pose::full_model_info::FullModelParameters
• set_parameter_as_res_list_in_pairs() : core::pose::full_model_info::FullModelParameters
• set_parameter_as_res_lists() : core::pose::full_model_info::FullModelParameters
• set_parent() : core::optimization::DOF_Node
• set_penalty() : core::scoring::MembraneEmbed
• set_peptoid_rotlib_n_bin_per_rot() : core::chemical::ResidueType
• set_peptoid_rotlib_n_rotameric_bins() : core::chemical::ResidueType
• set_peptoid_rotlib_path() : core::chemical::ResidueType
• set_perturbed_state() : core::pack::interaction_graph::FASTERNode
• set_pH() : core::scoring::methods::pHEnergy
• set_phi() : core::pose::Pose
• set_placeholder() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• set_polar_charge_cutoff() : core::scoring::sasa::SasaCalc
• set_polymeric_connection() : core::conformation::Conformation
• set_pos() : core::fragment::NonContinuousFrame
• set_pos_in_node_edgevector() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• set_pos_in_owners_list() : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• set_pose() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• set_pose_no_initialize() : core::pack::interaction_graph::SimpleInteractionGraph
• set_position() : core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity
• set_pr_idx() : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• set_preserve_crystinfo() : core::io::pdb::FileDataOptions
• set_preserve_header() : core::io::pdb::FileDataOptions
• set_prob() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::dunbrack::DunbrackRotamerSampleData
• set_probe_radius() : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• set_ProCorrection_values() : core::pack::interaction_graph::OnTheFlyEdge
• set_ProCorrection_values_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph
• set_property() : core::chemical::AtomType , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::orbitals::OrbitalType , core::chemical::ResidueProperties , core::chemical::ResidueSelector
• set_proton_chi() : core::chemical::ResidueType
• set_pseudobonds_to_residue() : core::conformation::Residue
• set_psi() : core::pose::Pose
• set_radii_set() : core::scoring::sasa::SasaMethod
• set_randomize_missing_coords() : core::io::pdb::FileDataOptions
• set_ranges_unmodifiable() : core::kinematics::MoveMap
• set_rb_center() : core::kinematics::Jump
• set_rb_delta() : core::kinematics::Jump
• set_rb_deltas() : core::kinematics::Jump
• set_reactivity() : core::io::rna::RDAT
• set_reactivity_error() : core::io::rna::RDAT
• set_read_annotation() : core::fragment::FragmentIO
• set_read_fold_tree() : core::import_pose::ImportPoseOptions
• set_read_link_records() : core::io::pdb::PDB_DReaderOptions
• set_read_pdb_header() : core::io::pdb::PDB_DReaderOptions
• set_recent_history_size() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• set_recent_history_sizes() : core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• set_record_source() : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• set_reference_energy() : core::pack::dunbrack::SingleLigandRotamerLibrary
• set_remember_unrecognized_res() : core::io::pdb::FileDataOptions
• set_remember_unrecognized_water() : core::io::pdb::FileDataOptions
• set_repack_list() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• set_res1_data() : core::scoring::hbonds::HBondResPairMinData
• set_res2_data() : core::scoring::hbonds::HBondResPairMinData
• set_res_high() : core::scoring::fiber_diffraction::FiberDiffractionOptions
• set_res_inds() : core::scoring::disulfides::DisulfMinData
• set_res_list() : core::pose::full_model_info::FullModelInfo
• set_res_low() : core::scoring::fiber_diffraction::FiberDiffractionOptions
• set_rescoords() : core::pack::scmin::ResidueAtomTreeCollection
• set_resid() : core::pack::rotamer_set::RotamerSet
• set_resid_2_connection_entry() : core::scoring::trie::RotamerTrieBase
• set_residue() : core::conformation::parametric::Parameters , core::fragment::FragData
• set_residue_as_background_residue() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_residue_numbers() : core::io::silent::SilentStruct
• set_residue_range_not_surface() : core::scoring::solid_surface::SurfaceEnergies
• set_residue_selector() : core::pack::task::residue_selector::NotResidueSelector
• set_residue_type_set() : core::import_pose::ImportPoseOptions
• set_residues_adjacent_for_subunit_pair() : core::pack::interaction_graph::SymmOnTheFlyEdge
• set_residues_adjacent_for_subunit_pair_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• set_residues_for_atom_name_remapping() : core::io::pdb::FileDataOptions
• set_resinfo() : core::pose::PDBInfo
• set_resnum() : core::pack::task::operation::AppendResidueRotamerSet
• set_restype_index() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• set_ring_conformation() : core::pose::Pose
• set_rna() : core::import_pose::ImportPoseOptions
• set_root_atom() : core::scoring::methods::GoapRsdType
• set_rotamer() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• set_rotamer_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• set_rotamer_dots_for_node_state() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• set_rotamer_dots_for_state() : core::pack::interaction_graph::HPatchNode< V, E, G >
• set_rotamer_operation() : core::pack::task::operation::AppendRotamer
• set_rotamer_set_operation() : core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamerSet
• set_rotamer_sets() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_RotamerLibraryName() : core::chemical::ResidueType
• set_rotamers() : core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• set_rotation() : core::kinematics::Jump , core::kinematics::RT
• set_rotation_matrix() : core::conformation::symmetry::SymmData
• set_rotwell() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_sa_length_scale() : core::pack::annealer::FASTERAnnealer
• set_sample_five_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• set_sample_rna_chi() : core::pack::task::rna::RNA_ResidueLevelTask
• set_sample_three_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• set_score() : core::fragment::FragData , core::optimization::Particle , core::scoring::motif::XformScore
• set_score_function() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• set_score_fxn() : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• set_score_multiply() : core::conformation::symmetry::SymmetryInfo
• set_score_multiply_from_subunit_factors() : core::conformation::symmetry::SymmetryInfo
• set_score_multiply_subunit() : core::conformation::symmetry::SymmData
• set_score_types() : core::scoring::methods::EnergyMethod
• set_score_weight() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• set_scorefunction() : core::pack::interaction_graph::SimpleInteractionGraph
• set_scorefxn_info() : core::scoring::Energies
• set_scoretypes() : core::scoring::etable::EtableEvaluator
• set_sd_ang() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_sd_dih() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_sd_dis() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_secstruct() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::SecstructSRFD , core::io::silent::RNA_SilentStruct , core::pose::Pose
• set_semirotameric_ncaa_rotlib() : core::chemical::ResidueType
• set_seq_sep_scale() : core::scoring::SecondaryStructureWeights
• set_seqpos() : core::io::rna::RDAT
• set_sequence() : core::fragment::FragData , core::fragment::SingleResidueFragData , core::io::rna::RDAT , core::io::silent::SimpleSequenceData
• set_sequence_profile() : core::scoring::constraints::SequenceProfileConstraint
• set_sequences() : core::io::rna::RDAT
• set_set_up_metal_bonds() : core::import_pose::ImportPoseOptions
• set_shadowing_atom() : core::chemical::ResidueType
• set_shared_silent_data() : core::io::silent::SilentFileData
• set_silent_file_data() : core::import_pose::pose_stream::SilentFilePoseInputStream
• set_silent_struct_type() : core::io::silent::SilentFileOptions
• set_size() : core::scoring::Energies
• set_skip_set_reasonable_fold_tree() : core::import_pose::ImportPoseOptions
• set_slide_info() : core::conformation::symmetry::SymmData
• set_slide_order() : core::conformation::symmetry::SymSlideInfo
• set_slide_type() : core::conformation::symmetry::SymSlideInfo
• set_SlideCriteriaType() : core::conformation::symmetry::SymSlideInfo
• set_SlideCriteriaVal() : core::conformation::symmetry::SymSlideInfo
• set_slope() : core::scoring::func::LinearPenaltyFunction
• set_sparse_aa_info() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• set_sparse_aa_info_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph
• set_ss_cutoff() : core::scoring::SecondaryStructureWeights
• set_ss_lowstrand() : core::scoring::SecondaryStructureWeights
• set_standard_stub_atoms() : core::fragment::DownJumpSRFD
• set_state_for_node() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• set_state_ind_for_this_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• set_stiffness() : core::scoring::dna::DNA_BasePotential
• set_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_strand_strand_weights() : core::scoring::methods::EnergyMethodOptions
• set_stretch_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_structure() : core::io::rna::RDAT
• set_structures() : core::io::rna::RDAT
• set_stub_atoms() : core::fragment::DownJumpSRFD
• set_stub_transform() : core::conformation::Conformation , core::kinematics::AtomTree
• set_subbin_type_i() : core::scoring::bin_transitions::BinTransitionData
• set_subbin_type_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_subunits() : core::conformation::symmetry::SymmData
• set_superenv() : core::environment::EnvCore
• set_surf() : core::scoring::packing::PoseBalls
• set_surface_score_weight() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_svn_version_and_url() : core::SVNVersion
• set_symm_transforms() : core::conformation::symmetry::SymmData
• set_symmetric_cenlist() : core::scoring::symmetry::SymmetricScoreFunction
• set_symmetric_residue_neighbors_hbonds() : core::scoring::symmetry::SymmetricScoreFunction
• set_symmetry_name() : core::conformation::symmetry::SymmData
• set_symmetry_type() : core::conformation::symmetry::SymmData
• set_tag_from_pose() : core::io::silent::SilentStruct
• set_takeoff_atom() : core::scoring::loop_graph::LoopScoreInfo
• set_takeoff_domain() : core::scoring::loop_graph::Loop
• set_takeoff_pos() : core::scoring::loop_graph::Loop
• set_target_function() : core::scoring::cryst::PhenixInterface
• set_task() : core::pack::rotamer_set::RotamerSets
• set_temperature() : core::pack::annealer::SimAnnealerBase
• set_theta() : core::conformation::Residue , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose
• set_throw_on_double_registration() : core::pack::task::residue_selector::ResidueSelectorFactory
• set_tmh_inserted() : core::scoring::MembraneTopology
• set_to_quench() : core::pack::annealer::SimAnnealerBase
• set_top_frag_num() : core::fragment::FragmentIO
• set_torsion() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::BBTorsionSRFD , core::pose::Pose
• set_torsion_angle() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_total_residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::solid_surface::SurfaceEnergies
• set_trace() : core::io::rna::RDAT
• set_translation() : core::kinematics::Jump , core::kinematics::RT
• set_translation_matrix() : core::conformation::symmetry::SymmData
• set_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• set_two_body_energy_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• set_type() : core::scoring::rna::data::RNA_Reactivity
• set_up_bin_cdfs() : core::scoring::bin_transitions::BinTransitionData
• set_up_bins() : core::scoring::bin_transitions::BinTransitionCalculator
• set_up_metal_bonds() : core::import_pose::ImportPoseOptions
• set_up_metal_constraints() : core::import_pose::ImportPoseOptions
• set_up_q() : core::scoring::saxs::SAXSEnergy
• set_up_spline_from_data() : core::scoring::nv::NVlookup
• set_up_subbins() : core::scoring::bin_transitions::BinTransitionData
• set_upper_connect_atom() : core::chemical::ResidueType
• set_use_big_polar_hydrogen() : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• set_use_nblist() : core::scoring::Energies
• set_use_ncaa_rotlib() : core::chemical::ResidueType
• set_use_peptoid_rotlib() : core::chemical::ResidueType
• set_use_symmetry() : core::conformation::symmetry::SymmetryInfo
• set_using() : core::scoring::methods::GoapRsdType
• set_valid() : core::fragment::FragData
• set_valid_energies() : core::io::silent::SilentStruct
• set_value() : core::scoring::rna::data::RNA_Reactivity
• set_variant_type() : core::chemical::ResidueProperties
• set_vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• set_verbose() : core::io::silent::SilentFileData , core::scoring::rna::RNA_TorsionPotential
• set_version() : core::io::rna::RDAT
• set_vertex_member_of_group() : core::pack::interaction_graph::InteractionGraphBase
• set_water_base_atm() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• set_weak_pointer_to_self() : core::kinematics::AtomTree
• set_weight() : core::scoring::CSA , core::scoring::DC , core::scoring::rna::data::RNA_Datum , core::scoring::ScoreFunction
• set_weight_if_zero() : core::scoring::ScoreFunction
• set_weights() : core::scoring::etable::EtableEvaluator
• set_well_depth() : core::scoring::func::LinearPenaltyFunction
• set_write_pdb_link_records() : core::io::pdb::FileDataOptions
• set_x_middle() : core::scoring::func::LinearPenaltyFunction
• set_xsel() : core::io::rna::RDAT
• set_xsel_refine() : core::io::rna::RDAT
• set_xyz() : core::conformation::Conformation , core::conformation::Residue , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose
• set_xyz_moved() : core::conformation::Conformation
• set_xyz_target() : core::scoring::constraints::LocalCoordinateConstraint
• set_zeta() : core::pose::Pose
• setAlgorithm() : core::scoring::cryst::PhenixInterface
• SetAtomicCharge() : core::chemical::SetAtomicCharge
• SetAtomType() : core::chemical::SetAtomType
• SetBackboneHeavyatom() : core::chemical::SetBackboneHeavyatom
• setBase() : core::grid::CartGrid< T >
• setDimensions() : core::grid::CartGrid< T >
• SetFormalCharge() : core::chemical::SetFormalCharge
• setFullOccupied() : core::grid::CartGrid< T >
• SetICoor() : core::chemical::SetICoor
• SetInterchangeabilityGroup_String() : core::chemical::SetInterchangeabilityGroup_String
• SetIO_String() : core::chemical::SetIO_String
• setK() : core::scoring::constraints::KofNConstraint
• SetMMAtomType() : core::chemical::SetMMAtomType
• setNames() : core::io::sequence_comparation::DesignContrast
• SetNbrAtom() : core::chemical::SetNbrAtom
• SetNbrRadius() : core::chemical::SetNbrRadius
• setNeighbors() : core::io::sequence_comparation::DesignContrast
• SetOrientAtom() : core::chemical::SetOrientAtom
• setparent() : core::kinematics::Node
• setPdbCodes() : core::io::sequence_comparation::DesignContrast
• SetPolymerConnectAtom() : core::chemical::SetPolymerConnectAtom
• setResLimits() : core::scoring::cryst::PhenixInterface
• SetRotamerCouplings() : core::pack::task::operation::SetRotamerCouplings
• SetRotamerLinks() : core::pack::task::operation::SetRotamerLinks
• sets() : core::graph::DisjointSets
• setScoreWindowContext() : core::scoring::electron_density::ElectronDensity
• setSCscaling() : core::scoring::electron_density::ElectronDensity
• SetSDFType() : core::chemical::Bond
• setSecStruct() : core::io::sequence_comparation::DesignContrast
• setTop() : core::grid::CartGrid< T >
• SetToType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• setTwinLaw() : core::scoring::cryst::PhenixInterface
• setup() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::NeighborList
• setup_approximate_vdw_radii() : core::scoring::AtomVDW
• setup_atom_map() : core::scoring::hbonds::HBondSet
• setup_atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_VDW_Energy
• setup_atom_ordering() : core::chemical::ResidueType
• setup_atom_tree() : core::conformation::Conformation
• setup_atom_weights() : core::scoring::methods::LKB_ResidueInfo
• setup_connectivity() : core::scoring::methods::GoapRsdType
• setup_constraints() : core::scoring::dna::DNATorsionPotential
• setup_csts() : core::scoring::constraints::FabConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues
• setup_d2_bounds() : core::scoring::methods::LK_BallEnergy
• setup_edge_counts() : core::kinematics::FoldTree
• setup_entropy_correction() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• setup_extra_patches() : core::io::silent::SilentFileData
• setup_extra_res() : core::io::silent::SilentFileData
• setup_fastscoring_first_time() : core::scoring::electron_density::ElectronDensity
• setup_for_derivatives() : core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::cryst::XtalMLEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::interface_::DDPscore , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPTerminiPenalty , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::vdwaals::VDW_Energy
• setup_for_derivatives_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::LK_BallEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore
• setup_for_derivatives_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• setup_for_fullatom() : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy
• setup_for_lr2benmeth_minimization_for_respair() : core::scoring::ScoreFunction
• setup_for_minimizing() : core::scoring::cryst::XtalMLEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• setup_for_minimizing_for_node() : core::scoring::ScoreFunction
• setup_for_minimizing_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy
• setup_for_minimizing_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::StackElecEnergy
• setup_for_minimizing_sr2b_enmeths_for_minedge() : core::scoring::ScoreFunction
• setup_for_packing() : core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::GenBornPotential , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::nv::NVscore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy
• setup_for_residue_pair_energies() : core::scoring::hbonds::HBondSet
• setup_for_scoring() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::cryst::XtalMLEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::methods::BurialEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::ProQPotential , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::ScoreFunction , core::scoring::SecondaryStructurePotential , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy
• setup_for_scoring_() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• setup_for_scoring_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::LK_BallEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore
• setup_for_scoring_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• setup_from_kill_hairpins_file() : core::scoring::SS_Killhairpins_Info
• setup_from_psipred() : core::scoring::SS_Killhairpins_Info
• setup_from_rotamer_dots() : core::pack::interaction_graph::InvRotamerDots
• setup_include_patches() : core::io::silent::SilentFileData
• setup_info_for_mg_calculation() : core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• setup_interpolation() : core::scoring::OmegaTether , core::scoring::Rama2BOffset
• setup_iterations() : core::pack::annealer::SimAnnealerBase
• setup_killhairpins() : core::scoring::SS_Killhairpins_Info
• setup_min_map() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• setup_other_poses() : core::io::silent::BinarySilentStruct
• setup_parallel_antiparallel_weights() : core::scoring::SecondaryStructureWeights
• setup_patterson_first_time() : core::scoring::electron_density::ElectronDensity
• setup_precise_zeta_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• setup_rotamer_couplings() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• setup_rotamer_links() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• setup_rots_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• setup_rsdtype() : core::scoring::methods::GoapRsdType
• setup_sasa_method() : core::scoring::sasa::SasaCalc
• setup_score_type_names() : core::scoring::ScoreTypeManager
• setup_sugar_ring_closure_constraints() : core::scoring::rna::RNA_SugarCloseEnergy
• setup_temperature() : core::pack::annealer::SimAnnealerBase
• setup_type_names() : core::scoring::hbonds::HBondTypeManager
• setup_weight_triple() : core::scoring::elec::FA_ElecEnergy
• setupBesselOrder() : core::scoring::fiber_diffraction::FiberDiffraction
• setupZones() : core::grid::CartGrid< T >
• setUseDensityInMinimizer() : core::scoring::electron_density::ElectronDensity
• setUseExactDerivatives() : core::scoring::electron_density::ElectronDensity
• setValue() : core::grid::CartGrid< T >
• setWindow() : core::scoring::electron_density::ElectronDensity
• sfd_req_1benmeths_begin() : core::scoring::MinimizationNode
• sfd_req_1benmeths_end() : core::scoring::MinimizationNode
• sfd_req_2benmeths_begin() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfd_req_2benmeths_end() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfs_req_1benmeths_begin() : core::scoring::MinimizationNode
• sfs_req_1benmeths_end() : core::scoring::MinimizationNode
• sfs_req_2benmeths_begin() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfs_req_2benmeths_end() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• SG_Dist_Func() : core::scoring::disulfides::SG_Dist_Func
• SGSG_Dihedral_Func() : core::scoring::disulfides::SGSG_Dihedral_Func
• ShapeComplementarityCalculator() : core::scoring::sc::ShapeComplementarityCalculator
• ShapeComplementarityCalculatorException() : core::scoring::sc::ShapeComplementarityCalculatorException
• SharedSilentData() : core::io::silent::SharedSilentData
• sheet_fraction() : core::fragment::SecondaryStructure
• sheets_from_dimers() : core::scoring::SecondaryStructurePotential
• shift() : core::conformation::membrane::Span , core::scoring::SmoothScoreTermCoeffs
• shift_by() : core::fragment::FragSet , core::fragment::Frame , core::fragment::NonContinuousFrame
• shift_span() : core::scoring::MembraneTopology
• shift_to() : core::fragment::Frame , core::fragment::NonContinuousFrame
• short_name() : core::chemical::carbohydrates::CarbohydrateInfo
• short_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• ShortestPathInFoldTree() : core::kinematics::ShortestPathInFoldTree
• ShortRangeTwoBodyEnergy() : core::scoring::methods::ShortRangeTwoBodyEnergy
• show() : core::chemical::Atom , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::ResidueType , core::chemical::RingConformerSet , core::conformation::Atom , core::conformation::membrane::EXCN_Illegal_Arguments , core::conformation::membrane::EXCN_Membrane , core::conformation::membrane::EXCN_Membrane_Bounds , core::conformation::membrane::EXCN_MembraneFoldTree , core::conformation::membrane::EXCN_NonMembrane , core::conformation::membrane::EXCN_Resource_Definition , core::conformation::membrane::EXCN_VirtualRsd , core::conformation::membrane::MembraneInfo , core::conformation::membrane::Span , core::conformation::membrane::SpanningTopology , core::conformation::Residue , core::conformation::symmetry::SymmData , core::environment::DofPassport , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::Frame , core::fragment::NonContinuousFrame , core::fragment::SecondaryStructure , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::id::SequenceMapping , core::kinematics::EXCN_InvalidFoldTree , core::kinematics::FoldTree , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pose::PDBInfo , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::CSA , core::scoring::DC , core::scoring::DipolarCoupling , core::scoring::Energies , core::scoring::etable::EtableOptions , core::scoring::func::Func , core::scoring::func::MixtureFunc , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBondSet , core::scoring::hbonds::Polynomial_1d , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::FreeDOF_Options , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::RDC , core::scoring::ResidualDipolarCoupling , core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::ScoreFunction
• show_all_atom_names() : core::chemical::ResidueType
• show_all_residue_tasks() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_available_silent_struct_types() : core::io::silent::SilentStructFactory
• show_classic() : core::fragment::FragData , core::fragment::Frame
• show_def() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint
• show_def_nopose() : core::scoring::constraints::NamedAtomPairConstraint
• show_definition() : core::scoring::constraints::BoundFunc , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc
• show_fragments() : core::fragment::Frame
• show_header() : core::fragment::Frame
• show_if_nonzero_weight() : core::scoring::EMapVector
• show_internals() : core::scoring::dssp::StrandPairing
• show_line() : core::scoring::ScoreFunction
• show_line_headers() : core::scoring::ScoreFunction
• show_nonzero() : core::scoring::EMapVector
• show_numbers() : core::scoring::constraints::ConstraintSet
• show_pos() : core::fragment::NonContinuousFrame
• show_pretty() : core::scoring::ScoreFunction
• show_rdc_values() : core::scoring::ResidualDipolarCoupling
• show_residue_connections() : core::conformation::Conformation
• show_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_tensor_matrix() : core::scoring::ResidualDipolarCoupling
• show_tensor_stats() : core::scoring::ResidualDipolarCoupling
• show_tensor_stats_nls() : core::scoring::ResidualDipolarCoupling
• show_total_headers() : core::scoring::Energies
• show_totals() : core::scoring::Energies
• show_values() : core::scoring::hbonds::Polynomial_1d
• show_violations() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CountViolFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::TopOutFunc
• show_weighted() : core::scoring::EMapVector
• showCachedScores() : core::scoring::electron_density::ElectronDensity
• shrink() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• shuffle_sBR_rotamers() : core::pack::annealer::FASTERAnnealer
• sibling() : core::scoring::trie::TrieNode< AT, CPDATA >
• sidechain_sidechain_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::TwoBodyEnergy
• sidechainAtoms_begin() : core::conformation::Residue
• SidechainStateAssignment() : core::pack::scmin::SidechainStateAssignment
• sigma() : core::scoring::SecondaryStructurePotential , core::sequence::ChemicalShiftSequence
• sigma1() : core::scoring::CSA
• sigma2() : core::scoring::CSA
• sigma3() : core::scoring::CSA
• sigmoid() : core::scoring::SmoothScoreTermCoeffs
• sigmoid_deps_dr() : core::scoring::etable::coulomb::Coulomb
• sigmoid_eps() : core::scoring::etable::coulomb::Coulomb
• SigmoidFunc() : core::scoring::func::SigmoidFunc
• sigmoidish_neighbor() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• SigmoidWeightedCenList() : core::scoring::SigmoidWeightedCenList< T >
• sign1() : core::scoring::DimerPairing
• sign2() : core::scoring::DimerPairing
• silent() : core::optimization::LineMinimizationAlgorithm , core::optimization::MinimizerOptions
• silent_energies() : core::io::silent::SilentStruct
• silent_file_data() : core::import_pose::pose_stream::SilentFilePoseInputStream
• SilentEnergy() : core::io::silent::SilentEnergy
• SilentFileData() : core::io::silent::SilentFileData
• SilentFileLoader() : core::io::silent::SilentFileLoader
• SilentFileLoaderCreator() : core::io::silent::SilentFileLoaderCreator
• SilentFileOptions() : core::io::silent::SilentFileOptions
• SilentFileOptionsCreator() : core::io::silent::SilentFileOptionsCreator
• SilentFilePoseInputStream() : core::import_pose::pose_stream::SilentFilePoseInputStream
• SilentStruct() : core::io::silent::SilentStruct
• SilentStructCreator() : core::io::silent::SilentStructCreator
• SilentStructFactory() : core::io::silent::SilentStructFactory
• SilentStructRegistrator() : core::io::silent::SilentStructRegistrator< T >
• SimAnnealerBase() : core::pack::annealer::SimAnnealerBase
• simple_tree() : core::kinematics::FoldTree
• SimpleDerivCheckResult() : core::optimization::SimpleDerivCheckResult
• SimpleEdge() : core::pack::interaction_graph::SimpleEdge
• SimpleInteractionGraph() : core::pack::interaction_graph::SimpleInteractionGraph
• SimpleNode() : core::pack::interaction_graph::SimpleNode
• SimplePDB() : core::scoring::packstat::SimplePDB
• SimplePDB_Atom() : core::scoring::packstat::SimplePDB_Atom
• SimpleScoringScheme() : core::sequence::SimpleScoringScheme
• SimpleSequenceCreator() : core::sequence::SimpleSequenceCreator
• SimpleSequenceData() : core::io::silent::SimpleSequenceData
• SingleLigandRotamerLibrary() : core::pack::dunbrack::SingleLigandRotamerLibrary
• SingleResidueCenrotLibrary() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• SingleResidueDunbrackLibrary() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• SingleResidueFragData() : core::fragment::SingleResidueFragData
• SingleResidueMultifunc() : core::optimization::SingleResidueMultifunc
• SingleResiduePeptoidLibrary() : core::pack::dunbrack::SingleResiduePeptoidLibrary
• SinXOverX() : core::scoring::saxs::SinXOverX
• SiteConstraint() : core::scoring::constraints::SiteConstraint
• SiteConstraintCreator() : core::scoring::constraints::SiteConstraintCreator
• SiteConstraintResidues() : core::scoring::constraints::SiteConstraintResidues
• SiteConstraintResiduesCreator() : core::scoring::constraints::SiteConstraintResiduesCreator
• size() : core::chemical::RingConformerSet , core::conformation::Conformation , core::conformation::PseudoBondCollection , core::fragment::FragData , core::fragment::FragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::Array0< T > , core::graph::EdgeList , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::AtomTree , core::kinematics::FoldTree , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::task::TaskFactory , core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , core::pose::MiniPose , core::pose::PDBPoseMap , core::scoring::CenListInfo , core::scoring::constraints::Constraints , core::scoring::constraints::MultiConstraint , core::scoring::constraints::ResidueConstraints , core::scoring::DenseEnergyContainer , core::scoring::dna::BasePartner , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::Energies , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::Hairpins , core::scoring::loop_graph::LoopCycle , core::scoring::MembraneEmbed , core::scoring::methods::LKB_ResiduesInfo , core::scoring::motif::Xfrag , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer , core::scoring::rna::data::RNA_DataInfo , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::saxs::DistanceHistogram , core::scoring::SigmoidWeightedCenList< T > , core::sequence::SequenceAlignment , core::sequence::SequenceProfile
• size1() : core::id::SequenceMapping
• size2() : core::id::SequenceMapping
• skip_set_reasonable_fold_tree() : core::import_pose::ImportPoseOptions
• SkipViolFunc() : core::scoring::func::SkipViolFunc
• Slice() : core::scoring::packstat::Slice
• slide() : core::conformation::UltraLightResidue
• slide_cutpoint() : core::kinematics::FoldTree
• slide_jump() : core::kinematics::FoldTree
• slope() : core::scoring::func::SigmoidFunc
• SmallAtNb() : core::scoring::SmallAtNb
• smallest_ring_size() : core::chemical::ResidueType
• smooth_etables() : core::scoring::etable::MembEtable
• smooth_etables_one_pair() : core::scoring::etable::Etable
• smooth_fa_elec() : core::scoring::etable::coulomb::Coulomb , core::scoring::methods::EnergyMethodOptions
• smooth_hb_env_dep() : core::scoring::hbonds::HBondOptions
• smooth_intensities() : core::scoring::electron_density::ElectronDensity
• smooth_nb() : core::scoring::packing::PoseBalls
• smooth_to_zero() : core::scoring::func::SOGFunc_Impl
• SmoothCenPairEnergy() : core::scoring::methods::SmoothCenPairEnergy
• SmoothEnvEnergy() : core::scoring::methods::SmoothEnvEnergy
• SmoothEnvPairPotential() : core::scoring::SmoothEnvPairPotential
• SmoothScoreTermCoeffs() : core::scoring::SmoothScoreTermCoeffs
• SoedingFunc() : core::scoring::func::SoedingFunc
• sog_cst_param() : core::scoring::func::SOGFunc_Impl
• SOGFunc() : core::scoring::func::SOGFunc
• SOGFunc_Impl() : core::scoring::func::SOGFunc_Impl
• sol_weight() : core::scoring::etable::EtableEvaluator
• solv1() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solv2() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solve_pb() : core::scoring::PoissonBoltzmannPotential
• solvF2BR() : core::scoring::FACTSResidueInfo
• solvF2d() : core::scoring::FACTSResidueInfo
• sort_by() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• sort_by_rms_and_energy() : core::scoring::motif::MotifHits
• sort_by_weighted_energy() : core::scoring::hbonds::HBondSet
• sort_R_function() : core::optimization::EItem
• sort_silent_scores() : core::io::silent::SilentStruct
• sp2_BAH180_rise() : core::scoring::hbonds::HBondOptions
• sp2_outer_width() : core::scoring::hbonds::HBondOptions
• spacegroup() : core::pose::CrystInfo
• Span() : core::conformation::membrane::Span
• span() : core::conformation::membrane::SpanningTopology
• span_begin() : core::scoring::MembraneTopology
• span_end() : core::scoring::MembraneTopology
• spanning() : core::conformation::membrane::SpanningTopology , core::scoring::MembraneEmbed
• spanning_topology() : core::conformation::membrane::MembraneInfo
• SpanningTopology() : core::conformation::membrane::SpanningTopology
• SparseMatrixIndex() : core::pack::interaction_graph::SparseMatrixIndex
• specialized_commands_exist_for_residue() : core::pack::task::ResfileContents
• SpecialSegmentsObserver() : core::pose::datacache::SpecialSegmentsObserver
• sphere() : core::scoring::packstat::CavityBall
• Sphere() : core::scoring::packstat::Sphere
• spherical() : core::kinematics::Stub , core::scoring::SecondaryStructurePotential
• spline_coeffs() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• spline_interpolation() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• SplineFunc() : core::scoring::func::SplineFunc
• SplineParameters() : core::scoring::etable::SplineParameters
• split() : core::grid::CartGrid< T >
• split_by_chain() : core::pose::Pose
• splitkv() : core::chemical::sdf::CtabV3000Parser
• square_distance() : core::scoring::EnergyEdge
• SquareWell2Func() : core::scoring::func::SquareWell2Func
• SquareWellFunc() : core::scoring::func::SquareWellFunc
• ss() : core::fragment::picking_old::vall::VallResidue , core::scoring::motif::Xfres
• ss1() : core::scoring::motif::ResPairMotif
• ss2() : core::scoring::motif::ResPairMotif
• ss_feature() : core::scoring::methods::ProQ_Energy
• SS_Killhairpins_Info() : core::scoring::SS_Killhairpins_Info
• ss_penalty() : core::fragment::picking_old::vall::eval::IdentityEval
• ss_penalty_initializer() : core::scoring::SecondaryStructurePotential
• ss_sc_feature() : core::scoring::methods::ProQ_Energy
• ss_str() : core::fragment::picking_old::vall::eval::IdentityEval
• sscomp() : core::scoring::motif::Xfrag
• ssdist_initializer() : core::scoring::SecondaryStructurePotential
• sspair() : core::scoring::SecondaryStructurePotential
• SSWeightParameters() : core::scoring::hbonds::SSWeightParameters
• st_atr() : core::scoring::etable::EtableEvaluator
• st_rep() : core::scoring::etable::EtableEvaluator
• st_sol() : core::scoring::etable::EtableEvaluator
• StackElecEnergy() : core::scoring::rna::StackElecEnergy
• start() : core::conformation::membrane::Span , core::fragment::Frame , core::kinematics::Edge , core::sequence::Sequence
• start_atom() : core::kinematics::Edge
• start_seq2() : core::sequence::DerivedSequenceMapping
• start_vertex() : core::chemical::RerootRestypeVisitor
• start_with_current() : core::pack::annealer::SimAnnealerBase
• starting_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• stat_motifs() : core::scoring::motif::MotifHits
• state_momento() : core::pack::scmin::SidechainStateAssignment
• state_unassigned() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• stddev() : core::scoring::dna::DNA_BasePotential
• steal() : core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::Frame , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD
• steal_def() : core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint
• steal_def_clone() : core::scoring::constraints::ConstraintSet
• steal_rotamer() : core::pack::rotamer_set::RotamerSubset
• stealBfactorsFromFile() : core::scoring::cryst::PhenixInterface
• steepness() : core::scoring::Membrane_FAEmbed
• step() : core::optimization::GA_Minimizer
• step_data() : core::optimization::SimpleDerivCheckResult
• stereochem() : core::chemical::carbohydrates::CarbohydrateInfo
• stiffness() : core::scoring::dna::DNA_BasePotential
• stop() : core::fragment::Frame , core::kinematics::Edge
• stop_atom() : core::kinematics::Edge
• store() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T > , core::indexed_structure_store::FragmentLookup
• store_active_energies() : core::scoring::EnergyEdge
• store_argv_in_file() : core::io::silent::SilentFileData
• store_classification() : core::io::pdb::HeaderInformation
• store_compound() : core::io::pdb::HeaderInformation
• store_curr_state_energy() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• store_current_derivatives() : core::optimization::LineMinimizationAlgorithm
• store_deposition_date() : core::io::pdb::HeaderInformation
• store_experimental_technique() : core::io::pdb::HeaderInformation
• store_experimental_techniques() : core::io::pdb::HeaderInformation
• store_header_record() : core::io::pdb::FileData
• store_heterogen_names() : core::io::pdb::FileData
• store_idCode() : core::io::pdb::HeaderInformation
• store_interaction_energy_first_node() : core::pack::interaction_graph::LazyEdge
• store_interaction_energy_second_node() : core::pack::interaction_graph::LazyEdge
• store_keywords() : core::io::pdb::HeaderInformation
• store_link_record() : core::io::pdb::FileData
• store_properties() : core::scoring::bin_transitions::BinTransitionCalculator
• store_record() : core::io::pdb::HeaderInformation
• store_residue_identities() : core::scoring::bin_transitions::BinTransitionCalculator
• store_title() : core::io::pdb::HeaderInformation
• store_top_energy() : core::pack::annealer::MultiCoolAnnealer
• store_trie() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• store_xyz() : core::scoring::FACTSResidueInfo
• str() : core::kinematics::Node , core::scoring::packstat::CavityBall
• str2cell() : core::io::rna::RDAT
• strand_fraction() : core::fragment::SecondaryStructure
• strand_pairing() : core::scoring::dssp::StrandPairingSet
• strand_pairing_set() : core::scoring::dssp::Dssp
• StrandPairing() : core::scoring::dssp::StrandPairing
• StrandPairingSet() : core::scoring::dssp::StrandPairingSet
• strands() : core::scoring::SS_Info
• Strands() : core::scoring::Strands
• strict_column_mode() : core::io::silent::SilentFileData
• stride_feature() : core::scoring::methods::ProQ_Energy
• string_list() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• string_properties() : core::chemical::ResidueProperties
• string_to_compound_token() : core::io::pdb::HeaderInformation
• string_to_experimental_technique() : core::io::pdb::HeaderInformation
• string_value() : core::io::silent::SilentEnergy
• StrongWolfe() : core::optimization::StrongWolfeLineMinimization
• StrongWolfeLineMinimization() : core::optimization::StrongWolfeLineMinimization
• structure() : core::io::rna::RDAT
• structure_has_moved() : core::scoring::Energies
• structure_list() : core::io::silent::SilentFileData
• structure_moved() : core::conformation::Conformation
• StructureDependentCalculator() : core::pose::metrics::StructureDependentCalculator
• structures() : core::io::rna::RDAT
• StructureStoreManager() : core::indexed_structure_store::StructureStoreManager
• Stub() : core::kinematics::Stub
• stub_atom() : core::chemical::Adduct , core::chemical::AtomICoor
• stub_atom1() : core::chemical::Adduct , core::chemical::AtomICoor , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• stub_atom1_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_atom2() : core::chemical::Adduct , core::chemical::AtomICoor , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• stub_atom2_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_atom3() : core::chemical::Adduct , core::chemical::AtomICoor , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• stub_atom3_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_defined() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_from_id() : core::conformation::Conformation , core::kinematics::AtomTree , core::pose::Pose
• StubID() : core::id::StubID
• stuck_in_network_state_loop() : core::pack::annealer::FASTERAnnealer
• sub_to_full() : core::pose::full_model_info::FullModelInfo
• SubArc() : core::scoring::sc::MolecularSurfaceCalculator
• subbin_cdf_i() : core::scoring::bin_transitions::BinTransitionData
• subbin_cdf_iplus1() : core::scoring::bin_transitions::BinTransitionData
• subbin_end_i() : core::scoring::bin_transitions::BinTransitionData
• subbin_end_iplus1() : core::scoring::bin_transitions::BinTransitionData
• subbin_start_i() : core::scoring::bin_transitions::BinTransitionData
• subbin_start_iplus1() : core::scoring::bin_transitions::BinTransitionData
• subbin_type_i() : core::scoring::bin_transitions::BinTransitionData
• subbin_type_iplus1() : core::scoring::bin_transitions::BinTransitionData
• SubCir() : core::scoring::sc::MolecularSurfaceCalculator
• SubDiv() : core::scoring::sc::MolecularSurfaceCalculator
• submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• submatrix_size() : core::pack::interaction_graph::DoubleLazyEdge
• subtract_neighbors_mass() : core::scoring::TenANeighborNode
• subtree_interaction_sphere_square_radius() : core::scoring::trie::TrieNode< AT, CPDATA >
• subunit_index() : core::conformation::symmetry::SymmetryInfo
• subunits() : core::conformation::symmetry::SymmetryInfo
• subunits_moved_by_jump() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• SuckerEnergy() : core::scoring::methods::SuckerEnergy
• sugar_edge_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• suggestRadius() : core::scoring::electron_density::ElectronDensity
• suiteness_bonus() : core::scoring::rna::RNA_EnergyMethodOptions
• sum() : core::grid::CartGrid< T > , core::scoring::EMapVector
• sum_deriv_contributions_for_atom_pair() : core::scoring::methods::LK_BallEnergy
• sum_deriv_contributions_for_atom_pair_one_way() : core::scoring::methods::LK_BallEnergy
• sum_energies() : core::scoring::etable::EtableEvaluator
• sum_of_neighbors_masses() : core::scoring::TenANeighborNode
• sum_profile() : core::scoring::methods::ProQ_Energy
• SumFunc() : core::scoring::func::SumFunc
• summarize_data() : core::scoring::bin_transitions::BinTransitionData
• summarize_stored_data() : core::scoring::bin_transitions::BinTransitionCalculator
• superenv() : core::environment::EnvCore
• surf() : core::scoring::packing::PoseBalls
• surf_feature() : core::scoring::methods::ProQ_Energy
• surface_exposed() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_score_weight() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• SurfaceBackgroundEdge() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• SurfaceBackgroundNode() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• SurfaceEdge() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• SurfaceEnergies() : core::scoring::solid_surface::SurfaceEnergies
• SurfaceEnergy() : core::pack::interaction_graph::SurfaceEnergy
• SurfaceInteractionGraph() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• SurfaceNode() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• SurfacePotential() : core::pack::interaction_graph::SurfacePotential
• SurfEnergy() : core::scoring::packing::SurfEnergy
• SurfVolEnergy() : core::scoring::packing::SurfVolEnergy
• svbksb() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• svdcmp() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• SVNVersion() : core::SVNVersion
• swap() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• swap_edge_energies() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph
• SymAtomTreeMinimizer() : core::optimization::symmetry::SymAtomTreeMinimizer
• SymAtomTreeMultifunc() : core::optimization::symmetry::SymAtomTreeMultifunc
• symbol2index() : core::util::ABEGOManager
• SymDof() : core::conformation::symmetry::SymDof
• symEnergy() : core::scoring::sym_e::symEnergy
• symm_info() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• SymmData() : core::conformation::symmetry::SymmData
• SymmDataOptions() : core::conformation::symmetry::SymmDataOptions
• SymmDataOptionsCreator() : core::conformation::symmetry::SymmDataOptionsCreator
• symmetric_transform() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetrical_allow_hbonds() : core::scoring::symmetry::SymmetricScoreFunction
• SymmetricConformation() : core::conformation::symmetry::SymmetricConformation
• SymmetricEnergies() : core::scoring::symmetry::SymmetricEnergies
• SymmetricLigandEnergy() : core::scoring::methods::SymmetricLigandEnergy
• SymmetricRotamerSet_() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• SymmetricRotamerSets() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• SymmetricScoreFunction() : core::scoring::symmetry::SymmetricScoreFunction
• symmetrize_by_intersection() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• symmetrize_by_union() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• Symmetry_Info() : core::conformation::symmetry::SymmetricConformation
• symmetry_info() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• SymmetryInfo() : core::conformation::symmetry::SymmetryInfo
• SymMinimizerMap() : core::optimization::symmetry::SymMinimizerMap
• SymmLinearMemEdge() : core::pack::interaction_graph::SymmLinearMemEdge
• SymmLinearMemNode() : core::pack::interaction_graph::SymmLinearMemNode
• SymmLinearMemoryInteractionGraph() : core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• SymmMinimalistEdge() : core::pack::interaction_graph::SymmMinimalistEdge
• SymmMinimalistInteractionGraph() : core::pack::interaction_graph::SymmMinimalistInteractionGraph
• SymmMinimalistNode() : core::pack::interaction_graph::SymmMinimalistNode
• SymmOnTheFlyEdge() : core::pack::interaction_graph::SymmOnTheFlyEdge
• SymmOnTheFlyInteractionGraph() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• SymmOnTheFlyNode() : core::pack::interaction_graph::SymmOnTheFlyNode
• SymSlideInfo() : core::conformation::symmetry::SymSlideInfo
• syn_G_potential_bonus() : core::scoring::rna::RNA_EnergyMethodOptions