Here is a list of all class members with links to the classes they belong to:

- s -

• S : core::chemical::gasteiger::GasteigerAtomTypeData
• s : core::optimization::lbfgs_iteration_data , core::scoring::fiber_diffraction::OneGaussianScattering , protocols::pockets::SmallMol
• s1() : protocols::fldsgn::topology::StrandPairing
• s1_ : protocols::fldsgn::topology::StrandPairing
• s1_end() : core::scoring::Hairpin
• s1_start() : core::scoring::Hairpin
• S2() : core::scoring::electron_density::ElectronDensity
• s2() : protocols::fldsgn::topology::StrandPairing , protocols::frag_picker::PhiPsiTalosIO
• s2_ : protocols::fldsgn::topology::StrandPairing
• s2_end() : core::scoring::Hairpin
• s2_start() : core::scoring::Hairpin
• S_ : core::scoring::ResidualDipolarCoupling
• s_ : protocols::normalmode::NormalMode
• s_atomic_env_outside_arom_ring_to_types_map : core::chemical::gasteiger::PossibleAtomTypesForAtom
• s_element_bonds_in_arom_ring_to_types_map : core::chemical::gasteiger::PossibleAtomTypesForAtom
• s_ik : protocols::cluster::Exemplar
• s_kk : protocols::cluster::DataPoint
• s_MaxElectronsInOrbital() : core::chemical::ElectronConfiguration
• s_mean : core::scoring::sc::_RESULTS
• s_median : core::scoring::sc::_RESULTS
• S_p_sp3 : core::scoring::orbitals::OrbitalsStatistics
• sa() : protocols::frag_picker::VallResidue
• sa_ : protocols::frag_picker::VallResidue
• SA_Energy() : core::scoring::methods::SA_Energy
• sa_inner_iterations_length_scale_ : core::pack::annealer::FASTERAnnealer
• sa_norm() : protocols::frag_picker::VallResidue
• sa_norm_ : protocols::frag_picker::VallResidue
• sa_scale_ : protocols::pack_daemon::FASTER_IG_Repacker
• sa_weight() : core::scoring::packing::HolesParams
• sa_weights_ : core::scoring::packing::HolesParams
• safe() : protocols::denovo_design::components::Segment
• safe_max_dis2 : core::scoring::etable::BaseEtableEnergy< Derived >
• safe_max_dis2_ : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::lkball::LK_BallEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::rna::RNA_LJ_BaseEnergy
• safe_root_ : protocols::forge::remodel::RemodelWorkingSet
• safe_secstruct() : protocols::jumping::JumpSample
• safely_append_polymer_residue_after_seqpos() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• safely_prepend_polymer_residue_before_seqpos() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• saferes_ : protocols::denovo_design::components::Segment
• salt_bridge_total_ : protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• saltbridge_correction_ : core::scoring::FACTSPotential
• SaltBridgeCalculator() : protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• SaltBridgeFeatures() : protocols::features::SaltBridgeFeatures
• SaltBridgeFeaturesCreator() : protocols::features::SaltBridgeFeaturesCreator
• same() : protocols::jd2::InnerJob , protocols::jd3::InnerLarvalJob , protocols::simple_moves::MinimalRotamer
• same_build_resids_for_all_csts_ : protocols::match::Matcher
• same_chain() : protocols::frag_picker::FragmentCandidate
• same_chain_prev_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• same_chi() : protocols::simple_moves::MinimalRotamer
• same_edge() : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• same_nonideal_geometry() : protocols::simple_moves::MinimalRotamer
• same_peak() : protocols::noesy_assign::CrossPeak
• same_residue_type() : protocols::simple_moves::MinimalRotamer
• same_strand_ : protocols::jumping::SameStrand , protocols::jumping::SheetBuilder
• same_type_as_me() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::id::SequenceMapping , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::aa_composition_energy::AACompositionConstraint , 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::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::Energies , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , 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::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::methods::LK_SigmoidalFunc , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies , core::sequence::DerivedSequenceMapping , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::environment::ProtectedConformation , protocols::jumping::ChainbreakDistFunc , protocols::pockets::EggshellGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketConstraint , protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• SameChiBinComboGrouper() : protocols::match::output::SameChiBinComboGrouper
• SamePose() : protocols::forge::remodel::RemodelMover
• SameRotamerComboGrouper() : protocols::match::output::SameRotamerComboGrouper
• SameSequenceAndDSPositionGrouper() : protocols::match::output::SameSequenceAndDSPositionGrouper
• SameSequenceGrouper() : protocols::match::output::SameSequenceGrouper
• SameSign : protocols::ligand_docking::rdf::RDFBase
• SameStrand() : protocols::jumping::SameStrand
• sample_all_conformers() : protocols::simple_moves::RingConformationMover
• sample_all_conformers_ : protocols::simple_moves::RingConformationMover
• sample_all_o2prime_ : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_alternative_chain_connection() : protocols::farna::movers::RNA_JumpMover
• sample_bb_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_beta() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• sample_beta_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• sample_both_sugar_base_rotamer() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• sample_both_sugar_base_rotamer_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• sample_by_monte_carlo_internal() : protocols::stepwise::monte_carlo::mover::AddMover
• sample_by_swa() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::FromScratchMover
• sample_cis_omega() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• sample_five_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• sample_five_prime_phosphate_ : core::pack::task::rna::RNA_ResidueLevelTask
• sample_index_ : protocols::toolbox::task_operations::MutationSetDesignOperation
• sample_level() : core::pack::task::operation::RotamerExplosion , protocols::match::upstream::SampleStrategyData
• sample_level_ : core::pack::task::operation::RotamerExplosion , protocols::match::upstream::SampleStrategyData
• sample_loops() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• sample_lower_nucleoside_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_near_a_form_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_near_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• sample_near_o2prime_torsion() : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_near_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• sample_nonpivot_torsions_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sample_nucleoside_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• sample_nucleoside_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• sample_nucleoside_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• sample_o2prime_hydrogen() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• sample_omega_for_pre_prolines_ : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• sample_omega_recursively() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• sample_ONLY_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sample_ONLY_multiple_virtual_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sample_orbital_frame() : protocols::magnesium::MgOrbitalFrameFinder
• sample_pc : protocols::flexpep_docking::FlexPepDockingFlags
• sample_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• sample_protein_linkage_ : protocols::carbohydrates::LinkageConformerMover
• sample_proton_chi() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• sample_proton_chi_ : core::pack::task::ResidueLevelTask_
• sample_range_large_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_range_small_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_res() : core::pose::full_model_info::FullModelInfo
• sample_residues_recursively() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• sample_rna_chi() : core::pack::task::rna::RNA_ResidueLevelTask
• sample_rna_chi_ : core::pack::task::rna::RNA_ResidueLevelTask
• sample_rotwells_unif_ : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• sample_scorefxn_ : protocols::stepwise::modeler::StepWiseModeler
• sample_sd_ : protocols::carbohydrates::LinkageConformerMover
• sample_strategy_for_chi() : protocols::match::upstream::BuildSet
• sample_strategy_for_chi_ : protocols::match::upstream::BuildSet
• sample_sugar : protocols::stepwise::modeler::rna::sugar::SugarModeling
• sample_suite_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• sample_three_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• sample_three_prime_phosphate_ : core::pack::task::rna::RNA_ResidueLevelTask
• sample_type_ : protocols::enzdes::DiffAtomSasaFilter , protocols::simple_moves::GenericMonteCarloMover
• sample_types() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_moves::GenericMonteCarloMover
• sample_types_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_moves::GenericMonteCarloMover
• sample_upper_nucleoside_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_virtual_sugar_string_list_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• sample_weight_const_ : protocols::loophash::LoopHashMoverWrapper
• sample_weight_str_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• sample_zero_probs_at() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• SampleApplier() : protocols::stepwise::screener::SampleApplier
• sampled_space_file_ : protocols::ligand_docking::Transform
• sampled_structures_ : protocols::simple_moves::CombinePoseMover
• sampled_sugar_index() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• SampleGrid() : protocols::magnesium::SampleGrid
• sampler_ : protocols::docking::TemperedDocking , protocols::match::upstream::ProteinUpstreamBuilder , protocols::nonlocal::Chunk , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::StepWiseSampleAndScreen
• sampler_assert_no_virt_sugar_sampling() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_assert_no_virt_sugar_sampling_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_beta_rotamer() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_beta_rotamer_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_epsilon_rotamer() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_epsilon_rotamer_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_include_torsion_value_in_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_include_torsion_value_in_tag_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::screener::TagDefinition
• sampler_max_centroid_distance() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_max_centroid_distance_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_movemap_union_ : protocols::simple_moves::BBDihedralSamplerMover
• sampler_num_pose_kept() : protocols::stepwise::options::StepWiseBasicOptions
• sampler_num_pose_kept_ : protocols::stepwise::options::StepWiseBasicOptions
• sampler_perform_phosphate_pack() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_perform_phosphate_pack_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_silent_file() : protocols::stepwise::options::StepWiseBasicOptions
• sampler_silent_file_ : protocols::stepwise::options::StepWiseBasicOptions
• sampler_torsion_types_ : protocols::simple_moves::BBDihedralSamplerMover
• sampler_try_sugar_instantiation() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_try_sugar_instantiation_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• samplers_ : protocols::simple_moves::BBDihedralSamplerMover
• samples() : protocols::helical_bundle::PerturbBundleOptions , protocols::match::upstream::DunbrackSCSampler , protocols::match::upstream::ProteinSCSampler
• samples_ : core::chemical::AddProtonChi , core::pack::rotamer_set::ContinuousRotamerSet , protocols::helical_bundle::PerturbBundleOptions
• SampleStrategyData() : protocols::match::upstream::SampleStrategyData
• SampleTiltAngles() : protocols::membrane::benchmark::SampleTiltAngles
• sampling_chunk_ : protocols::hybridization::ChunkTrialMover
• sampling_cutoff_ : protocols::antibody::CDRSetOptions
• sampling_data() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT
• sampling_data_ : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT
• sampling_data_setup() : core::scoring::carbohydrates::CHIEnergyFunction
• sampling_fold_tree() : protocols::abinitio::KinematicControl
• sampling_fold_tree_ : protocols::abinitio::KinematicControl
• sampling_id_for_current_rotamer() : core::pack::rotamer_set::ContinuousRotamerSet
• sampling_mode_ : protocols::matdes::SymDofMover
• sampling_protocol() : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicTaskControl
• sampling_protocol_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicTaskControl
• sampling_score_fxn_ : protocols::residue_optimization::MetapatchEnumeration
• sampling_step_size_ : protocols::simple_moves::bb_sampler::SugarBBSampler
• sampling_successful() : protocols::stepwise::modeler::StepWiseModeler
• sampling_temperature() : protocols::simple_moves::sidechain_moves::SidechainMover
• sampling_temperature_ : protocols::simple_moves::sidechain_moves::SidechainMover
• sampling_type_ : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• samplingrot_offsets_ : core::pack::rotamer_set::ContinuousRotamerSet
• sandboxed_copy() : protocols::environment::ClientMover
• SandwichFeatures() : protocols::features::strand_assembly::SandwichFeatures
• SandwichFeaturesCreator() : protocols::features::strand_assembly::SandwichFeaturesCreator
• SandwichFragment() : protocols::features::strand_assembly::SandwichFragment
• SaneMinMover() : protocols::simple_moves::SaneMinMover
• sanity_check() : core::conformation::symmetry::SymmData , core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• sasa() : core::scoring::FACTSResidueInfo , core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere
• SASA : protocols::analysis::PerResidueInterfaceData
• sasa() : protocols::features::helixAssembly::HelicalFragment
• sasa_ : core::pack::interaction_graph::RotamerDots , core::scoring::FACTSResidueInfo
• Sasa_ : protocols::analysis::InterfaceAnalyzerMover
• sasa_ : protocols::features::helixAssembly::HelicalFragment
• sasa_arrays_initialized_ : core::pack::interaction_graph::RotamerDots
• sasa_calc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• sasa_core() : core::select::util::SelectResiduesByLayer , protocols::flxbb::LayerDesignOperation
• sasa_cutoff_ : protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::simple_moves::ConsensusDesignMover
• sasa_filter_ : protocols::features::helixAssembly::HelixBundleFeatures , protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• sasa_for_cc_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• sasa_is_current_ : core::pack::interaction_graph::RotamerDots
• sasa_surface() : core::select::util::SelectResiduesByLayer , protocols::flxbb::LayerDesignOperation
• sasa_threshold_ : protocols::simple_filters::ChiWellRmsdEvaluator
• SasaCalc() : core::scoring::sasa::SasaCalc
• SasaCalculator2() : core::pose::metrics::simple_calculators::SasaCalculator2
• SasaCalculatorLegacy() : core::pose::metrics::simple_calculators::SasaCalculatorLegacy
• sasaF2() : core::scoring::FACTSResidueInfo
• sasaF2_ : core::scoring::FACTSResidueInfo
• SasaMethod() : core::scoring::sasa::SasaMethod
• SasaOptions() : core::scoring::packstat::SasaOptions
• SasaResult() : core::scoring::packstat::SasaResult
• satellite_suites : core::pose::rna::RNA_SuiteName
• satisfaction_cutoff() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• satisfies() : protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::GlobalRequirement , protocols::sewing::sampling::requirements::IntraSegmentRequirement , protocols::sewing::sampling::requirements::RequirementSet , protocols::sewing::sampling::requirements::ResidueRetentionRequirement , protocols::sewing::sampling::requirements::SegmentDsspRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement
• save_all_in_one() : protocols::toolbox::KClusterData
• save_all_solutions_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• save_archive() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• save_archive_time_interval_ : protocols::jd2::archive::ArchiveManager
• save_best_exemplars() : protocols::cluster::APCluster
• save_binary() : protocols::cluster::APCluster
• save_candidates() : protocols::frag_picker::FragmentPicker
• save_cluster_tree() : protocols::toolbox::KClusterData
• save_data() : core::io::rna::RDAT
• save_data_with_idx() : core::io::rna::RDAT
• save_db() : protocols::loophash::LoopHashLibrary
• save_decoys() : protocols::jd2::archive::ArchiveBase
• 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::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborIterator
• save_fragments() : protocols::frag_picker::FragmentPicker
• save_in_jump_library() : protocols::farna::libraries::RNA_JumpLibrary
• save_into_pose() : protocols::denovo_design::components::StructureData
• save_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover
• save_momento() : core::pack::scmin::ResidueAtomTreeCollection
• save_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• save_MSAcst_file() : protocols::simple_moves::StructProfileMover
• save_pending_decoys() : protocols::abinitio::HedgeArchive
• save_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• save_phi_psi_omega_over_loop_residues() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• save_pose_as_submotif() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• save_remarks_to_datacache() : protocols::denovo_design::components::StructureData
• save_res_lists_to_chain_connections_and_clear() : protocols::farna::setup::RNA_DeNovoParameters
• save_scalar_variable() : protocols::pack_daemon::DynamicAggregateFunction
• save_state() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• save_state_auto() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• save_state_interval_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• save_status() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase
• save_times() : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• save_times_ : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• save_to_file() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeCentroid , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• save_trial_number_to_checkpoint() : protocols::simple_moves::GenericMonteCarloMover
• save_vector_variable() : protocols::pack_daemon::DynamicAggregateFunction
• SaveAndRetrieveSidechains() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• saved_accept_file_name() : protocols::simple_moves::GenericMonteCarloMover
• saved_accept_file_name_ : protocols::simple_moves::GenericMonteCarloMover
• saved_bb_constraints_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• saved_coord_constraints_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_ft_ : protocols::hybridization::HybridizeFoldtreeDynamic
• saved_input_pose_ : protocols::protein_interface_design::PatchdockReader
• saved_input_tag_ : protocols::protein_interface_design::PatchdockReader
• saved_n_residue_ : protocols::hybridization::HybridizeFoldtreeDynamic
• saved_native_pose_ : protocols::protein_interface_design::PatchdockReader
• saved_native_tag_ : protocols::protein_interface_design::PatchdockReader
• saved_placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• saved_pose_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_prevent_repacking_ : protocols::protein_interface_design::movers::PlaceStubMover
• saved_state_poses_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• saved_structs_ : protocols::jd2::SilentFileJobOutputter
• saved_stub_sets_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_transformations_ : protocols::protein_interface_design::PatchdockReader
• saved_trial_number_file() : protocols::simple_moves::GenericMonteCarloMover
• saved_trial_number_file_ : protocols::simple_moves::GenericMonteCarloMover
• saveGDB() : protocols::sparta::GDB
• SavePoseConstraintToFileFilter() : protocols::simple_filters::SavePoseConstraintToFileFilter
• SavePoseMover() : protocols::rosetta_scripts::SavePoseMover
• SaveResfileToDiskFilter() : protocols::simple_filters::SaveResfileToDiskFilter
• saxs_score_variant_ : core::scoring::saxs::SAXSEnergy
• 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
• SAXSScoreFilter() : protocols::simple_filters::SAXSScoreFilter
• sBR() : core::pack::annealer::FASTERAnnealer
• sBR_ : core::pack::interaction_graph::FASTERInteractionGraph
• sBR_limit_ : core::pack::annealer::FASTERAnnealer
• sBR_rotamers_ : core::pack::annealer::FASTERAnnealer
• sc : core::scoring::sc::_RESULTS
• sc_ : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid
• 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_bounding_spheres_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• sc_H_orbital() : core::scoring::orbitals::OrbitalsStatistics
• sc_hbond_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• sc_interface_builder_ : protocols::ligand_docking::MoveMapBuilder
• sc_interface_padding_ : protocols::ligand_docking::LigandBaseProtocol
• sc_min() : protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy
• sc_min_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• sc_min_only : protocols::simple_moves::ShakeStructureMover
• SC_ONLY : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• sc_only() : protocols::hotspot_hashing::HotspotStubSet , protocols::simple_filters::TaskAwareSASAFilter
• sc_only_ : protocols::hotspot_hashing::HotspotStubSet , protocols::simple_filters::TaskAwareSASAFilter
• sc_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• sc_prob_ : protocols::backrub::BackrubProtocol
• sc_prob_uniform_ : protocols::backrub::BackrubProtocol
• sc_prob_withinrot_ : protocols::backrub::BackrubProtocol
• sc_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• SC_SC_EnergyInvoker() : core::scoring::etable::SC_SC_EnergyInvoker< Evaluator >
• sc_scale_ : protocols::cryst::LoadDensityMapMover
• sc_scale_byres_ : core::scoring::electron_density::FastDensEnergy
• SC_scaling_ : core::scoring::electron_density::ElectronDensity
• sc_value : protocols::analysis::InterfaceData
• SC_Whole_EnergyInvoker() : core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator >
• scaf_name() : protocols::match::output::PDBWriter
• scaf_name_ : protocols::match::output::PDBWriter
• scaffold_build_id() : protocols::match::Hit , protocols::match::upstream_hit
• scaffold_fragment_data : protocols::motif_grafting::movers::MotifMatch
• scaffold_match() : protocols::hotspot_hashing::HotspotStub
• scaffold_movemap() : protocols::grafting::AnchoredGraftMover
• scaffold_movemap_ : protocols::grafting::AnchoredGraftMover
• scaffold_status_ : protocols::hotspot_hashing::HotspotStub
• ScaffoldBuildPoint() : protocols::match::upstream::ScaffoldBuildPoint
• scaffoldHigh : protocols::motif_grafting::movers::motif2scaffold_indexes
• scaffoldLow : protocols::motif_grafting::movers::motif2scaffold_indexes
• ScaffoldRotamerPair : protocols::match::output::UpstreamHitCacher
• ScaffoldRotamerTuple : protocols::match::output::UpstreamHitCacher
• scafrot_pair_for_conf_ : protocols::match::output::UpstreamHitCacher
• scalar_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• scalar_expressions_ : protocols::pack_daemon::DynamicAggregateFunction
• scalar_variable_names_dec_line_ : protocols::pack_daemon::DynamicAggregateFunction
• ScalarWeightedFunc() : core::scoring::func::ScalarWeightedFunc
• scale() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• scale_axis_stagger() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scale_axis_stagger_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scale_dna_torsion_sd_ : core::scoring::dna::DNATorsionPotential
• scale_dna_torsion_tether_ : core::scoring::dna::DNATorsionPotential
• scale_dynamic_ : protocols::normalmode::NormalModeRelaxMover
• scale_factor() : core::scoring::GenBornResidueInfo , protocols::frag_picker::SidechainContactDistCutoff , protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scale_factor_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::GenBornResidueInfo , protocols::frag_picker::SidechainContactDistCutoff , protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scale_inneriterations() : core::pack::annealer::SimAnnealerBase
• scale_outeriterations() : core::pack::annealer::SimAnnealerBase
• scale_rna_torsion_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• scale_rna_torsion_tether_ : core::scoring::rna::RNA_SugarCloseEnergy
• scale_target_proximity_to_other_conformations() : protocols::enzdes::EnzdesFlexibleRegion
• scale_target_proximity_to_starting_conformation() : protocols::enzdes::EnzdesFlexibleRegion
• scale_temp_cycles_ : protocols::loop_modeling::LoopProtocol
• ScaleAnnealerTemperatureOperation() : protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scaled_logodds_profile_ : core::scoring::methods::ProQ_Energy
• scaleIntensities() : core::scoring::electron_density::ElectronDensity
• ScaleMapIntensities() : protocols::electron_density::ScaleMapIntensities
• scaling() : protocols::protein_interface_design::movers::SetTemperatureFactor
• scaling_ : protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_moves::FavorSequenceProfile
• scan_magnesiums() : protocols::magnesium::MgScanner
• scan_output_and_setup_to_receive() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• scan_res_ : protocols::magnesium::SampleGrid
• scanner_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• scc_ : protocols::simple_filters::ShapeComplementarityFilter
• scCD_ : core::scoring::methods::ProClosureEnergy
• SCdisplay_state : protocols::viewer::GraphicsState
• scfxn_ : protocols::features::DatabaseJobInputter , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::StructureScoresFeatures , protocols::rotamer_recovery::RotamerRecoveryMover
• scfxn_name_ : protocols::features::ScoreFunctionFeatures
• scfxn_rules_for_energy() : core::scoring::orbitals::OrbitalsScore
• scfxn_rules_for_weight() : core::scoring::orbitals::OrbitalsScore
• sch_stage_ : protocols::mpi_refinement::MPI_Refine_Master
• scheduled_ : protocols::md::MDBase
• Scheduler() : protocols::mpi_refinement::Scheduler
• scheduler_ : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• schema() : protocols::features::FeaturesReporter
• scheme_file_ : protocols::antibody::AntibodyNumberingParser
• scheme_types_ : core::sequence::ScoringSchemeFactory
• SchemePlaceMotifsMover() : protocols::matdes::SchemePlaceMotifsMover
• schemes_defined_ : protocols::antibody::AntibodyNumberingParser
• scmin_ : protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scmin_mover_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• scmin_numerical_derivative_check() : core::pack::scmin::SCMinMultifunc
• scminmap_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• SCMinMinimizerMap() : core::pack::scmin::SCMinMinimizerMap
• SCMinMultifunc() : core::pack::scmin::SCMinMultifunc
• scNV_ : core::scoring::methods::ProClosureEnergy
• score() : core::fragment::FragData , core::fragment::picking_old::vall::scores::VallFragmentScore , core::optimization::Particle , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::aa_composition_energy::SequenceConstraint , 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::NamedDihedralConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::DimerPairing , core::scoring::dna::DirectReadoutPotential , core::scoring::mm::MMBondAngleScore , core::scoring::mm::MMBondLengthScore , core::scoring::mm::MMLJEnergyTable , core::scoring::mm::MMLJScore , core::scoring::mm::MMTorsionScore , core::scoring::motif::ResPairMotif
• Score : core::scoring::motif::XformScore
• score : core::scoring::packing::HolesResult , 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 , protocols::abinitio::IterativeBase , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::filters::Filter , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::BFactor , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::ConstScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::DisulfideIdentity , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SequenceIdentity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::hybridization::TMalign , protocols::jd2::archive::EvaluatedArchive , protocols::loophash::MPI_LoopHashRefine , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::MatchEvaluator , protocols::mpi_refinement::MPI_Refinement , protocols::nonlocal::SmoothPolicy::Candidate , protocols::pmut_scan::AlterSpecDisruptionDriver , protocols::pmut_scan::PointMutScanDriver , protocols::pockets::PocketConstraint , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::rbsegment_relax::SequenceShiftMover , protocols::residue_optimization::MetapatchEnumeration , protocols::sewing::Hasher , protocols::sewing::scoring::AssemblyScoreFunction , protocols::sewing::scoring::AssemblyScorer , protocols::sewing::scoring::BlosumScorer , protocols::sewing::scoring::ClashScorer , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::PartnerMotifScorer , protocols::sic_dock::CBScore , protocols::sic_dock::CBScoreVisitor , protocols::sic_dock::ConstraintSetScore , protocols::sic_dock::JointScore , protocols::sic_dock::LinkerScore , protocols::sic_dock::RigidScore , protocols::sic_dock::scores::MotifHashRigidScore , protocols::sic_dock::scores::TrisBpyScore , protocols::sic_dock::XfoxmScore , protocols::simple_filters::SAXSScoreFilter , protocols::simple_moves::FragmentCost , protocols::simple_moves::GunnCost , protocols::simple_moves::LookupResultPlus , protocols::stepwise::legacy::modeler::rna::Cluster_Member
• score1 : core::scoring::motif::MotifHit
• score2 : core::scoring::motif::MotifHit
• score_ : core::fragment::FragData , core::scoring::DimerPairing , core::scoring::rna::RNA_SuitePotential , core::scoring::TMscore , core::sequence::Cell , core::util::ChainbreakUtil , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::Template , protocols::electron_density::RBfitResult , protocols::electron_density::RefinementResult , protocols::fldsgn::topology::DimerPairing , protocols::moves::MoverStatistics , protocols::nonlocal::SmoothPolicy::Candidate , protocols::residue_optimization::MetapatchEnumeration , protocols::simple_filters::PDDFScoreFilter
• score_all_particles() : core::optimization::ParticleSwarmMinimizer , protocols::pockets::DarcParticleSwarmMinimizer
• score_and_output() : protocols::docking::DockingPrepackProtocol
• score_atom_centrally() : core::scoring::methods::MMBondAngleEnergy
• score_atom_pair() : core::scoring::elec::FA_ElecEnergy
• score_basis() : protocols::sewing::Hasher
• score_basis_125() : protocols::sewing::Hasher
• score_best_ : protocols::membrane::OptimizeMembranePositionMover
• score_bias_ : core::scoring::saxs::SAXSEnergy
• score_by_scoretype() : core::scoring::ScoreFunction
• score_chi_ : core::scoring::methods::DNA_DihedralEnergy
• score_criteria_ : core::conformation::symmetry::SymSlideInfo
• score_cut() : protocols::magnesium::MgScanner
• score_cut_ : protocols::magnesium::MgScanner
• score_cut_count : protocols::stepwise::modeler::rna::Filterer_Count
• score_cut_PDB() : protocols::magnesium::MgScanner
• score_cut_PDB_ : protocols::magnesium::MgScanner
• score_cut_per_batch_ : protocols::abinitio::HedgeArchive
• score_cutoff_ : protocols::docking::DockingProtocol , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::task_operations::InteractingRotamerExplosion
• score_d2() : protocols::simple_filters::SymmetricMotifFilter
• score_d8 : protocols::hybridization::TMalign
• score_data_ : protocols::analysis::InterfaceAnalyzerMover
• score_delta_ : core::scoring::methods::DNA_DihedralEnergy , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential , core::scoring::disulfides::DisulfideMatchingPotential
• score_expression_ : protocols::pack_daemon::EntityFunc
• score_extra() : protocols::sic_dock::scores::TrisBpyScore
• score_file() : protocols::jd2::archive::Batch
• score_file_tags_ : protocols::jd2::ScoreOnlyJobOutputter
• score_filt_ : protocols::loophash::LoopHashSampler
• score_filter() : core::io::silent::SilentFileData , protocols::flexpep_docking::FlexPepDockingFlags
• score_fragment() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::PValuedFragmentScoreManager
• score_fragment_from_cache() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::PValuedFragmentScoreManager
• score_fun() : core::scoring::TMscore
• score_fun8() : protocols::hybridization::TMalign
• score_func_type_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy
• 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 , protocols::canonical_sampling::BiasedMonteCarlo , protocols::ddg::ddGMover , protocols::dna::PDBOutput , protocols::farna::movers::RNA_Minimizer , protocols::medal::MedalMover , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::SimulatedTempering , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::PackDaemon , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::ScoreMover
• score_function_ : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::cryst::ReportGradientsMover , protocols::cryst::SetCrystWeightMover , protocols::dna::PDBOutput , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::RotamerDump::RotamerDumpMover , protocols::simple_moves::ScoreMover
• score_function_info_ : core::scoring::ScoreFunction
• score_function_info_current_ : core::scoring::ScoreFunction
• score_function_ref_ : protocols::cryst::SetCrystWeightMover
• score_fxn() : protocols::ligand_docking::InterfaceScoreCalculator
• score_fxn_ : core::pack::task::residue_selector::ClashBasedRepackShellSelector , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CyclizationMover
• score_high_res_ : protocols::surface_docking::FullatomRelaxMover
• score_ligand_interface() : protocols::optimize_weights::IterativeOptEDriver
• SCORE_LINE_STRINGS : core::pose::datacache::CacheableDataType
• score_list_ : protocols::optimize_weights::OptEMultifunc
• score_log_file() : protocols::protein_interface_design::filters::FilterScanFilter
• score_log_file_ : protocols::protein_interface_design::filters::FilterScanFilter
• score_low_res_ : protocols::surface_docking::CentroidRelaxMover
• SCORE_MAP : core::pose::datacache::CacheableDataType
• score_map() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::qsar::qsarOptData
• score_map_ : protocols::antibody_legacy::AntibodyModeler , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::qsar::scoring_grid::GridManager , protocols::simple_moves::ScoreMover , protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• score_map_from_scored_pose() : protocols::jd2::ScoreMap
• score_margin_ : protocols::docking::DockingHighResFilter
• score_matrix_rmsd() : protocols::hybridization::TMalign
• score_matrix_rmsd_sec() : protocols::hybridization::TMalign
• score_meta() : protocols::sic_dock::scores::MotifHashRigidScore
• score_min_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_min_defined_ : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_mode1() : protocols::simple_moves::TailsScoreMover
• score_mode2() : protocols::simple_moves::TailsScoreMover
• score_mode3() : protocols::simple_moves::TailsScoreMover
• score_multiply() : core::conformation::symmetry::SymmetryInfo
• score_multiply_ : core::conformation::symmetry::SymmetryInfo
• score_multiply_factor() : core::conformation::symmetry::SymmetryInfo
• score_multiply_factor_ : core::conformation::symmetry::SymmetryInfo
• score_multiply_subunit_ : core::conformation::symmetry::SymmData
• score_name_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• score_normal_center() : core::scoring::MembranePotential
• score_of_bin() : core::scoring::motif::XformScore
• score_of_bin_normalized() : core::scoring::motif::XformScore
• score_offset_ : protocols::canonical_sampling::SimulatedTempering
• score_one() : protocols::sewing::Hasher
• score_only : protocols::flexpep_docking::FlexPepDockingFlags , protocols::symmetric_docking::SymDockProtocol
• score_only_ : protocols::enzdes::DetectProteinLigandInterface
• score_or_matchrt_ : protocols::denovo_design::DisulfidizeMover
• score_output_file_name() : protocols::match::MatcherTask
• score_output_file_name_ : protocols::match::MatcherTask
• score_output_filename_ : protocols::match::output::MatchScoreWriter
• score_pairmatrix() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• score_pairmatrix_ : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• score_patch : core::init::pre_talaris_2013_behavior_settings
• score_pose() : protocols::sparta::Sparta
• score_pose_per_residue() : protocols::sparta::Sparta
• score_position_data() : protocols::optimize_weights::IterativeOptEDriver
• score_post_apply_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• score_pre_apply_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• score_prefix_ : protocols::domain_assembly::PostDockAssemblyScorer
• score_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• score_selection_ : protocols::qsar::qsarOptFunc
• score_separated_chains() : protocols::analysis::InterfaceAnalyzerMover
• score_sidechain_pack_ : protocols::surface_docking::SurfaceDockingProtocol
• score_stage1_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage2_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage2_beginning : protocols::relax::ClassicRelax
• score_stage2_end : protocols::relax::ClassicRelax
• score_stage2_half : protocols::relax::ClassicRelax
• score_stage2_quarter : protocols::relax::ClassicRelax
• score_stage3a_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage3b_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage4_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage4rot_ : protocols::abinitio::ClassicAbinitio
• score_stage4rot_sc_ : protocols::abinitio::ClassicAbinitio
• score_stage5_ : protocols::abinitio::ClassicAbinitio
• score_stride_ : protocols::canonical_sampling::SilentTrajectoryRecorder
• score_subunit_ : core::conformation::symmetry::SymmData
• score_term_ : protocols::features::TopCountOfAllInputs , protocols::features::TopCountOfEachInput
• score_this_disulfide() : core::scoring::disulfides::FullatomDisulfidePotential
• score_this_disulfide_old() : core::scoring::disulfides::FullatomDisulfidePotential
• score_threshold() : protocols::hotspot_hashing::HotspotStubSet
• score_threshold_ : protocols::hotspot_hashing::HotspotStubSet , protocols::hybridization::CartesianSampler , protocols::hybridization::FragmentBiasAssigner , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_filters::MotifScoreFilter
• score_torsion() : protocols::simple_moves::TorsionDOFMover
• score_tuple() : protocols::frag_picker::scores::GunnCost , protocols::simple_moves::GunnCost
• score_type() : core::scoring::constraints::Constraint , core::scoring::constraints::DOF_Constraint , protocols::helical_bundle::BundleReporterFilter , protocols::mpi_refinement::MethodParams , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type2name_ : core::scoring::ScoreTypeManager
• score_type_ : core::scoring::constraints::Constraint , core::scoring::constraints::DOF_Constraint , core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , protocols::canonical_sampling::PatchOperation , protocols::enzdes::EnzScoreFilter , protocols::helical_bundle::BundleReporterFilter , protocols::moves::RampingMover , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ConstrainToIdealMover , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type_2_active() : core::scoring::EnergyGraph
• score_type_2_active_ : core::scoring::EnergyGraph
• score_type_features_ : protocols::features::ProteinSilentReport
• score_type_from_name() : core::scoring::ScoreTypeManager
• score_type_name() : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type_name_ : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type_threshold() : protocols::helical_bundle::BundleReporterFilter
• score_type_threshold_ : protocols::helical_bundle::BundleReporterFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ScoreTypeFilter
• score_type_weights_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::UnfoldedStateEnergy
• score_types() : core::scoring::methods::EnergyMethod , core::scoring::PolymerBondedEnergyContainer
• score_types_ : core::scoring::methods::EnergyMethod , core::scoring::PolymerBondedEnergyContainer , protocols::simple_filters::ScoreCutoffFilter
• score_types_by_method_type() : core::scoring::ScoreFunction
• 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::aa_composition_energy::AACompositionEnergyCreator , core::scoring::aa_repeat_energy::AARepeatEnergyCreator , 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_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::lkball::LK_BallEnergyCreator , core::scoring::loop_graph::LoopCloseEnergyCreator , core::scoring::magnesium::MgEnergyCreator , core::scoring::magnesium::RNA_MgPointEnergyCreator , 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::carbohydrates::SugarBackboneEnergyCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::CenPairMotifDegreeEnergyCreator , core::scoring::methods::CenPairMotifEnergyCreator , 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::DNA_DihedralEnergyCreator , core::scoring::methods::DNA_EnvPairEnergyCreator , core::scoring::methods::DNA_ReferenceEnergyCreator , 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_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::MultipoleElecEnergyCreator , 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::P_AA_ss_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::RamachandranEnergy2BCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::RamaPreProEnergyCreator , 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::RingClosureEnergyCreator , 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::SplitUnfoldedTwoBodyEnergyCreator , core::scoring::methods::SSElementMotifContactEnergyCreator , core::scoring::methods::SuckerEnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::VdWTinkerEnergyCreator , 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_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 , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::scoring::methods::EnsembleEnergyCreator , protocols::scoring::methods::InterchainEnvEnergyCreator , protocols::scoring::methods::InterchainPairEnergyCreator , protocols::scoring::methods::pcs2::PcsEnergyCreator , protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator , protocols::scoring::methods::pcsTs1::PseudocontactShiftEnergyCreator_Ts1 , protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2 , protocols::scoring::methods::pcsTs3::PseudocontactShiftEnergyCreator_Ts3 , protocols::scoring::methods::pcsTs4::PseudocontactShiftEnergyCreator_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegmentsCreator , protocols::scoring::methods::saxs::PDDFEnergyCreator , protocols::scoring::methods::SpecialRotamerEnergyCreator
• score_types_to_ignore_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• score_upper_ : core::scoring::func::SOGFunc_Impl
• score_value_ : protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter
• score_variation() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• score_variations() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• score_variations_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• score_variations_are_clean_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• score_weights : core::init::pre_talaris_2013_behavior_settings
• score_weights_ : protocols::frag_picker::scores::FragmentScoreManager
• score_window_context_ : core::scoring::electron_density::ElectronDensity
• score_zero_scores() : protocols::frag_picker::scores::FragmentScoreManager
• ScoreConstIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoreCutoffFilter() : protocols::simple_filters::ScoreCutoffFilter
• scored_base_pair_list() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_base_pair_list_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_base_stack_list() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_base_stack_list_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• scored_context_pose_ : protocols::flexpack::OtherContextScoreFunction
• scored_core_ : protocols::abinitio::IterativeBase
• scored_frag_close() : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• scored_frag_cycle_ratio() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• scored_frag_cycle_ratio_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• scored_frag_ids() : core::fragment::CacheWrapper< T, XCacheUnit >
• scored_fragpick_list() : protocols::abinitio::Templates
• ScoredFrag : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoredList : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreEValuator() : protocols::frag_picker::scores::ScoreEValuator
• ScoreEvaluator() : protocols::simple_filters::ScoreEvaluator
• scorefile() : protocols::enzdes::EnzdesJobOutputter , protocols::jd2::FileJobOutputter
• scorefile_ : protocols::jobdist::PlainPdbJobDistributor , protocols::simple_moves::ScoreMover
• scorefile_name() : protocols::jd2::FileJobOutputter
• scorefile_name_ : protocols::jd2::FileJobOutputter , protocols::jobdist::PlainPdbJobDistributor
• scorefile_writer_ : protocols::enzdes::EnzdesJobOutputter
• ScoreFileData() : core::io::raw_data::ScoreFileData
• ScoreFileSilentStruct() : core::io::silent::ScoreFileSilentStruct
• ScoreFileSilentStructCreator() : core::io::silent::ScoreFileSilentStructCreator
• scorefilter_ : protocols::docking::DockingHighResFilter
• ScoreFunction : core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::OnTheFlyInteractionGraph
• scorefunction() : core::pack::interaction_graph::SimpleInteractionGraph
• ScoreFunction : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::scoring::ScoreFunction , protocols::dna::PDBOutput
• scorefunction() : protocols::docking::SlideIntoContact
• ScoreFunction : protocols::fldsgn::BluePrintBDR
• scorefunction() : protocols::fldsgn::BluePrintBDR
• ScoreFunction : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies
• scorefunction() : protocols::fldsgn::potentials::SetSecStructEnergies
• ScoreFunction : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild
• scorefunction() : protocols::forge::components::VarLengthBuild
• ScoreFunction : protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover
• scorefunction() : protocols::forge::remodel::RemodelDesignMover
• ScoreFunction : protocols::forge::remodel::RemodelGlobalFrame
• scorefunction() : protocols::forge::remodel::RemodelGlobalFrame
• ScoreFunction : protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover
• scorefunction() : protocols::forge::remodel::RemodelLoopMover
• ScoreFunction : protocols::forge::remodel::RemodelMover
• scorefunction() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• ScoreFunction : protocols::matdes::SymDofMover , protocols::moves::MonteCarlo , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::Revert , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker
• scorefunction() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• ScoreFunction : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• scorefunction_ : protocols::docking::DockingHighResFilter
• scorefunction_initialized : protocols::simple_moves::ShakeStructureMover
• ScoreFunctionCOP : core::fragment::picking_old::vall::eval::EnergyEval , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FlxbbDesignPack , protocols::forge::remodel::RemodelAccumulator , protocols::matdes::SymDofMover , protocols::moves::MonteCarlo , protocols::normalmode::NormalModeMinimizer , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::Revert , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• ScoreFunctionFactory : protocols::forge::remodel::RemodelAccumulator
• ScoreFunctionFeatures() : protocols::features::ScoreFunctionFeatures
• ScoreFunctionFeaturesCreator() : protocols::features::ScoreFunctionFeaturesCreator
• ScoreFunctionInfo : core::scoring::Energies , core::scoring::ScoreFunctionInfo
• ScoreFunctionLoader() : protocols::jd2::parser::ScoreFunctionLoader
• ScoreFunctionOP : core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::matdes::SymDofMover , protocols::moves::MonteCarlo , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::Revert , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover
• scorefxn() : protocols::abinitio::abscript::AbscriptStageMover , protocols::denovo_design::connection::BridgeChains , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::features::TotalScoreFeatures , protocols::flxbb::DesignTask , protocols::helical_bundle::BundleReporterFilter , protocols::jd2::archive::EvaluatedArchive
• SCOREFXN : protocols::loop_modeling::ToolboxKeys
• scorefxn() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::magnesium::MgScanner , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::md::MDBase , protocols::multistate_design::MultiStateFitnessFunction , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::RandomMutation , protocols::seeded_abinitio::SeedFoldTree , protocols::simple_filters::AlaScan , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ddG , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::SwitchChainOrderMover , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::StepWiseModeler , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• scorefxn_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::analysis::PeptideDeriverPoseOutputter , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::RefineOneCDRLoop , protocols::backrub::BackrubProtocol , protocols::carbohydrates::GlycanRelaxMover , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::ddg::ddGMover , protocols::denovo_design::connection::BridgeChains , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::docking::DockingLowRes , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::FaDockingSlideIntoContact , protocols::docking::SlideIntoContact , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::farna::FARNA_Optimizer , protocols::farna::movers::RNA_Minimizer , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::InterfaceFeatures , protocols::features::TotalScoreFeatures , protocols::flexpack::FlexPacker , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::DesignTask , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::helical_bundle::BundleReporterFilter , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::hybridization::DomainAssembly , protocols::hybridization::FoldTreeHybridize , protocols::jd2::archive::EvaluatedArchive , protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::RigidSearchMover , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::magnesium::MgScanner , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::md::MDBase , protocols::motifs::MotifDnaPacker , protocols::moves::JumpOutMover , protocols::moves::RampingMover , protocols::moves::SimulatedTempering , protocols::multistate_design::MultiStateFitnessFunction , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMinimizer , protocols::pmut_scan::PointMutScanDriver , protocols::pose_length_moves::InsertResMover , protocols::pose_reporters::EnergyReporter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::Revert , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , protocols::relax::WorkUnit_BatchRelax , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::JScoreEvaluator , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ScoreEvaluator , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ddG , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::Scorer , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::symmetric_docking::SymSidechainMinMover , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• scorefxn_cart_graft_ : protocols::antibody::design::AntibodyDesignMover
• scorefxn_cen_cst() : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashLibrary
• scorefxn_cen_cst_ : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashDiversifier
• scorefxn_centroid_ : protocols::abinitio::Protocol
• scorefxn_deriver_ : protocols::analysis::PeptideDeriverFilter
• scorefxn_design_ : protocols::flxbb::FlxbbDesign
• scorefxn_docking() : protocols::docking::DockMCMProtocol
• scorefxn_fa_ : protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher
• scorefxn_high_ : protocols::docking::DockingEnsemble
• scorefxn_hires_ : protocols::symmetric_docking::SymDockBaseProtocol
• scorefxn_info_ : core::scoring::Energies
• scorefxn_input_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• scorefxn_low() : protocols::docking::DockingEnsemble
• scorefxn_low_ : protocols::antibody::AntibodyCDRGrafter , protocols::docking::DockingEnsemble
• scorefxn_lowres_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::symmetric_docking::SymDockBaseProtocol
• scorefxn_min_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol
• scorefxn_minimize() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• scorefxn_minimize_ : protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::DesignRepackMover
• scorefxn_minimizer_ : protocols::analysis::PeptideDeriverFilter
• scorefxn_name_ : protocols::simple_moves::symmetry::TaskAwareSymMinMover
• scorefxn_non_const() : protocols::jd2::archive::EvaluatedArchive
• scorefxn_obj_ : protocols::md::MDBase
• scorefxn_pack() : protocols::docking::DockingHighRes
• scorefxn_pack_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scorefxn_packing() : protocols::docking::DockMCMProtocol
• scorefxn_rama_cst() : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashLibrary
• scorefxn_rama_cst_ : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashDiversifier
• scorefxn_rb_ : protocols::RBSegmentRelaxImpl
• scorefxn_relax_ : protocols::flxbb::FlxbbDesign
• scorefxn_repack() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• scorefxn_repack_ : protocols::enzdes::BackboneSampler , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::DesignRepackMover
• scorefxn_repack_greedy_ : protocols::enzdes::PackRotamersMoverPartGreedy
• scorefxn_sampling_ : protocols::rbsegment_relax::OptimizeThreadingMover
• scorefxn_weights_ : core::scoring::Energies
• scorefxns() : protocols::comparative_modeling::LoopRelaxMover
• ScoreIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoreJumpFileSilentStruct() : core::io::silent::ScoreJumpFileSilentStruct
• ScoreJumpFileSilentStructCreator() : core::io::silent::ScoreJumpFileSilentStructCreator
• ScoreLessThanComparator() : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• scoreline_prefix() : core::io::silent::SilentStruct
• scoreline_prefix_ : core::io::silent::SilentStruct
• ScoreList : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreMap : core::scoring::motif::XformScore
• ScoreMover() : protocols::simple_moves::ScoreMover
• scorename_ : protocols::filters::Filter
• ScoreNormalization() : protocols::qsar::scoring_grid::ScoreNormalization
• ScoreOnlyJobOutputter() : protocols::jd2::ScoreOnlyJobOutputter
• Scorer() : protocols::stepwise::screener::Scorer
• scorer_ : protocols::nonlocal::SmoothPolicy
• ScorerMap : protocols::sewing::scoring::AssemblyScoreFunction
• scorers_ : protocols::sewing::scoring::AssemblyScoreFunction
• Scores : core::fragment::picking_old::vall::VallLibrarian
• scores() : core::fragment::picking_old::vall::VallLibrarian , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::sequence::SequenceAlignment
• Scores : protocols::sic_dock::RigidScore
• scores_ : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::scoring::motif::XformScore , core::sequence::SequenceAlignment , protocols::analysis::LoopAnalyzerMover , protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity , protocols::sic_dock::JointScore
• scores_are_clean_ : protocols::jd2::archive::EvaluatedArchive
• scores_heap_ : protocols::match::output::BestMatchesCollection
• scores_hist_ : core::scoring::custom_pair_distance::DistanceFunc
• scores_present() : core::scoring::ScoreFunctionInfo
• scores_present_ : core::scoring::ScoreFunctionInfo
• scores_to_probs_() : core::sequence::SequenceProfile
• scorescale_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• ScoreStructJSON() : core::io::raw_data::ScoreStructJSON
• ScoreStructText() : core::io::raw_data::ScoreStructText
• scoreSymmComplex_ : core::scoring::electron_density::FastDensEnergy
• ScoreType : core::scoring::Energies , protocols::simple_moves::ddG
• scoretype_ : protocols::docking::SlideIntoContact , protocols::pose_reporters::EnergyReporter
• ScoreTypeFeatures() : protocols::features::ScoreTypeFeatures
• ScoreTypeFeaturesCreator() : protocols::features::ScoreTypeFeaturesCreator
• ScoreTypeFilter() : protocols::simple_filters::ScoreTypeFilter
• ScoreTypes : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::simple_moves::GreenPacker
• scoretypes_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• scoring() : core::scoring::Energies , protocols::simple_moves::GenericMonteCarloMover
• scoring_ : core::scoring::Energies , protocols::frag_picker::CompareTotalScore
• scoring_begin() : core::pose::Pose , core::scoring::Energies
• scoring_end() : core::pose::Pose , core::scoring::Energies
• scoring_mask_ : core::scoring::electron_density::ElectronDensity
• scoring_matrix() : core::sequence::MatrixScoringScheme
• scoring_matrix_ : core::sequence::DP_Matrix , core::sequence::MatrixScoringScheme
• scoring_scheme_ : protocols::frag_picker::CustomScoreSelector
• scoring_schemes() : core::sequence::CompositeScoringScheme
• scoring_schemes_ : core::sequence::CompositeScoringScheme
• scoring_subunit_ : core::conformation::symmetry::SymmetryInfo
• scoringEval_counter : protocols::match::downstream::ScoringSecMatchRPE
• ScoringGridLoader() : protocols::qsar::scoring_grid::ScoringGridLoader
• ScoringManager() : core::scoring::ScoringManager
• ScoringScheme() : core::sequence::ScoringScheme
• ScoringSchemeFactory() : core::sequence::ScoringSchemeFactory
• ScoringSchemeTypes : core::sequence::ScoringSchemeFactory
• ScoringSecMatchRPE() : protocols::match::downstream::ScoringSecMatchRPE
• scrambled_job_order_ : protocols::jd2::ShuffleFileSystemJobDistributor
• scratch_ : protocols::simple_moves::sidechain_moves::SidechainMover
• scratch_dir() : protocols::simple_filters::ExternalEvaluator
• scratch_dir_ : protocols::simple_filters::ExternalEvaluator
• scratch_pose() : protocols::farna::libraries::BasePairStepLibrary
• scratch_pose_ : core::pose::copydofs::CopyDofs
• scratch_poses_ : protocols::farna::libraries::BasePairStepLibrary
• scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• screen() : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• screen_all() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• screen_all_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• screen_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• screen_for_donor_contact_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• screen_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• screen_three_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• screener_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• screener_whose_counts_to_check_ : protocols::stepwise::screener::IntegrationTestBreaker
• screeners_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::StepWiseSampleAndScreen
• screening_moving_rsd_at_origin_ : protocols::stepwise::screener::VDW_BinScreener
• screening_pose_ : protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::VDW_BinScreener
• screening_pose_list_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• ScreeningFeatures() : protocols::features::ScreeningFeatures
• ScreeningFeaturesCreator() : protocols::features::ScreeningFeaturesCreator
• ScreeningJobInputter() : protocols::jd2::ScreeningJobInputter
• scrfxn_ : protocols::make_rot_lib::MakeRotLibMover
• script_ : protocols::relax::FastRelax
• script_file_specified_ : protocols::relax::FastRelax
• script_max_accept_ : protocols::relax::FastRelax
• ScriptCM() : protocols::environment::ScriptCM
• scsc_energy_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• scsc_energy_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• ScValue : core::scoring::sc::MolecularSurfaceCalculator
• sd() : core::scoring::constraints::BoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::HarmonicFunc , core::scoring::func::MinMultiHarmonicFunc , protocols::simple_moves::symmetry::SetupNCSMover
• sd_ : core::scoring::constraints::BoundFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::KarplusFunc , core::scoring::func::MinMultiHarmonicFunc , core::scoring::methods::D2H_SA_Energy
• SD_ : core::scoring::ResidualDipolarCoupling
• sd_ : protocols::simple_moves::symmetry::SetupNCSMover
• sd_ang() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_ang_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dih() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dih_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dis() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_dis_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• sd_range() : protocols::match::upstream::SampleStrategyData
• sd_range_ : protocols::match::upstream::SampleStrategyData
• sdens : core::scoring::APBSConfig::R_PARAM
• sdev() : core::scoring::constraints::BigBinConstraint
• sdev1_ : core::scoring::func::SoedingFunc
• sdev2_ : core::scoring::func::SoedingFunc
• sdev_ : core::chemical::AddChiRotamer , core::scoring::constraints::BigBinConstraint
• sdevs_ : core::scoring::func::SOGFunc_Impl
• sdf_type() : core::chemical::sdf::MolFileIOBond
• sdf_type_ : core::chemical::sdf::MolFileIOBond
• SDFParser() : core::chemical::sdf::SDFParser
• sds_ : core::scoring::disulfides::Cb_Distance_Func
• seal_foldtree_ : protocols::forge::remodel::RemodelLoopMover
• search13_ : protocols::pockets::PocketGrid
• search_density_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• search_memb_center() : core::scoring::MembranePotential
• search_memb_normal() : core::scoring::MembranePotential
• search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• search_points_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• search_random_poses() : protocols::pockets::PlaidFingerprint
• search_reversed_map() : protocols::topology_broker::SequenceNumberResolver
• search_stubs_ : protocols::hotspot_hashing::SearchPatternRotSetOp
• search_typ_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• SearchPatternExpansion() : protocols::hotspot_hashing::SearchPatternExpansion
• SearchPatternRotSetOp() : protocols::hotspot_hashing::SearchPatternRotSetOp
• SearchPatternTransform() : protocols::hotspot_hashing::SearchPatternTransform
• Searchpoints() : protocols::hotspot_hashing::CartesianSearchPattern , protocols::hotspot_hashing::ComposeSearchPatterns , protocols::hotspot_hashing::ConstPattern , protocols::hotspot_hashing::LSMSearchPattern , protocols::hotspot_hashing::PartitionedSearchPattern , protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SearchPattern , protocols::hotspot_hashing::SearchPatternExpansion , protocols::hotspot_hashing::SearchPatternTransform , protocols::hotspot_hashing::SICPatternAtTransform , protocols::hotspot_hashing::SphericalRotationSearchPattern , protocols::hotspot_hashing::SurfaceSearchPattern , protocols::hotspot_hashing::TestPattern
• searchpoints_ : protocols::hotspot_hashing::CartesianSearchPattern , protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SphericalRotationSearchPattern
• SearchTyp : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• sec_matcher_ : protocols::match::downstream::SecondaryMatchUpstreamResProcessor
• sec_shift_data_ : protocols::frag_picker::VallResidue
• sec_str() : protocols::hybridization::TMalign
• sec_struc_char_to_enum_map() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• sec_struct_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• secant_interpolation() : core::optimization::LineMinimizationAlgorithm
• secmatch_prot_ : protocols::enzdes::PoseFoundResiduesCombination
• secmatch_scotypes_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• secmatch_value_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• SecMatchResiduePairEvaluator() : protocols::match::downstream::SecMatchResiduePairEvaluator
• second : core::fragment::FragID , protocols::match::downstream_hit , protocols::match::Hit , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• second_ : protocols::match::downstream_hit , protocols::match::Hit
• second_atom_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• second_mover_ : protocols::moves::JumpOutMover
• second_node_num_states_per_aatype_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• second_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• secondary_shifts() : protocols::frag_picker::VallResidue
• secondary_shifts_ : protocols::frag_picker::CS2ndShift
• secondary_structure_ : protocols::jumping::SameStrand , protocols::jumping::SheetBuilder
• secondary_structure_potential_ : core::scoring::ScoringManager
• secondary_structure_weights() : core::scoring::methods::EnergyMethodOptions
• SecondaryIdentity() : protocols::frag_picker::scores::SecondaryIdentity
• SecondaryMatcherToDownstreamResidue() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• SecondaryMatcherToUpstreamResidue() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• SecondaryMatchProtocol() : protocols::enzdes::SecondaryMatchProtocol
• SecondaryMatchUpstreamResProcessor() : protocols::match::downstream::SecondaryMatchUpstreamResProcessor
• SecondarySimilarity() : protocols::frag_picker::scores::SecondarySimilarity
• SecondaryStructure() : core::fragment::SecondaryStructure
• SecondaryStructureCountFilter() : protocols::fldsgn::filters::SecondaryStructureCountFilter
• SecondaryStructureEnergy() : core::scoring::methods::SecondaryStructureEnergy
• SecondaryStructureFilter() : protocols::fldsgn::filters::SecondaryStructureFilter
• SecondaryStructureHasResidueFilter() : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• SecondaryStructureMPM() : protocols::match::SecondaryStructureMPM
• SecondaryStructurePool() : protocols::frag_picker::quota::SecondaryStructurePool
• SecondaryStructurePotential() : core::scoring::SecondaryStructurePotential
• SecondaryStructureSegmentFeatures() : protocols::features::SecondaryStructureSegmentFeatures
• SecondaryStructureSegmentFeaturesCreator() : protocols::features::SecondaryStructureSegmentFeaturesCreator
• SecondaryStructureSelector() : core::select::residue_selector::SecondaryStructureSelector
• SecondaryStructureWeights() : core::scoring::SecondaryStructureWeights
• SecondLoop() : core::scoring::sc::MolecularSurfaceCalculator
• seconds() : protocols::simple_filters::ExpiryFilter
• seconds_ : protocols::simple_filters::ExpiryFilter
• seconds_to_keep_files_alive_ : protocols::jd2::MpiFileBuffer
• 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 , protocols::farna::fragments::FullAtomRNA_Fragments , protocols::farna::fragments::TorsionSet , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::SS_Info2 , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• SecStruct : protocols::toolbox::task_operations::DsspDesignOperation
• secstruct_ : core::conformation::Conformation , core::fragment::SecstructSRFD , core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::scoring::packing::PoseBalls , protocols::abinitio::TemplateJumpSetup , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::topology::SS_Info2 , protocols::frags::RMSVallData , protocols::frags::TorsionFragment , protocols::frags::VallData , protocols::hybridization::InsertChunkMover , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSelector , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::viewer::ConformationViewer
• secstruct_defined_ : protocols::farna::setup::RNA_DeNovoParameters
• secstruct_input_ : protocols::fldsgn::filters::SheetTopologyFilter
• SecStructFinder() : protocols::ncbb::SecStructFinder
• SecStructGen() : core::fragment::picking_old::vall::gen::SecStructGen
• SecStructMinimizeMover() : protocols::ncbb::SecStructMinimizeMover
• SecStructMinimizeMultiFunc() : protocols::ncbb::SecStructMinimizeMultiFunc
• SecStructResidues : protocols::toolbox::task_operations::DsspDesignOperation
• secstructs_ : core::io::sequence_comparation::DesignContrast
• SecstructSRFD() : core::fragment::SecstructSRFD
• secstructure_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• section_index() : core::fragment::picking_old::vall::VallResidue
• section_index_ : core::fragment::picking_old::vall::VallResidue
• sections() : core::fragment::picking_old::vall::VallLibrary
• secx : protocols::hybridization::TMalign
• secy : protocols::hybridization::TMalign
• seed() : core::pose::full_model_info::SubMotifInfo
• seed_ : core::pose::full_model_info::SubMotifInfo
• seed_centroids() : protocols::make_rot_lib::MakeRotLibMover
• seed_exceptions_ : protocols::seeded_abinitio::CAcstGenerator
• seed_foldtree_ : protocols::seeded_abinitio::GrowPeptides
• seed_vector_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::SeedSetupMover
• SeedFoldTree() : protocols::seeded_abinitio::SeedFoldTree
• seeds_only_ : protocols::seeded_abinitio::SeedFoldTree
• seeds_pdb_ : protocols::seeded_abinitio::SwapSegment
• seeds_presence_ : protocols::seeded_abinitio::SwapSegment
• SeedSetupMover() : protocols::seeded_abinitio::SeedSetupMover
• seg1 : protocols::denovo_design::components::BondInfo
• seg2 : protocols::denovo_design::components::BondInfo
• seg2node_ : protocols::denovo_design::components::FoldGraph
• seg_end_it_ : protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T >
• seg_it_ : protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T >
• seg_len_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• seg_size : protocols::forge::remodel::RemodelGlobalFrame
• seg_type : protocols::rbsegment_relax::RBResidueRange
• seg_vector_ : protocols::seeded_abinitio::SegmentHybridizer
• Segment : core::pose::datacache::SpecialSegmentsObserver
• segment() : protocols::backrub::BackrubMover , protocols::denovo_design::components::FoldGraph
• Segment() : protocols::denovo_design::components::Segment
• segment() : protocols::denovo_design::components::StructureData , protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T >
• segment1 : protocols::denovo_design::connection::Connection::ConnectionInfo
• segment2 : protocols::denovo_design::connection::Connection::ConnectionInfo
• segment_ : protocols::rbsegment_relax::RBSegmentMover
• segment_definitions_ : protocols::scoring::ResidualDipolarCouplingRigidSegments
• segment_group() : protocols::denovo_design::components::StructureData
• segment_id() : protocols::backrub::BackrubMover , protocols::features::SecondaryStructureSegment , protocols::sewing::HashValue , protocols::sewing::segment
• segment_id_ : protocols::sewing::SewSegment
• segment_ids() : protocols::sewing::Model , protocols::sewing::ModelNode
• segment_IDs_ : core::io::silent::SilentStruct
• segment_ids_ : protocols::sewing::ModelNode
• segment_length() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• segment_match_counts : protocols::sewing::HashResult
• segment_matches : protocols::sewing::HashResult
• segment_name() : protocols::denovo_design::components::StructureData
• segment_names() : protocols::denovo_design::components::NamedMover
• segment_names_ : protocols::denovo_design::components::NamedMover
• segment_nonconst() : protocols::denovo_design::components::StructureData
• segment_order_ : protocols::denovo_design::components::StructureData
• SegmentDsspRequirement() : protocols::sewing::sampling::requirements::SegmentDsspRequirement
• SegmentHybridizer() : protocols::seeded_abinitio::SegmentHybridizer
• segmentID : core::io::AtomInformation , core::io::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBInfo
• segmentID_ : core::io::ResidueInformation
• SegmentInsert() : protocols::forge::build::SegmentInsert
• SegmentLengthRequirement() : protocols::sewing::sampling::requirements::SegmentLengthRequirement
• SegmentRebuild() : protocols::forge::build::SegmentRebuild
• segments() : core::pose::datacache::SpecialSegmentsObserver , protocols::denovo_design::components::StructureData , protocols::sewing::Assembly
• segments_ : core::pose::datacache::SpecialSegmentsObserver , protocols::backrub::BackrubMover , protocols::denovo_design::components::EXCN_PreFilterFailed , protocols::denovo_design::components::StructureData , protocols::rbsegment_relax::RBSegment , protocols::sewing::Assembly , protocols::sewing::Model
• segments_begin() : protocols::denovo_design::components::EXCN_PreFilterFailed , protocols::denovo_design::components::StructureData
• segments_end() : protocols::denovo_design::components::EXCN_PreFilterFailed , protocols::denovo_design::components::StructureData
• segments_fixed() : protocols::denovo_design::connection::BridgeChains
• segments_in_movable_group() : protocols::denovo_design::components::StructureData
• SegmentSwap() : protocols::forge::build::SegmentSwap
• select_around_resnums_ : protocols::simple_filters::EnergyPerResidueFilter
• select_best_solution() : protocols::denovo_design::components::FoldGraph
• select_chain_by_index() : core::select::residue_selector::ChainSelector
• select_chain_by_pdb_chain_char() : core::select::residue_selector::ChainSelector
• select_conf_and_move_ligand_() : protocols::pockets::PlaidFingerprint
• select_connection_info() : protocols::denovo_design::connection::Connection
• select_core_loops() : protocols::abinitio::DoubleLayerKinematicAbinitio
• select_designable_ : protocols::residue_selectors::TaskSelector
• select_final_loop() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• select_fixed_ : protocols::residue_selectors::TaskSelector
• select_fragments() : protocols::frag_picker::BestTotalScoreSelector , protocols::frag_picker::CompositeFragmentSelector , protocols::frag_picker::CustomScoreSelector , protocols::frag_picker::DiversifyCrmsdByClustering , protocols::frag_picker::DiversifyCrmsdSelector , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::FragmentSelectingRule , protocols::frag_picker::quota::QuotaSelector
• select_fragments_200() : protocols::frag_picker::quota::QuotaSelector
• select_fragments_25_200() : protocols::frag_picker::quota::QuotaSelector
• select_hit_representatives() : protocols::match::Matcher
• select_jump() : protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider , protocols::simple_moves::symmetry::RandomSymmetrySlider , protocols::simple_moves::symmetry::SequentialSymmetrySlider , protocols::simple_moves::symmetry::SymmetrySlider
• select_loops() : protocols::abinitio::LoopJumpFoldCst , protocols::loops::loop_mover::IndependentLoopMover
• select_low_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• select_next_job() : protocols::jd3::JobDistributor
• select_one_loop() : protocols::LoopRebuild
• select_orient_atoms() : core::chemical::ResidueType , core::conformation::Residue
• select_packable_ : protocols::residue_selectors::TaskSelector
• select_parts() : protocols::abinitio::abscript::RigidChunkCM , protocols::topology_broker::RigidChunkClaimer
• select_points() : protocols::electron_density::DockIntoDensityMover
• select_poses() : protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::TopNByProperty , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::PoseSelector
• select_positive_phi() : core::select::residue_selector::PhiSelector
• select_positive_phi_ : core::select::residue_selector::PhiSelector
• select_random() : protocols::jumping::JumpSelector
• select_random_move() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• select_range_ : protocols::fldsgn::filters::HelixKinkFilter
• select_relevant_states() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::MultistateAggregateFunction
• select_residues() : protocols::simple_filters::SaveResfileToDiskFilter
• select_resnums_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::simple_filters::EnergyPerResidueFilter
• select_rotamer() : protocols::simple_moves::BoltzmannRotamerMover
• select_rotamer_subset() : protocols::pack_daemon::PackDaemon
• select_score() : protocols::jd2::archive::EvaluatedArchive
• select_solution() : protocols::generalized_kinematic_closure::GeneralizedKIC
• select_weights_ : protocols::jd2::archive::EvaluatedArchive
• SelectByDeltaScoreOperation() : protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• SelectByDensityFitOperation() : protocols::toolbox::task_operations::SelectByDensityFitOperation
• SelectBySASAOperation() : protocols::toolbox::task_operations::SelectBySASAOperation
• selected_ : core::scoring::SelectedResPredicate
• selected_boundary_residues() : core::select::util::SelectResiduesByLayer
• selected_boundary_residues_ : core::select::util::SelectResiduesByLayer
• selected_core_residues() : core::select::util::SelectResiduesByLayer
• selected_core_residues_ : core::select::util::SelectResiduesByLayer
• selected_pairings_ : protocols::jumping::MembraneJump
• selected_resis() : protocols::simple_filters::SaveResfileToDiskFilter
• selected_resis_ : protocols::simple_filters::SaveResfileToDiskFilter
• selected_resis_property() : protocols::simple_filters::SaveResfileToDiskFilter
• selected_resis_property_ : protocols::simple_filters::SaveResfileToDiskFilter
• selected_ss_ : core::select::residue_selector::SecondaryStructureSelector
• selected_surface_residues() : core::select::util::SelectResiduesByLayer
• selected_surface_residues_ : core::select::util::SelectResiduesByLayer
• SelectedResPredicate() : core::scoring::SelectedResPredicate
• SelectGdtEvaluator() : protocols::simple_filters::SelectGdtEvaluator
• selection() : protocols::protein_interface_design::filters::RmsdFilter
• selection_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::TruncatedScoreEvaluator
• selection_bias_ : protocols::hybridization::CartesianSampler
• selection_from_segment_cache_ : protocols::protein_interface_design::filters::RmsdFilter
• selection_low() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• selection_operation() : protocols::pose_selectors::AndSelector , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::OrSelector
• SelectMaxsubEvaluator() : protocols::simple_filters::SelectMaxsubEvaluator
• selectmode_ : protocols::md::MDBase
• selector() : core::chemical::PatchCase , core::pack::task::operation::OperateOnResidueSubset , core::scoring::aa_composition_energy::AACompositionConstraint , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim , protocols::simple_moves::BackboneMover
• selector_ : core::chemical::Metapatch , core::chemical::Patch , core::chemical::PatchCase , core::scoring::aa_composition_energy::AACompositionConstraint , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::constraints::CoordinateConstraintGenerator , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim , protocols::frag_picker::FragmentPicker , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::simple_movers::DeleteRegionMover , protocols::loops::loop_mover::LoopCM , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::BackboneMover
• Selector_AA() : core::chemical::Selector_AA
• Selector_CMDFLAG() : core::chemical::Selector_CMDFLAG
• selector_filters_ : protocols::rosetta_scripts::MultiplePoseMover
• selector_list_ : protocols::environment::claims::EnvClaim
• 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_sfxn_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• selector_tag_ : protocols::rosetta_scripts::MultiplePoseMover
• Selector_UPPER_POSITION() : core::chemical::Selector_UPPER_POSITION
• Selector_VARIANT_TYPE() : core::chemical::Selector_VARIANT_TYPE
• selectors_ : core::chemical::ResidueTypeSelector , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::OrResidueSelector , protocols::frag_picker::CompositeFragmentSelector , protocols::match::MatcherMover , protocols::pose_selectors::LogicalSelector , protocols::rosetta_scripts::MultiplePoseMover
• selectortype_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• SelectRDC_Evaluator() : protocols::simple_filters::SelectRDC_Evaluator
• SelectResiduesByLayer() : core::select::util::SelectResiduesByLayer
• SelectResiduesWithinChainOperation() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• SelectRmsdEvaluator() : protocols::simple_filters::SelectRmsdEvaluator
• SelectStubIteratively() : protocols::protein_interface_design::movers::PlaceStubMover
• self_and_bg_dots_for_states_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• self_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• self_transition_ : protocols::canonical_sampling::SimulatedTempering
• selfmerge() : core::scoring::dssp::StrandPairingSet
• semi_energy_dist_ : protocols::make_rot_lib::RotData
• semi_prob_dist_ : protocols::make_rot_lib::RotData
• semiexpl_water_cutoff_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• semiexpl_water_hbgeom_score() : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• SemiExplicitWaterUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• semirotameric_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::make_rot_lib::RotData
• semirotameric_ncaa_rotlib() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• semirotameric_ncaa_rotlib_ : core::chemical::rotamers::NCAARotamerLibrarySpecification
• SemiRotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• send_accepted() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• send_colors() : protocols::moves::PyMolMover
• send_energy() : protocols::moves::PyMolMover
• send_error_message_to_remote_daemon_sets() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• send_go_signal() : protocols::jd2::MPIWorkPoolJobDistributor
• send_job_to_slave() : protocols::jd2::MPIFileBufJobDistributor
• send_level_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• send_membrane_planes() : protocols::moves::PyMolMover
• send_MPI_workunit() : protocols::wum::MPI_WorkUnitManager
• send_newest_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• send_next_WU_on_request() : protocols::wum::MPI_WorkUnitManager
• send_random_library_struct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• send_random_library_structs() : protocols::mpi_refinement::MPI_Refinement
• send_RAW_Energies() : protocols::moves::PyMolMover
• send_receive_and_write_structures() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• send_rotamer_energies_to_master_cpu() : protocols::optimize_weights::IterativeOptEDriver
• send_rotamer_recovery_data_to_master_cpu() : protocols::optimize_weights::IterativeOptEDriver
• send_sequence_recovery_data_to_master_cpu() : protocols::optimize_weights::IterativeOptEDriver
• send_silent_struct_to_rank() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• send_sortedpick_library_structs() : protocols::mpi_refinement::MPI_Refinement
• send_spin_down_signal() : protocols::pack_daemon::MPIMultistateFitnessFunction
• send_stop_to_jobdistributor() : protocols::jd2::archive::ArchiveManager
• send_success_message_to_remote_daemon_set() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• send_swap_invites() : protocols::canonical_sampling::AsyncMPITemperingBase
• send_to_stdout() : core::optimization::NumericalDerivCheckResult
• send_to_stdout_ : core::optimization::NumericalDerivCheckResult
• send_update() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• send_wu_time_ : protocols::wum::MPI_WorkUnitManager
• send_wu_time_n_ : protocols::wum::MPI_WorkUnitManager
• send_xyz() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• sendMessage() : protocols::moves::UDPSocketClient
• sendRAWMessage() : protocols::moves::UDPSocketClient
• sent_termination_ : protocols::mpi_refinement::MPI_Refine_Master
• sentCount_ : protocols::moves::UDPSocketClient
• sep : core::scoring::sc::MolecularSurfaceCalculator
• sep_aa1_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_aa2_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_aa_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_bfac_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_dist_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_dssp_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_hb_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_lj_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_nbrs_ : core::scoring::motif::ResPairMotifMetaBinner
• sep_ss() : core::scoring::packing::HolesParams
• sep_ss_ : core::scoring::motif::ResPairMotifMetaBinner , core::scoring::packing::HolesParams
• separate_moving_residue_to_estimate_baseline_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• separate_protein_and_ligand() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• separate_prt_ligand_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• separate_scores_ : core::scoring::rna::data::RNA_DMS_Potential
• separated_energy : protocols::analysis::PerResidueInterfaceData
• separated_interface_score : protocols::analysis::InterfaceData
• separated_SASA : protocols::analysis::InterfaceData
• separated_sasa : protocols::analysis::PerResidueInterfaceData
• separated_total_energy : protocols::analysis::InterfaceData
• SeparateDnaFromNonDna() : protocols::dna::SeparateDnaFromNonDna
• seq() : core::sequence::CompositeSequence
• seq1() : core::sequence::DerivedSequenceMapping
• seq1_ : core::sequence::DerivedSequenceMapping
• seq2() : core::sequence::DerivedSequenceMapping
• seq2_ : core::sequence::DerivedSequenceMapping
• seq_ : core::import_pose::pose_stream::ExtendedPoseInputStream , core::sequence::Sequence , protocols::antibody::design::NativeAntibodySeq , protocols::seeded_abinitio::GrowPeptides
• seq_design_creator_ : protocols::antibody::design::AntibodyDesignMover
• seq_design_options_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• seq_design_strategy_enum_to_string() : protocols::antibody::design::AntibodyDesignEnumManager
• seq_design_strategy_is_present() : protocols::antibody::design::AntibodyDesignEnumManager
• seq_design_strategy_string_to_enum() : protocols::antibody::design::AntibodyDesignEnumManager
• seq_design_strategy_to_enum_ : protocols::antibody::design::AntibodyDesignEnumManager
• seq_design_strategy_to_string_ : protocols::antibody::design::AntibodyDesignEnumManager
• seq_end() : protocols::features::helixAssembly::HelicalFragment
• seq_from_file() : core::sequence::SequenceFactory
• seq_num : core::scoring::rna::chemical_shift::ChemicalShiftData , protocols::stepwise::modeler::rna::Residue_info
• seq_pos_ : protocols::simple_moves::a3b_hbs::A3BHbsMover
• seq_recovery_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• seq_sep : protocols::jumping::DisulfPairing
• seq_sep_ : core::scoring::hbonds::HBEvalTuple
• seq_sep_intercept() : protocols::abinitio::abscript::AbscriptStageMover
• seq_sep_scale_ : core::scoring::SecondaryStructureWeights
• seq_sep_stage1_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• seq_sep_stage3_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• seq_sep_stage4_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• seq_sep_type2name_ : core::scoring::hbonds::HBondTypeManager
• seq_sep_type_from_name() : core::scoring::hbonds::HBondTypeManager
• seq_separation_ : protocols::seeded_abinitio::CAcstGenerator
• seq_start() : protocols::features::helixAssembly::HelicalFragment
• seq_types_ : core::sequence::SequenceFactory
• seqfrags_only_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• seqid() : core::environment::FoldTreeSketch::Node
• seqid_ : core::environment::FoldTreeSketch::Node
• SeqLabelMap : core::environment::SequenceAnnotation
• seqmap() : protocols::forge::remodel::RemodelConstraintGenerator
• seqmap_ : protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelConstraintGenerator
• seqmapping_ : protocols::frag_picker::scores::FragmentChunkCrms
• seqNum : core::io::ModifiedResidueInformation
• seqNum1 : core::io::CisPeptideInformation
• seqNum2 : core::io::CisPeptideInformation
• 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 , protocols::contact_map::ContactPartner , protocols::motifs::BuildPosition , protocols::simple_filters::nmer_svm_res_data
• seqpos1() : protocols::constraints_additional::SequenceCouplingConstraint
• seqpos1_ : core::scoring::constraints::ResidueTypeLinkingConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• seqpos2() : protocols::constraints_additional::SequenceCouplingConstraint
• seqpos2_ : core::scoring::constraints::ResidueTypeLinkingConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• seqpos_ : core::conformation::Residue , core::io::PositionDdGInfo::PositionDdGInfo , core::io::rna::RDAT , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::contact_map::ContactPartner , protocols::enzdes::ResidueConformerFilter , protocols::metal_interface::MetalSiteResidue , protocols::motifs::BuildPosition , protocols::pockets::PocketConstraint , protocols::simple_moves::PeptideStapleMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• seqpos_aa_vals_vec_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• seqpos_aligned_start_ : protocols::hybridization::InsertChunkMover
• seqpos_aligned_stop_ : protocols::hybridization::InsertChunkMover
• seqpos_for_geomcst() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• seqpos_for_geomcst_ : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• seqpos_map_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqpos_map_begin() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqpos_map_end() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqpos_map_size() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqpos_moved_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• seqpos_start_ : protocols::hybridization::InsertChunkMover
• seqpos_stop_ : protocols::hybridization::InsertChunkMover
• SeqposTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqprof() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqprof_ : protocols::simple_moves::ConsensusDesignMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqprof_filename_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqprof_wt_aa() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• SeqprofConsensusOperation() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqs() : core::sequence::CompositeSequence
• seqs_ : core::sequence::CompositeSequence
• seqsep_intcpt_ : protocols::abinitio::abscript::AbscriptStageMover
• seqsep_slope_ : protocols::abinitio::abscript::AbscriptStageMover
• seqtable_ : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• 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 , protocols::antibody::CDRDBSequence , protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet , protocols::frag_picker::FragmentCandidate , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::loophash::BBExtraData , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::ResonanceList , protocols::simple_moves::ExtendedPoseMover , protocols::sparta::Sparta::SpartaLib , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• sequence_ : core::fragment::SingleResidueFragData , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::rna::RDAT , core::io::silent::SilentStruct , core::io::silent::SimpleSequenceData , core::pose::MiniPose , protocols::abinitio::AbrelaxApplication , protocols::frag_picker::CSTalosIO , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::TorsionBinIO , protocols::frag_picker::VallChunk , protocols::frags::RMSVallData , protocols::frags::TorsionFragment , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::ResonanceList , protocols::simple_moves::ExtendedPoseMover , protocols::toolbox::AtomID_Mapper , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• sequence_alignment_ : protocols::hybridization::InsertChunkMover
• sequence_alignment_local_ : protocols::hybridization::InsertChunkMover
• sequence_alignments_ : protocols::hybridization::ChunkTrialMover
• sequence_chunks_ : protocols::seeded_abinitio::GrowPeptides
• sequence_claim_ : protocols::topology_broker::SequenceClaimer
• sequence_claims_ : protocols::topology_broker::TopologyBroker
• sequence_constraint() : core::scoring::constraints::ConstraintSet
• sequence_constraints_ : core::scoring::constraints::ConstraintSet
• sequence_coupling() : protocols::constraints_additional::SequenceCouplingConstraint
• sequence_coupling_ : protocols::constraints_additional::SequenceCouplingConstraint
• sequence_file_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• sequence_indexer_ : protocols::match::output::SameSequenceGrouper
• sequence_indices() : core::sequence::SequenceAlignment
• sequence_length_ : protocols::frag_picker::JCouplingIO
• sequence_map_ : protocols::antibody::AntibodyInfo
• sequence_mapping() : core::sequence::SequenceAlignment , protocols::forge::build::BuildManager
• sequence_match_position_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_match_sequence_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_matched_fragments_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_matches() : core::conformation::Conformation
• sequence_number_resolver() : protocols::topology_broker::TopologyBroker
• sequence_number_resolver_ : protocols::topology_broker::TopologyBroker
• sequence_pos_map_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• SEQUENCE_PROFILE : core::pose::datacache::CacheableDataType
• sequence_profile() : core::scoring::constraints::SequenceProfileConstraint
• sequence_profile_ : core::scoring::constraints::SequenceProfileConstraint
• sequence_protocol() : protocols::rosetta_scripts::ParsedProtocol
• sequence_rama_tables_ : protocols::frag_picker::scores::RamaScore
• sequence_recovery() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• sequence_sep() : core::scoring::hbonds::HBEvalTuple
• sequence_shift_ : protocols::topology_broker::FibrilModelingClaimer
• sequence_space() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• SequenceAlignment() : core::sequence::SequenceAlignment
• SequenceAnnotation() : core::environment::SequenceAnnotation , protocols::environment::Environment
• SequenceAnnotationCOP : protocols::environment::EnvClaimBroker , protocols::environment::Environment , protocols::environment::ProtectedConformation
• SequenceAnnotationOP : protocols::environment::EnvClaimBroker , protocols::environment::Environment
• SequenceClaim() : protocols::topology_broker::claims::SequenceClaim
• SequenceClaimer() : protocols::topology_broker::SequenceClaimer
• SequenceComparison() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• SequenceConstraint() : core::scoring::aa_composition_energy::SequenceConstraint
• SequenceCoupling() : core::sequence::SequenceCoupling , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCoupling1BDConstraint() : protocols::constraints_additional::SequenceCoupling1BDConstraint
• SequenceCoupling1BDConstraintCreator() : protocols::constraints_additional::SequenceCoupling1BDConstraintCreator
• SequenceCouplingConstraint() : protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCouplingConstraintCreator() : protocols::constraints_additional::SequenceCouplingConstraintCreator
• SequenceCouplingCOP : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCouplingCreator() : core::sequence::SequenceCouplingCreator
• SequenceCouplingOP : protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCreator() : core::sequence::SequenceCreator
• SequenceCreatorMap : core::sequence::SequenceFactory
• SequenceDependentRefEnergy() : core::scoring::methods::SequenceDependentRefEnergy
• SequenceFactory() : core::sequence::SequenceFactory
• SequenceIdentity() : protocols::frag_picker::scores::SequenceIdentity
• SequenceLigPosMap : protocols::match::output::SameSequenceAndDSPositionGrouper
• SequenceMap : protocols::match::output::SameSequenceGrouper
• SequenceMapping() : core::id::SequenceMapping , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::forge::build::BuildManager
• SequenceMappingCOP : protocols::forge::build::BuildManager
• SequenceMappingOP : protocols::forge::build::BuildManager
• SequenceMover() : protocols::moves::SequenceMover
• SequenceNumberResolver() : protocols::topology_broker::SequenceNumberResolver
• SequenceProfile : core::scoring::constraints::SequenceProfileConstraint , core::sequence::SequenceProfile
• SequenceProfileConstraint() : core::scoring::constraints::SequenceProfileConstraint
• SequenceProfileConstraintCreator() : core::scoring::constraints::SequenceProfileConstraintCreator
• SequenceProfileCOP : core::scoring::constraints::SequenceProfileConstraint
• SequenceProfileCreator() : core::sequence::SequenceProfileCreator
• SequenceProfileMover() : protocols::simple_moves::SequenceProfileMover
• SequenceRecoveryFilter() : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• SequenceRegistrator() : core::sequence::SequenceRegistrator< T >
• sequences() : core::io::rna::RDAT
• sequences_ : core::io::rna::RDAT , core::sequence::SequenceAlignment , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::toolbox::task_operations::JointSequenceOperation
• sequences_are_in_frame() : core::sequence::SequenceAlignment
• sequenceSep_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• SequenceShiftMover() : protocols::rbsegment_relax::SequenceShiftMover
• sequential_distribution() : protocols::jd2::MPIWorkPoolJobDistributor
• sequential_distribution_ : protocols::jd2::MPIWorkPoolJobDistributor
• sequential_order() : protocols::loops::Loops
• SequentialSymmetrySlider() : protocols::simple_moves::symmetry::SequentialSymmetrySlider
• seqx : protocols::hybridization::TMalign
• seqy : protocols::hybridization::TMalign
• serial : core::io::AtomInformation
• serial_data() : protocols::wum::WorkUnitBase
• serial_data_ : protocols::wum::WorkUnitBase
• Serial_Refine() : protocols::mpi_refinement::Serial_Refine
• serialize() : core::grid::CartGrid< T > , protocols::denovo_design::components::Segment , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeAtom , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::SilentStructStore , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnitBase
• serialize_to_file() : protocols::wum::SilentStructStore
• serialize_weights() : core::scoring::ScoreFunction
• SerializedLoopList : protocols::loops::Loops
• 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::EMapVector , protocols::cyclic_peptide::DeclareBond , protocols::hybridization::TemplateHistory , protocols::jobdist::BasicJob , protocols::toolbox::AtomLevelDomainMap
• set1_selector_ : protocols::denovo_design::DisulfidizeMover
• set2_selector_ : protocols::denovo_design::DisulfidizeMover
• set_2D_torsion_to_pose() : protocols::simple_moves::bb_sampler::BBDihedralSampler2D
• set_3D_torsion_to_pose() : protocols::simple_moves::bb_sampler::BBDihedralSampler3D
• set_a_form_range() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_A_index() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• set_aa() : core::chemical::ResidueTypeSelector
• set_aa_composition_setup_files() : core::scoring::methods::EnergyMethodOptions
• set_aa_periodicity() : protocols::optimize_weights::IterativeOptEDriver
• set_aa_probabilities() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_aa_probability_set() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• set_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• set_aatypes_for_node() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_ab_fold_tree() : protocols::protein_interface_design::movers::SetAtomTree
• set_ab_info() : protocols::antibody::AntibodyFeatures
• set_abego() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::forge::components::VarLengthBuild
• set_abgar() : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• set_abort_on_failed_loop() : protocols::LoopRebuild
• set_absolute_stereochemistry() : core::chemical::Atom
• set_accept_aborted_loops_() : protocols::loops::loop_mover::IndependentLoopMover
• set_accept_blocks_missing_header() : protocols::enzdes::AddOrRemoveMatchCsts
• set_active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• set_active_restype_index() : core::pack::scmin::ResidueAtomTreeCollection
• set_active_site_grid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• set_active_site_residue_list_to_preexisting_partial_match() : protocols::match::MatcherTask
• set_add_base_pair_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_add_delete_frequency() : protocols::magnesium::MgMonteCarlo , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_add_hetatm() : protocols::hybridization::FoldTreeHybridize
• set_add_lead_zero_to_tag() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_add_ligand_to_pose() : protocols::forge::constraints::InvrotTreeRCG
• set_add_non_init_chunks() : protocols::hybridization::FoldTreeHybridize
• set_add_peptide_plane_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_add_proposal_density_factor() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_add_target_to_pose() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• set_add_to_current() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• set_add_virt_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_add_virt_res_as_root() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_additional_task_operarations() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• set_adduct_flag() : core::chemical::ResidueType
• set_adp_strategy() : core::scoring::cryst::PhenixInterface
• set_Aform_torsions() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• set_aggregate_function() : protocols::multistate_design::MultiStateFitnessFunction
• set_akash_dyepos() : protocols::anchored_design::AnchorMoversData
• set_align_file() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_align_only_over_base_atoms() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_align_to_native() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_aligned_chunk() : protocols::hybridization::InsertChunkMover
• set_alignment_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_all_bb() : protocols::ligand_docking::MoveMapBuilder
• set_all_chi() : core::conformation::Residue , protocols::ligand_docking::MoveMapBuilder
• set_all_current_jobs_as_deletable() : protocols::jd2::JobsContainer
• set_all_energies() : protocols::toolbox::DecoySetEvaluation
• set_all_extra_parameters() : core::chemical::AtomType
• set_all_jumps_minimizable() : protocols::enzdes::EnzdesBaseProtocol
• set_all_lores_score_final() : protocols::farna::RNA_FragmentMonteCarlo
• set_all_nu() : core::conformation::Residue
• set_all_ring_nu() : core::conformation::Residue
• set_all_rna_fragments_file() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_all_target_res() : protocols::toolbox::match_enzdes_util::InvrotTarget
• set_allocated() : core::graph::NegSpaceElement< T >
• set_allow_anchor_repack() : protocols::anchored_design::AnchorMoversData
• set_allow_base_pair_only_centroid_screen() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_allow_base_pair_only_screen() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• set_allow_bondangles() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_allow_bondlengths() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_allow_bulge() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_allow_bulge_at_chainbreak() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_allow_chain_boundary_jump_partner_right_at_fixed_BP() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_allow_consecutive_bulges() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_allow_cyclic() : protocols::denovo_design::connection::Connection
• set_allow_delete() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• set_allow_design_cdr() : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_allow_design_neighbor_antigen() : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_allow_design_neighbor_framework() : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_allow_dihedrals() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_allow_dof() : core::conformation::symmetry::SymDof
• set_allow_fixed_res_at_moving_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_allow_fragment_moves_in_bps() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_allow_insert_res() : protocols::farna::setup::RNA_DeNovoParameters
• set_allow_internal_hinge_moves() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_allow_internal_local_moves() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_allow_phosphate_virtualization() : core::pack::task::rna::RNA_ResidueLevelTask
• set_allow_rebuild_bulge_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_allow_scoring() : core::scoring::MembraneTopology
• set_allow_split_off() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_allow_submotif_split() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_allow_syn_pyrimidine() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_allow_tmh_scoring() : core::scoring::MembraneTopology
• set_allow_variable_bond_geometry() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• set_allow_virtual_o2prime_hydrogens() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_allow_virtual_side_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_allowed_aas() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• set_allowed_bulge_res() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_allowed_failure_before_extend() : protocols::LoopRebuild
• set_allowed_failure_before_stop() : protocols::LoopRebuild
• set_allowed_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• set_alpha() : core::pose::Pose , protocols::stepwise::sampler::rigid_body::EulerAngles
• set_alpha_beta_pattern() : protocols::ncbb::SecStructMinimizeMover
• set_alt_aa_offsets_from_edge() : core::pack::interaction_graph::PDNode
• set_alt_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_alt_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• 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 , protocols::flexpack::interaction_graph::FlexbbNode
• set_alternate_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• set_alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• set_alternate_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• set_always_use_dssp() : core::select::residue_selector::SecondaryStructureSelector
• set_amino_acid_types() : core::pack::interaction_graph::PDNode , protocols::flexpack::interaction_graph::FlexbbNode
• set_anchor_noise_constraints_mode() : protocols::anchored_design::AnchorMoversData
• set_anchor_offset() : protocols::multistate_design::PartitionAggregateFunction< T >
• set_anchor_res() : protocols::seeded_abinitio::SeedFoldTree
• set_anchor_residue() : core::conformation::symmetry::SymmData
• set_anchor_via_constraints() : protocols::anchored_design::AnchorMoversData
• set_and_reinit() : protocols::stepwise::sampler::StepWiseSamplerBase
• set_ang_D1D2D3() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_ang_U1D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_ang_U2D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_angle() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::stepwise::sampler::MC_OneTorsion
• set_angle_atom() : core::scoring::methods::GoapRsdType
• set_angle_exponent() : core::select::residue_selector::LayerSelector , core::select::util::SelectResiduesByLayer
• set_angle_max() : protocols::relax::RangeRelaxMover , protocols::simple_moves::bb_sampler::SmallBBSampler
• set_angle_params_helices_on_sheet() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_angle_params_helix_sheet() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_angle_range() : protocols::simple_moves::TorsionDOFMover , protocols::stepwise::sampler::MC_OneTorsion
• set_angle_ranges() : protocols::matdes::SymDofMoverSampler
• set_angle_shift_factor() : core::select::residue_selector::LayerSelector , core::select::util::SelectResiduesByLayer
• set_angle_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_angle_tolerance() : protocols::fldsgn::SheetConstraintGenerator
• set_angle_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_angles() : protocols::matdes::SymDofMoverSampler , protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• set_annotations() : core::io::rna::RDAT
• set_antibody_info() : protocols::antibody::SnugDock
• set_antiparallel_weight() : core::scoring::SecondaryStructureWeights
• set_apply_residue_alternative_sampler_() : protocols::stepwise::screener::SampleApplier
• set_apply_vdw_cut() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_apply_virtual_res_variant_at_dinucleotide() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_approved() : protocols::topology_broker::claims::DofClaim
• set_archive() : protocols::jd2::archive::BaseArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• set_array() : core::graph::NegSpaceElement< T >
• set_array_size() : core::graph::ArrayPool< T >
• set_assert_jump_point_in_fixed_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_assign_state_to_all_nodes_immediately() : core::pack::annealer::RotamerAssigningAnnealer
• set_assume_atom_ids_invariant() : protocols::stepwise::modeler::align::StepWiseClusterer
• set_atmid() : core::scoring::methods::GoapRsdType
• set_atom_base() : core::chemical::ResidueType
• set_atom_level_domain_map() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::farna::libraries::RNA_ChunkLibrary , protocols::farna::movers::RNA_LoopCloser , protocols::farna::movers::RNA_Minimizer , protocols::simple_moves::ConstrainToIdealMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• set_atom_type() : core::chemical::ResidueType
• set_atoms() : protocols::environment::claims::JumpClaim
• set_atoms_per_residue() : protocols::helical_bundle::parameters::BundleParameters
• set_atr_rep_screen() : protocols::stepwise::options::StepWiseBasicOptions
• set_atr_rep_screen_for_docking() : protocols::stepwise::options::StepWiseBasicOptions
• set_atrdist_params_helix_strands() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_attach_boinc_ghost_observer() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• set_attached_res() : protocols::stepwise::monte_carlo::mover::Attachment
• set_attachment_type() : protocols::stepwise::monte_carlo::mover::Attachment
• set_attachments() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• set_auto_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_auto_tune() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_auto_update() : core::scoring::NeighborList
• set_autofilter() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_autofilter_score_quantile() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_autofoldtree() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• set_autoinitialize() : protocols::anchored_design::AnchoredDesignMover
• set_autotemp() : protocols::moves::MonteCarlo
• set_babmotifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• set_backbone() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• 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_backbone_only() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• set_background_residue_rotamer_dots() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• set_backrub_mover() : protocols::backrub::BackrubProtocol
• set_bad() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob
• set_bad_nter() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::ModelCDRH3
• set_ball_radius() : core::select::residue_selector::LayerSelector
• set_base_and_pucker_state() : protocols::stepwise::modeler::rna::sugar::SugarModeling
• set_base_centroid_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• set_base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• set_base_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• set_base_type_cop() : core::chemical::ResidueType
• set_batch_description() : protocols::features::ReportToDB
• set_batch_id() : protocols::jd2::JobDistributor
• set_batch_name() : protocols::features::ReportToDB
• set_batch_relax() : protocols::hybridization::HybridizeProtocol
• set_bb() : core::kinematics::MoveMap , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::make_rot_lib::RotData , protocols::simple_moves::symmetry::SetupNCSMover
• set_bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• set_bb_bb() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_bb_bbE() : core::pack::interaction_graph::SimpleEdge
• set_bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• set_bb_dihedral_tolerance() : protocols::fldsgn::SheetConstraintGenerator
• set_bb_don_avail() : core::scoring::hbonds::HBondResidueMinData
• set_bb_grid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::UpstreamBuilder
• set_bb_id() : protocols::make_rot_lib::RotData
• set_bb_true_range() : core::kinematics::MoveMap
• set_bb_xyz_aligned() : protocols::hybridization::InsertChunkMover
• set_bbmove() : protocols::hybridization::CartesianSampler
• set_BenchMark() : protocols::antibody::AntibodyModelerProtocol
• set_benchmark() : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::RefineOneCDRLoopCentroid
• set_bendangle() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_best_score() : protocols::multistate_design::SingleState
• set_bestpose() : protocols::flxbb::FilterStructs
• set_beta() : core::pose::Pose , protocols::stepwise::sampler::rigid_body::EulerAngles
• set_bias_sampling() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• set_bIdealLoopClosing() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_big_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_big_fragments() : protocols::hybridization::MRMover
• set_bin() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::stepwise::modeler::rna::checker::VDW_Grid
• set_bin_size() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_bin_width() : protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid
• set_binary_rna_output() : protocols::farna::options::RNA_DeNovoProtocolOptions
• set_binfile_and_load() : protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• set_bInitDofs() : protocols::topology_broker::FragmentClaimer
• set_binname() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• 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_block_stack_above_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_block_stack_below_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_blueprint() : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::toolbox::task_operations::DsspDesignOperation
• set_boltz_rank() : protocols::simple_moves::GenericMonteCarloMover
• set_boltzmann_rotamer_mover() : protocols::simple_moves::CoupledMover
• set_boltzmann_temp() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• set_bond_angle() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , protocols::environment::ProtectedConformation
• set_bond_length() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , protocols::denovo_design::components::StructureData , protocols::environment::ProtectedConformation
• set_bootstrap() : protocols::rbsegment_relax::RBSegmentRelax
• set_boundary() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• set_bounding_box() : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_bps_moves() : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::setup::RNA_DeNovoPoseSetup
• set_branch_atom() : core::scoring::methods::GoapRsdType
• set_branches() : core::kinematics::MoveMap
• set_branches_true_range() : core::kinematics::MoveMap
• set_bridge_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_broker() : protocols::topology_broker::TopologyClaimer
• set_buffer_length() : protocols::simple_moves::WobbleMover
• set_build_abego() : protocols::denovo_design::connection::Connection
• set_build_all_loops_() : protocols::loops::loop_mover::IndependentLoopMover
• set_build_attempts_() : protocols::loops::loop_mover::IndependentLoopMover
• set_build_ideal_geometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_build_len() : protocols::denovo_design::connection::Connection
• set_build_round1_hits_twice() : protocols::match::downstream::ClassicMatchAlgorithm
• set_build_ss() : protocols::denovo_design::connection::Connection
• set_bulge_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_bump_check() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• set_bump_overlap_factor() : core::pack::task::residue_selector::ClashBasedRepackShellSelector , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_bump_tolerance() : protocols::match::Matcher
• set_bundle_parameters() : protocols::helical_bundle::MakeBundleHelix
• set_bundle_symmetry() : protocols::helical_bundle::parameters::BundleParametersSet
• set_bundle_symmetry_copies() : protocols::helical_bundle::parameters::BundleParametersSet
• set_bundleparametersset_index() : protocols::helical_bundle::PerturbBundle
• set_c_repeat() : core::scoring::fiber_diffraction::FiberDiffractionOptions
• set_ca_only() : protocols::simple_moves::SuperimposeMover
• set_cacb_dihedral_tolerance() : protocols::fldsgn::SheetConstraintGenerator
• set_cache_limit() : protocols::trajectory::DbTrajectoryWriter
• set_cache_selection() : core::select::residue_selector::LayerSelector
• set_cache_size() : protocols::match::output::UpstreamHitCacher
• set_cacheable_cluster_data_to_pose() : protocols::antibody::clusters::CDRClusterSet
• set_cached_string() : protocols::denovo_design::components::StructureData
• set_calc_hbond_sasaE() : protocols::analysis::InterfaceAnalyzerMover
• set_calc_rms_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_calculate_silent_Es() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• 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_calculator_by_name() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• set_camelid() : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::GraftMover
• set_camelid_constraints() : protocols::antibody::GraftCDRLoopsProtocol
• set_can_be_deleted() : protocols::jd2::Job
• set_candidates_collector() : protocols::frag_picker::FragmentPicker
• set_cap_ends() : protocols::helical_bundle::BackboneGridSampler
• set_careful_base_pair_classifier() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• set_cart_min() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_cartesian() : core::pack::RTMin , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::relax::CentroidRelax , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin , protocols::simple_moves::CombinePoseMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• set_cartesian_bonded_linear() : core::scoring::methods::EnergyMethodOptions
• set_cartesian_bonded_parameters() : core::scoring::methods::EnergyMethodOptions
• set_cartesian_minimize() : protocols::normalmode::NormalModeRelaxMover
• set_cartfrag_overlap() : protocols::hybridization::CartesianHybridize
• set_catalytic_atoms() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_ccd_close() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_ccd_close_res() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• set_cdr() : protocols::antibody::CDRSetOptions , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::antibody::design::GeneralAntibodyModeler
• set_CDR_cluster() : protocols::antibody::AntibodyInfo
• set_cdr_design_fallback_option() : protocols::antibody::design::CDRSeqDesignOptionsParser
• set_cdr_design_options() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_cdr_design_primary_option() : protocols::antibody::design::CDRSeqDesignOptionsParser
• set_cdr_graft_general_option() : protocols::antibody::design::CDRGraftDesignOptionsParser
• set_cdr_graft_mintype_options() : protocols::antibody::design::CDRGraftDesignOptionsParser
• set_cdr_graft_neighbor_mintype_options() : protocols::antibody::design::CDRGraftDesignOptionsParser
• set_cdr_only() : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_cdr_override() : protocols::antibody::design::AntibodyDesignMover
• set_cdr_range() : protocols::antibody::design::GeneralAntibodyModeler
• set_cdr_set_exclude_options() : protocols::antibody::CDRSetOptionsParser
• set_cdr_set_general_option() : protocols::antibody::CDRSetOptionsParser
• set_cdr_set_include_options() : protocols::antibody::CDRSetOptionsParser
• set_cdr_set_mintype_options() : protocols::antibody::CDRSetOptionsParser
• set_cdr_set_options() : protocols::antibody::design::AntibodyDesignMover
• set_cdrs() : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_cdrs_to_use() : protocols::antibody::clusters::CDRClusterFeatures
• set_cen_cst_weight() : protocols::hybridization::MRMover
• set_cen_dist() : protocols::make_rot_lib::RotData
• set_cen_scorefunction() : protocols::grafting::AnchoredGraftMover
• set_cen_scorefxn() : protocols::floppy_tail::FloppyTailMover , protocols::loop_modeling::LoopModeler
• set_cenrot() : protocols::hybridization::CartesianHybridize
• set_censcale() : protocols::hybridization::MRMover
• set_center() : core::scoring::MembraneEmbed , protocols::docking::DockingInitialPerturbation , protocols::membrane::geometry::EmbeddingDef , protocols::qsar::scoring_grid::SingleGrid
• set_center_vector() : protocols::viewer::ConformationViewer
• set_centroid() : core::import_pose::ImportPoseOptions , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::topology_broker::ConstraintClaimer
• set_centroid_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_centroid_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_centroid_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_centroid_density_weight() : protocols::hybridization::MRMover
• set_centroid_loop_building() : protocols::antibody_legacy::CDRH3Modeler
• set_centroid_output() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_centroid_score_diff_cut() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_centroid_scorefunction() : protocols::anchored_design::AnchorMoversData
• set_centroid_scorefxn() : protocols::abinitio::Protocol , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_centroid_screen() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_centroid_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_chain() : protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::toolbox::task_operations::JointSequenceOperation
• set_chain_boundaries() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_chain_connections() : protocols::farna::movers::RNA_JumpMover
• set_chain_strings() : core::select::residue_selector::ChainSelector
• set_chain_to_design() : protocols::hotspot_hashing::HotspotStubSet
• set_chainbreak_bias() : protocols::rigid::RigidBodyMotionMover
• set_chainbreak_max() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_chainbreak_ramping() : protocols::abinitio::abscript::AbscriptStageMover
• set_chainbreak_weight() : protocols::anchored_design::AnchorMoversData , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_chains() : core::io::silent::SilentStruct , core::pose::PDBInfo , protocols::simple_moves::DeleteChainsMover
• set_chains_whose_residues_are_separate_chemical_entities() : core::io::StructFileRepOptions
• set_change_chi_without_replacing_residue() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• set_changed() : core::scoring::FACTSResidueInfo
• set_charged_residues_map() : core::scoring::methods::PBLifetimeCache
• set_check_abego() : protocols::denovo_design::connection::Connection
• set_check_if_residues_are_Ctermini() : core::io::StructFileRepOptions
• set_check_if_residues_are_Ntermini() : core::io::StructFileRepOptions
• set_check_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_check_ss() : protocols::simple_moves::ClassicFragmentMover
• set_checkpoint_gzip() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_checkpoint_prefix() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_checkpoint_rename() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_checkpoint_write_interval() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_chemical_bond_from_upstream_to_downstream() : protocols::match::output::UpstreamDownstreamCollisionFilter
• set_chi() : core::conformation::Residue , core::kinematics::MoveMap , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose , protocols::simple_moves::symmetry::SetupNCSMover
• 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_choices() : protocols::genetic_algorithm::DiscreteRandomizer
• set_choose_best_solution() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_choose_random() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• set_chunk_coverage() : protocols::farna::RNA_FragmentMonteCarlo
• set_chunk_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_chunk_pdb_files() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_chunk_silent_files() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_ciBR_only() : core::pack::annealer::FASTERAnnealer , protocols::pack_daemon::FASTER_IG_Repacker
• set_cif_files() : core::scoring::cryst::PhenixInterface
• set_claim_right() : protocols::topology_broker::FragmentClaimer
• set_clash_check_types() : protocols::match::downstream::TargetRotamerCoords
• set_clash_checking() : protocols::match::downstream::TargetRotamerCoords
• set_client() : protocols::environment::ScriptCM
• set_close_loops() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_close_loops_after_each_move() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_closest_states_on_other_bbs() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode
• set_closure_attempts() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_cluster() : protocols::antibody::clusters::BasicCDRClusterSet , protocols::toolbox::KClusterElement
• set_cluster_by_all_atom() : protocols::cluster::GatherPosesMover
• set_cluster_by_all_atom_rmsd() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_cluster_by_protein_backbone() : protocols::cluster::GatherPosesMover
• set_cluster_csts_data_cutoff() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_cluster_csts_use_mean_cst_data() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_cluster_csts_use_outlier_data() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_cluster_data() : protocols::antibody::clusters::CDRClusterSet
• set_cluster_num() : protocols::make_rot_lib::RotData
• set_cluster_radius() : protocols::cluster::ClusterBase , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_cluster_rmsd() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::options::StepWiseBasicOptions
• set_clusters() : protocols::antibody::clusters::BasicCDRClusterSet
• set_cmd_line_defaults() : protocols::carbohydrates::GlycanRelaxMover
• set_combine_long_loop_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_combine_ratio() : protocols::constraints_additional::ConstraintEvaluator , protocols::topology_broker::ConstraintClaimer
• set_command() : protocols::simple_filters::ExternalEvaluator
• set_commandline_options() : protocols::simple_moves::RingConformationMover
• set_comments() : core::io::rna::RDAT
• set_comp1_ids() : protocols::denovo_design::connection::Connection
• set_comp2_ids() : protocols::denovo_design::connection::Connection
• set_comp_constraint_aa() : protocols::fldsgn::potentials::AACompositionEnergy
• set_comparer_info() : protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• set_completed() : protocols::jd2::Job
• set_compute_interface_delta_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• set_compute_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• set_compute_interface_sc() : protocols::analysis::InterfaceAnalyzerMover
• set_compute_packstat() : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• set_compute_separated_sasa() : protocols::analysis::InterfaceAnalyzerMover
• set_computed() : core::scoring::PolymerBondedEnergyContainer
• set_conformational_data() : core::scoring::methods::PBLifetimeCache
• set_connect_info_cutoff() : core::io::StructFileRepOptions
• set_connecting_bond_dist() : protocols::denovo_design::connection::Connection
• set_cons_design_data_source() : protocols::antibody::task_operations::AddCDRProfilesOperation
• set_conserved() : core::pose::datacache::PositionConservedResiduesStore
• set_consider_already_bonded() : protocols::cyclic_peptide::TryDisulfPermutations
• set_consideration() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• set_considering_alternate_state() : protocols::flexpack::interaction_graph::FlexbbNode
• set_const_data() : core::pose::Pose
• set_constrain() : protocols::ncbb::SecStructMinimizeMover
• set_constrain_bb_angle() : protocols::fldsgn::SheetConstraintGenerator
• set_constrain_bb_cacb_dihedral() : protocols::fldsgn::SheetConstraintGenerator
• set_constrain_bb_dihedral() : protocols::fldsgn::SheetConstraintGenerator
• set_constrain_ca_ca_dist() : protocols::fldsgn::SheetConstraintGenerator
• set_constrain_cter() : protocols::antibody::AntibodyModelerProtocol
• set_constrain_vlvh_qq() : protocols::antibody::AntibodyModelerProtocol
• set_constraint() : protocols::md::MDBase
• set_constraint_file() : protocols::fldsgn::BluePrintBDR , protocols::hybridization::FoldTreeHybridize
• set_constraint_func() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::forge::constraints::InverseRotamersRCG
• set_constraint_weight() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::relax::FastRelax , protocols::simple_moves::DisulfideInsertionMover
• set_constraints() : core::scoring::constraints::CstMinimizationData , protocols::simple_filters::ConstraintScoreCutoffFilter
• set_constraints_from_link_records() : core::io::StructFileRepOptions
• set_constraints_NtoC() : protocols::fldsgn::BluePrintBDR
• set_contents() : protocols::checkpoint::FileBuffer
• set_context_pose() : protocols::flexpack::OtherContextScoreFunction
• set_context_update_step() : protocols::md::MDBase
• set_conventional_chains() : core::pose::full_model_info::FullModelParameters
• set_conventional_numbering() : core::pose::full_model_info::FullModelParameters
• set_coord_cst_weight_array() : protocols::abinitio::LoopJumpFoldCst
• set_coord_frame_ref() : core::scoring::MultipoleElecResidueInfo
• set_coordinate_cacher() : protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• set_coordinate_constraints_during_minimize() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• set_coordinates() : core::fragment::BBTorsionSRFD
• set_coordinates_for_rotamer() : protocols::match::downstream::TargetRotamerCoords
• set_coords() : core::io::silent::RNA_SilentStruct
• set_coords_for_clash_check() : protocols::match::downstream::TargetRotamerCoords
• set_coords_for_residue() : protocols::features::ResidueConformationFeatures
• set_coords_for_residue_from_compact_schema() : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• set_coords_for_residues() : protocols::features::ProteinResidueConformationFeatures
• set_copy_DOF() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_copy_dofs_info() : protocols::simple_moves::CopyDofMover
• set_core_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• set_count_data() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• set_couplings() : core::pack::task::operation::SetRotamerCouplings
• set_create_db() : protocols::loophash::LoopHashLibrary
• set_crossover() : core::scoring::etable::count_pair::CountPairGeneric
• set_crystinfo() : core::pose::PDBInfo
• set_cst_action() : protocols::enzdes::AddOrRemoveMatchCsts
• set_cst_block() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• set_cst_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• set_cst_file() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::topology_broker::ConstraintClaimer
• set_cst_file_name() : protocols::simple_moves::SequenceProfileMover
• set_cst_root() : protocols::topology_broker::CoordConstraintClaimer
• set_cst_sdev() : protocols::normalmode::NormalModeRelaxMover
• set_cst_source() : protocols::constraints_additional::ConstraintEvaluator
• set_cst_string() : core::pose::full_model_info::FullModelParameters
• set_cst_weight() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::docking::DockingProtocol , protocols::rbsegment_relax::RBSegmentRelax
• set_cst_width() : protocols::rbsegment_relax::RBSegmentRelax
• set_cstAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• set_cstfile() : protocols::denovo_design::constraints::FileConstraintGenerator , protocols::forge::constraints::InvrotTreeRCG
• set_cstid_list() : protocols::enzdes::RepackWithoutLigandFilter
• set_cstInfo() : protocols::jumping::ResiduePairJump
• set_cstio() : protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• set_cstweight() : protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_Relax
• set_CterInsert() : protocols::antibody::AntibodyModelerProtocol
• set_cterm_included() : protocols::denovo_design::components::Segment
• set_cumulative_peak_volume() : protocols::noesy_assign::CrossPeak
• set_cur_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_curr_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• set_curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• set_curr_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• set_current() : core::pack::interaction_graph::SimpleNode
• set_current_confnum() : protocols::docking::DockingEnsemble
• set_current_cycle() : protocols::features::TrajectoryMapFeatures
• set_current_distance() : core::scoring::loop_graph::LoopScoreInfo
• set_current_job() : protocols::moves::Mover
• set_current_job_by_index() : protocols::jd2::JobDistributor
• set_current_jump() : protocols::simple_moves::symmetry::SymmetrySlider
• set_current_no_E_update() : core::pack::interaction_graph::SimpleNode
• set_current_pose() : protocols::simple_moves::MSDMover
• set_current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• set_current_tag() : protocols::moves::Mover , protocols::moves::MoverContainer
• set_current_temp() : protocols::canonical_sampling::TemperingBase
• set_current_weight() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• set_custom_angle() : protocols::backrub::BackrubMover
• set_custom_data() : protocols::antibody::design::MutateFrameworkForCluster
• set_custom_rama_table() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• set_cut() : protocols::loops::Loop
• set_cut_resi() : protocols::denovo_design::connection::Connection
• set_cut_resis() : protocols::denovo_design::connection::Connection
• set_cutoff() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ScoreCutoffFilter
• set_cutoff_distance() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• set_cutoff_lr() : core::scoring::CenHBPotential
• set_cutoff_sr() : core::scoring::CenHBPotential
• set_cutoffs() : core::select::residue_selector::LayerSelector
• set_cutpoint() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• set_cutpoint_closed_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_cutpoint_open_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_cutpoints_closed() : protocols::farna::setup::RNA_DeNovoParameters
• set_cutpoints_open() : protocols::farna::setup::RNA_DeNovoParameters
• set_cycle() : protocols::noesy_assign::PeakAssignmentParameters
• set_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::farna::FARNA_Optimizer , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::magnesium::MgMonteCarlo , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_cycles_adjust() : protocols::abinitio::abscript::AbscriptStageMover
• set_cycles_inner() : protocols::docking::membrane::MPDockingMover
• set_cycles_outer() : protocols::docking::membrane::MPDockingMover
• set_cyd_res_at_termini() : protocols::simple_moves::DisulfideInsertionMover
• set_cyd_seqpos() : protocols::simple_moves::DisulfideInsertionMover
• set_cys_types() : protocols::denovo_design::DisulfidizeMover
• 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_data_int() : protocols::denovo_design::components::StructureData
• set_data_real() : protocols::denovo_design::components::StructureData
• set_data_source() : protocols::toolbox::task_operations::ConservativeDesignOperation
• set_data_str() : protocols::denovo_design::components::StructureData
• set_database_name() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• set_database_pq_schema() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• set_db_path() : protocols::loophash::LoopHashLibrary
• set_dcut() : protocols::noesy_assign::DistanceScoreMover
• set_ddG_cutoff() : protocols::pmut_scan::PointMutScanDriver
• set_ddG_filter() : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• set_debug() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• set_decoy_compatibility() : protocols::noesy_assign::PeakAssignment
• set_decoy_tag() : core::io::silent::SilentStruct
• set_decoys_returned() : protocols::jd2::archive::Batch
• set_deep_optimization() : protocols::antibody::GraftedStemOptimizer
• set_default() : core::scoring::FACTSPotential , core::scoring::methods::GoapEnergy , core::scoring::TMscore , protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CloseOneCDRLoop , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::docking::DockTaskFactory , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::InterfaceSidechainMinMover , protocols::docking::SidechainMinMover , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::mpi_refinement::Scheduler , protocols::mpi_refinement::StructAvrgMover , protocols::relax::ClassicRelax , protocols::simple_moves::CombinePoseMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• set_default_allow_bondangles() : protocols::helical_bundle::MakeBundle
• set_default_allow_bondlengths() : protocols::helical_bundle::MakeBundle
• set_default_allow_dihedrals() : protocols::helical_bundle::MakeBundle
• set_default_cen_scorefunction() : protocols::grafting::AnchoredGraftMover
• set_default_coordinate_settings() : protocols::relax::RelaxProtocolBase
• set_default_crick_params_file() : protocols::helical_bundle::MakeBundle
• set_default_delta_omega0() : protocols::helical_bundle::MakeBundle
• set_default_delta_omega1_all() : protocols::helical_bundle::MakeBundle
• set_default_delta_t() : protocols::helical_bundle::MakeBundle
• set_default_fa_scorefunction() : protocols::grafting::AnchoredGraftMover
• set_default_helix_length() : protocols::helical_bundle::MakeBundle
• set_default_invert() : protocols::helical_bundle::MakeBundle
• set_default_layer_residues() : protocols::flxbb::LayerDesignOperation
• set_default_mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::LoopRebuild , protocols::symmetric_docking::SymDockingLowRes
• set_default_minimization_settings() : protocols::relax::RelaxProtocolBase
• set_default_minimizer() : protocols::relax::ClassicRelax
• set_default_minoption() : protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::NormalModeRelaxMover , protocols::normalmode::TorsionNormalModeMover
• set_default_modes() : protocols::normalmode::NormalModeMultifunc
• set_default_move_map() : protocols::symmetric_docking::SymDockingLowRes
• set_default_movemap() : protocols::grafting::AnchoredGraftMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::RelaxProtocolBase
• set_default_moveset_phase1() : protocols::relax::ClassicRelax
• set_default_moveset_phase2() : protocols::relax::ClassicRelax
• set_default_moveset_phase3() : protocols::relax::ClassicRelax
• set_default_omega0() : protocols::helical_bundle::MakeBundle
• set_default_omega1() : protocols::helical_bundle::MakeBundle
• set_default_options() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• set_default_protocol() : protocols::symmetric_docking::SymDockingLowRes
• set_default_r0() : protocols::helical_bundle::MakeBundle
• set_default_rama_table_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• set_default_repeating_unit_offset() : protocols::helical_bundle::MakeBundle
• set_default_residue_name() : protocols::helical_bundle::MakeBundle
• set_default_score_functions() : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashLibrary
• set_default_scores() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• set_default_settings() : protocols::loop_build::LoopMover_SlidingWindow , protocols::LoopRebuild , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_default_sse_residues() : protocols::toolbox::task_operations::DsspDesignOperation
• set_default_value() : protocols::helical_bundle::PerturbBundleOptions
• set_default_z0_offset() : protocols::helical_bundle::MakeBundle
• set_default_z1() : protocols::helical_bundle::MakeBundle
• set_default_z1_offset() : protocols::helical_bundle::MakeBundle
• set_defaults() : core::scoring::func::SOGFunc_Impl , core::scoring::sasa::SasaCalc , protocols::abinitio::AbrelaxMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::analysis::InterfaceAnalyzerMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::CDRSetOptions , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::antibody_legacy::Antibody , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::LinkageConformerMover , protocols::docking::DockSetupMover , protocols::docking::membrane::MPDockingMover , protocols::docking::TemperedDocking , protocols::features::InterfaceFeatures , protocols::grafting::AnchoredGraftMover , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::loophash::LoopHashSampler , protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::loophash::WorkUnit_LoopHash , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_mover::IndependentLoopMover , protocols::md::MDBase , protocols::membrane::FlipMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::TiltMover , protocols::mpi_refinement::Clusterer , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::MultiObjective , protocols::mpi_refinement::Serial_Refine , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Relax , protocols::relax::CentroidRelax , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::WobbleMover , protocols::toolbox::task_operations::ConservativeDesignOperation , protocols::toolbox::task_operations::MutationSetDesignOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer , protocols::wum::WorkUnit_MoverWrapper
• set_defaults_() : protocols::comparative_modeling::LoopRelaxMover , protocols::simple_moves::SaneMinMover
• set_defaults_from_cmdline() : protocols::canonical_sampling::CanonicalSamplingMover
• set_degree_vicinity() : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• set_degrees() : protocols::nonlocal::HelixRotate
• set_delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• set_delta() : core::pose::Pose
• set_delta_omega0() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_delta_omega1() : protocols::helical_bundle::parameters::BundleParameters
• set_delta_omega1_all() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_delta_omega1_guesses() : protocols::helical_bundle::FitSimpleHelix
• set_delta_t() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_delta_z1() : protocols::helical_bundle::parameters::BundleParameters
• set_delta_z1_guesses() : protocols::helical_bundle::FitSimpleHelix
• set_denovo_scorefxn() : protocols::farna::RNA_FragmentMonteCarlo
• set_density_sc_scale_byres() : core::scoring::methods::EnergyMethodOptions
• set_deriv_check() : protocols::farna::options::RNA_MinimizerOptions
• set_deriv_check_result() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , protocols::normalmode::NormalModeMultifunc
• set_deriv_cutoff() : core::optimization::BrentLineMinimization
• set_derivative_graph() : core::scoring::symmetry::SymmetricEnergies
• set_design() : protocols::cryst::DockLatticeMover , protocols::docking::DockingProtocol , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzRepackMinimize , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• set_design_chains() : protocols::docking::DockTaskFactory
• set_design_framework_conservative() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_design_framework_conserved_res() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_design_H3_stem() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_design_layer() : core::select::util::SelectResiduesByLayer
• set_design_layers() : protocols::flxbb::LayerDesignOperation
• set_design_loop() : protocols::toolbox::task_operations::RestrictToLoops
• set_design_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• set_design_options() : protocols::antibody::task_operations::AddCDRProfilesOperation
• set_design_protocol() : protocols::antibody::design::AntibodyDesignMover
• set_design_shell() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• set_design_target_res() : protocols::enzdes::DetectProteinLigandInterface
• set_design_taskset() : protocols::flxbb::FlxbbDesign
• set_designable_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• set_desymmeterize() : protocols::match::upstream::DunbrackSCSampler
• set_detect_bonds() : protocols::simple_moves::DeleteChainsMover
• set_detect_pseudobonds() : protocols::simple_moves::DeleteChainsMover
• set_dihedral() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• set_dihedral_constraint_weight() : protocols::antibody::AntibodyCDRGrafter
• set_dihedral_pattern() : protocols::ncbb::SecStructMinimizeMover
• set_dihedrals() : protocols::ncbb::SecStructMinimizeMover
• set_dis() : protocols::forge::remodel::ResidueVicinityInfo
• set_dis_D1D2() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_dis_D2D3() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_disable_packing_and_design() : protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation
• set_disable_sampling_of_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_disabled() : protocols::checkpoint::CheckPointer
• set_disallow_bps_at_extra_min_res() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_disallow_deletion_of_last_residue() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• set_disallow_quench() : core::pack::annealer::SimAnnealerBase
• set_disallow_realign() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• set_discovered_out() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• set_dist() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_dist_exponent() : core::select::residue_selector::LayerSelector , core::select::util::SelectResiduesByLayer
• set_dist_midpoint() : core::select::util::SelectResiduesByLayer
• set_dist_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• 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_dist_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_distance() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::select::residue_selector::NeighborhoodResidueSelector , protocols::fldsgn::SheetConstraintGenerator , protocols::forge::constraints::NtoCConstraintGenerator , protocols::nonlocal::SheetTranslate
• set_distance_cutoff() : protocols::contact_map::ContactMap
• set_distance_sphere() : protocols::qsar::scoring_grid::SingleGrid
• set_distance_sphere_for_atom() : protocols::qsar::scoring_grid::SingleGrid
• set_distance_tolerance() : protocols::fldsgn::SheetConstraintGenerator
• set_distinguish_pucker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_disulf() : protocols::hybridization::MRMover
• set_disulfide_atom_name() : core::chemical::ResidueType
• set_disulfide_file() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_dlig_nmeg_limit() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• set_do_add_delete() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_do_checks() : protocols::stepwise::modeler::align::StepWiseClusterer
• set_do_minimize() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• set_do_not_sample_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_do_remodel() : protocols::denovo_design::connection::Connection
• set_do_screen() : protocols::stepwise::screener::AlignRMSD_Screener
• set_do_screens() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• set_do_sfxn_eval_every_iteration() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_dock_high_res_scorefunction() : protocols::antibody::design::GeneralAntibodyModeler
• set_dock_jump() : protocols::antibody::LHRepulsiveRamp
• set_dock_low_res_scorefunction() : protocols::antibody::design::GeneralAntibodyModeler
• set_dock_mcm_protocol() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_dock_min() : protocols::docking::DockingProtocol
• set_dock_min_protocol() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_dock_pert() : protocols::docking::DockingInitialPerturbation
• set_dock_post_graft() : protocols::antibody::design::AntibodyDesignMover
• set_dock_ppk() : protocols::docking::DockingPrepackProtocol , protocols::symmetric_docking::SymDockProtocol
• set_dock_ppk_protocol() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_dock_rounds() : protocols::antibody::design::AntibodyDesignMover
• set_dock_rtmin() : protocols::symmetric_docking::SymDockProtocol
• set_dock_score_func() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• set_docking_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_docking_highres_mover() : protocols::docking::DockingProtocol
• set_docking_local_refine() : protocols::docking::DockingProtocol
• set_docking_pose() : protocols::enzdes::PredesignPerturbMover
• set_dof() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pose::Pose , protocols::environment::ProtectedConformation
• set_DOF() : protocols::simple_moves::TorsionDOFMover
• set_dof_moved() : core::conformation::Conformation
• set_dofs() : core::conformation::symmetry::SymmetryInfo
• set_dofs_from_tag() : protocols::helical_bundle::MakeBundle
• set_domain() : protocols::toolbox::AtomLevelDomainMap
• set_donor_structure() : protocols::antibody::AntibodyCDRGrafter
• set_downstream_algorithm() : protocols::match::upstream::BuildSet
• set_downstream_builder() : protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::PDBWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::output::UpstreamDownstreamCollisionFilter
• set_downstream_master() : protocols::match::output::DownstreamCoordinateKinemageWriter , protocols::match::output::SingleDownstreamResidueWriter
• set_downstream_orientation_atoms() : protocols::match::MatcherTask
• set_downstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::UpstreamDownstreamCollisionFilter
• set_downstream_restype() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_downstream_writer() : protocols::match::output::WriteKinemageOutputter , protocols::match::output::WriteUpstreamCoordinateKinemage
• set_drift() : protocols::simple_moves::GenericMonteCarloMover
• set_ds_atom_ids_needed() : protocols::match::downstream::TargetRotamerCoords
• set_ds_coords_needed() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_dSASA_cutoff() : protocols::features::InterfaceFeatures
• set_dsbuilder() : protocols::match::downstream::DownstreamAlgorithm
• set_dswriter() : protocols::match::output::WriteUpstreamHitKinemage
• set_dt() : protocols::md::MDBase
• set_dump() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• set_dump_pdb() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_BasicOptions
• set_dump_weights_file() : protocols::abinitio::LoopJumpFoldCst
• set_e2g2_diubi_fold_tree() : protocols::ub_e2c::ubi_e2c_modeler
• set_ecounter() : protocols::surface_docking::FullatomRelaxMover
• set_edge() : core::scoring::rna::data::RNA_Datum
• set_edge1() : core::pose::rna::BasePair
• set_edge2() : core::pose::rna::BasePair
• 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 , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• set_effective_sequence_separation() : core::scoring::constraints::MultiConstraint
• set_elec_sigmoidal_die_params() : core::scoring::methods::EnergyMethodOptions
• set_eliminated_due_to_dist_violations() : protocols::noesy_assign::CrossPeak
• set_elimination_candidate() : protocols::noesy_assign::CrossPeak
• set_elimination_comment() : protocols::noesy_assign::CrossPeak
• set_else() : protocols::filters::IfThenFilter
• set_empty_voxel_color() : protocols::match::Bool3DGridKinemageWriter
• set_enable_design() : protocols::relax::FastRelax
• set_end() : protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::rbsegment_relax::RBResidueRange
• set_end_bias() : protocols::simple_moves::ClassicFragmentMover
• set_energy() : core::scoring::PolymerBondedEnergyContainer , protocols::make_rot_lib::RotData
• set_energy_cutoff() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_energy_method_options() : core::scoring::ScoreFunction
• set_energy_reportstep() : protocols::md::MDBase
• set_energy_state() : core::scoring::methods::PBLifetimeCache
• set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• set_energy_to_beat() : protocols::vip::VIP_Mover
• set_enforce_bb_contiguity() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_ensemble1() : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingProtocol
• set_ensemble2() : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingProtocol
• set_ensemble_diversity() : protocols::simple_moves::ShakeStructureMover
• set_entity_correspondence() : protocols::pack_daemon::PackDaemon
• set_entity_element() : protocols::genetic_algorithm::Entity
• set_entity_length() : protocols::genetic_algorithm::EntityRandomizer
• set_entity_resfile() : protocols::pack_daemon::DaemonSet
• set_entity_template() : protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::GeneticAlgorithmBase
• set_enumerate() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_enumerate_ligand_rotamers() : protocols::match::MatcherTask
• set_enumeration_shell() : core::scoring::FACTSResidueInfo
• set_environment() : protocols::environment::ProtectedConformation
• set_enz_input_data() : protocols::match::MatcherTask
• set_enzdes_loops_file() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• set_enzio_param() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• set_epitope_residues() : protocols::antibody::design::AntibodyDesignMover
• set_eps() : protocols::make_rot_lib::RotData
• set_epsilon() : core::pose::Pose
• set_equiv() : core::pack::rotamer_set::RotamerLinks , protocols::simple_moves::symmetry::NCSResMapping
• set_erraser() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_error_out_on_complex_cycles() : core::scoring::loop_graph::LoopGraph
• set_errorfull_deltaE_threshold() : core::pack::interaction_graph::AnnealableGraphBase , 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::MultiplexedAnnealableGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• set_etable() : core::scoring::ScoreFunction
• set_euler_alpha_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_angle_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_angle_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_angle_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_bin_widths() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_euler_gamma_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_z_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_z_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_z_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_euler_z_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_evaluate_local() : protocols::jd2::archive::EvaluatedArchive
• set_evaluation() : protocols::abinitio::Protocol , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_evaluator() : protocols::match::output::MatchProcessor
• set_evaluators() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• set_excise_mini_pose() : protocols::magnesium::MgHydrater , protocols::magnesium::MgWaterHydrogenPacker
• set_exclude_polar_atoms_by_charge() : core::scoring::sasa::SasaCalc
• set_excluded_positions() : protocols::helix_capper::HelixNCapperMover , protocols::vip::VIP_Mover
• set_excluded_residues() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• set_existing_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• set_exit_if_missing_heavy_atoms() : core::io::StructFileRepOptions
• set_exit_on_fail() : protocols::stepwise::legacy::screener::RNA_AtrRepScreener
• set_expand_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_expecting_n_ligands() : protocols::metal_interface::ZincSiteFinder
• set_experimental_ddg() : protocols::optimize_weights::DDGMutationOptEData
• set_experimental_ddg_bind() : protocols::optimize_weights::DDGBindOptEData
• set_explicit_hydrogen_included_radii_set() : core::scoring::sasa::SasaCalc
• set_extend_h3() : protocols::antibody::ModelCDRH3
• set_extend_h3_before_modeling() : protocols::antibody::AntibodyModelerProtocol
• set_extend_ss() : protocols::denovo_design::connection::Connection
• set_extended() : protocols::loops::Loop , protocols::loops::Loops
• set_extended_loop() : protocols::LoopRebuild
• set_extended_torsions() : protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• set_extended_torsions_and_idealize_loops() : protocols::abinitio::KinematicTaskControl
• set_external_position() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• set_external_position_for_resA() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• set_external_position_for_resA_in_parameter_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• set_external_position_for_resB() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• set_external_position_for_resB_in_parameter_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• set_extra_beta() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_extra_chi() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_extra_data_1() : protocols::wum::WorkUnitBase
• set_extra_data_2() : protocols::wum::WorkUnitBase
• set_extra_data_3() : protocols::wum::WorkUnitBase
• set_extra_epsilon() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_extra_loose_rep_cutoff() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• set_extra_minimize_chi_res() : protocols::farna::options::RNA_MinimizerOptions
• set_extra_minimize_res() : protocols::farna::options::RNA_MinimizerOptions , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_extra_parameter() : core::chemical::AtomType
• set_extra_penalty() : protocols::rbsegment_relax::SequenceShiftMover
• set_extra_samples() : core::pack::rotamer_set::RotamerSet_
• set_extrapolate_scale() : protocols::normalmode::NormalModeRelaxMover
• set_fa_cst_weight() : protocols::hybridization::MRMover
• set_fa_dun_cutoff() : protocols::match::upstream::BuildSet
• set_fa_dun_cutoff_for_constraint() : protocols::match::Matcher
• set_fa_score_function() : protocols::relax::CentroidRelax
• set_fa_scorefunction() : protocols::grafting::AnchoredGraftMover , protocols::hybridization::CartesianSampler
• set_fa_scorefxn() : protocols::floppy_tail::FloppyTailMover , protocols::loop_modeling::LoopModeler
• set_facet_alpha() : protocols::match::Bool3DGridKinemageWriter
• set_facet_color() : protocols::match::Bool3DGridKinemageWriter
• set_facet_master() : protocols::match::Bool3DGridKinemageWriter
• set_fallback_strategy() : protocols::antibody::task_operations::AddCDRProfilesOperation
• set_farray_from_sso() : core::pose::datacache::SpecialSegmentsObserver
• set_fast() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• 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_figure_out_prepack_res() : protocols::stepwise::modeler::StepWiseModeler
• set_file_reading_token() : protocols::loops::Loops
• set_filename() : core::io::silent::SilentFileData , protocols::anchored_design::Anchor , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base
• set_filename_root() : protocols::dna::DnaInterfacePacker
• set_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• set_filter() : protocols::cluster::GatherPosesMover , protocols::docking::DockMCMProtocol , protocols::hotspot_hashing::HotspotStub , protocols::moves::FilterReporterMover
• set_filter_attach_boinc_ghost_observer() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_filter_behaviour() : protocols::helical_bundle::BundleReporterFilter
• set_filter_bin() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_filter_by_lj() : protocols::match::output::MatchCollisionFilter
• set_filter_by_phipsi() : protocols::loophash::LoopHashSampler
• set_filter_chain_closure() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_filter_chain_closure_distance() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_filter_chain_closure_halfway() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_filter_complex_cycles() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_filter_during_design() : protocols::flxbb::FlxbbDesign
• set_filter_for_previous_clash() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_filter_for_previous_contact() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_filter_lores_base_pairs() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_filter_lores_base_pairs_early() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_filter_native_big_bins() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_filter_off() : protocols::flxbb::FilterStructs
• set_filter_omega() : protocols::anchored_design::AnchoredDesignMover
• set_filter_on() : protocols::flxbb::FilterStructs
• set_filter_rama_cutoff_energy() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_filter_resnum() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_filter_SASA() : protocols::anchored_design::AnchoredDesignMover
• set_filter_score() : protocols::anchored_design::AnchoredDesignMover
• set_filter_structs() : protocols::flxbb::DesignTask
• set_filter_templates() : protocols::hybridization::FoldTreeHybridize
• set_filter_type() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• set_filter_user_alignment_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_filter_virtual_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_filter_weight() : protocols::topology_broker::ConstraintClaimer
• set_filters() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_final_fold_tree() : protocols::abinitio::KinematicControl
• set_final_solution() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_finer_sampling_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_finish_scorefxn() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• set_finish_stage() : protocols::abinitio::IterativeBase
• set_first() : core::scoring::packstat::trace
• set_first_cycle() : protocols::docking::DockMCMProtocol
• set_fitness() : protocols::genetic_algorithm::Entity
• set_five_prime_chain_break_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_five_prime_phosphate_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• set_fix_backbone() : protocols::simple_moves::CoupledMover
• set_fix_cataa() : protocols::enzdes::EnzdesBaseProtocol
• set_fix_catalytic_aa() : protocols::enzdes::SetCatalyticResPackBehavior
• set_fix_ligands() : protocols::rbsegment_relax::RBSegmentRelax
• set_fixed_energies() : core::scoring::MinimizationGraph
• set_fixed_if_moving() : protocols::toolbox::AtomLevelDomainMap
• set_fixed_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_fixed_residues() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_fixed_stub() : core::scoring::constraints::LocalCoordinateConstraint
• set_flags() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• set_flank_relax() : protocols::antibody::RefineOneCDRLoop
• set_flank_residue_min() : protocols::antibody::AntibodyModelerProtocol , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_flank_residue_size() : protocols::antibody::AntibodyModelerProtocol
• set_flank_size() : protocols::antibody::GraftOneCDRLoop , protocols::antibody::RefineOneCDRLoop
• set_flat_bottom_constraints() : protocols::fldsgn::SheetConstraintGenerator
• set_flat_score_multiply() : core::conformation::symmetry::SymmetryInfo
• set_flexseg_considering_alt_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_flip_rate() : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• set_floating_base() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_floating_base_anchor_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_focus() : core::select::residue_selector::NeighborhoodResidueSelector
• set_focus_selector() : core::select::residue_selector::NeighborhoodResidueSelector
• set_focused_geomcst_id() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_fold_tree() : core::io::silent::RNA_SilentStruct , protocols::denovo_design::components::StructureData , protocols::rigid::RigidBodyMotionMover , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_fold_tree_and_chainbreaks() : protocols::jumping::JumpSample
• set_fold_tree_and_cutpoints() : protocols::anchored_design::AnchoredDesignMover
• set_fold_tree_from_loops() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• set_fold_tree_from_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• set_fold_tree_in_pose() : protocols::jumping::JumpSample
• set_fold_tree_io() : core::import_pose::ImportPoseOptions , core::io::pose_to_sfr::PoseToStructFileRepConverter , core::io::StructFileRepOptions
• set_fold_tree_root() : protocols::simple_moves::SetTorsion
• set_folding_window() : protocols::noesy_assign::CrossPeakInfo
• set_foldtree() : protocols::docking::EllipsoidalRandomizationMover , protocols::moves::ChangeFoldTreeMover , protocols::seeded_abinitio::SeedFoldTree
• set_force_align() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_force_anti_chi_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_force_bitflip() : core::io::silent::SilentStruct
• set_force_centroid_interaction() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_force_cluster() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• set_force_ideal_chainbreak() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_force_internal() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_force_job_purging() : protocols::jd2::JobsContainer
• set_force_nonideal() : protocols::relax::FastRelax
• set_force_north_paper_db() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• set_force_north_sugar_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_force_phosphate_instantiation() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_force_repack() : protocols::loop_modeling::utilities::PrepareForFullatom
• set_force_south_sugar_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_force_submotif_without_intervening_bulge() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_force_syn_chi_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_force_unique_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• set_force_user_defined_jumps() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_forced_silent_struct_type() : protocols::jd2::SilentFileJobOutputter
• set_forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• set_format_from_peak() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• set_frac_by_recomb() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_fraction() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaConfig , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• set_fractions() : core::fragment::SecondaryStructure
• set_frag3() : protocols::anchored_design::AnchorMoversData
• set_frag_1mer_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_frag_files() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_frag_size() : protocols::farna::movers::RNA_FragmentMover
• set_frag_sizes() : protocols::hybridization::CartesianSampler
• set_frag_weight_aligned() : protocols::hybridization::FoldTreeHybridize
• set_fragment_probs() : protocols::hybridization::CartesianHybridize
• set_fragments() : protocols::jd2::parser::FragmentReader , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign , protocols::simple_moves::FragmentMover , protocols::topology_broker::FragmentClaimer
• set_frags() : protocols::anchored_design::AnchorMoversData
• set_fragset() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• set_frame() : protocols::magnesium::MgHydrater
• set_frames() : protocols::flexpack::FlexPacker , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• set_freeze_domains() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_freq() : protocols::noesy_assign::CrossPeak::Spin
• set_frequency() : protocols::trajectory::DbTrajectoryWriter
• set_from_cdr() : protocols::antibody::design::NativeAntibodySeq
• set_from_extra_data() : core::chemical::sdf::MolFileIOMolecule
• set_from_other_chains() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_from_residue_list_string() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• set_from_residue_selector() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• set_from_same_chain() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_from_scratch_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_ft_mover() : protocols::simple_moves::ChangeAndResetFoldTreeMover
• set_full_length_loop_rmsd_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_full_model_parameters() : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• set_full_repack() : protocols::relax::ClassicRelax
• set_full_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_full_to_sub() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_fullatom() : protocols::cryst::DockLatticeMover , protocols::hybridization::CartesianSampler , protocols::symmetric_docking::SymDockProtocol , protocols::topology_broker::ConstraintClaimer
• set_fullatom_density_weight() : protocols::hybridization::MRMover
• set_fullatom_loop_building() : protocols::antibody_legacy::CDRH3Modeler
• set_fullatom_pose() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• set_fullatom_scorefunction() : protocols::anchored_design::AnchorMoversData
• set_fullatom_scorefxn() : protocols::abinitio::Protocol , protocols::hybridization::HybridizeProtocol
• set_func() : core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::loop_graph::LoopScoreInfo , protocols::genetic_algorithm::GeneticAlgorithm
• set_func_for_weight() : protocols::moves::RampingMover
• set_Fv() : protocols::antibody_legacy::Antibody
• set_gamma() : core::pose::Pose
• set_Gamma() : protocols::md::MDBase
• set_gamma() : protocols::stepwise::sampler::rigid_body::EulerAngles
• set_gap_size() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_gasteiger_atom_type() : core::chemical::ResidueType
• set_gasteiger_typeset() : core::chemical::ResidueType
• set_gaussian() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• set_gaussian_stdev() : protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_general_overlap_tolerance() : protocols::match::BumpGrid
• set_general_phi_sd() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_general_psi_sd() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_generator() : protocols::forge::constraints::RemoveConstraints
• set_genericRBMoveStepsize() : protocols::rbsegment_relax::RBSegmentRelax
• set_geomcst_for_superposition_from_enz_io() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• set_ghost_loops() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_global() : protocols::mpi_refinement::WorkUnit_LoopHash
• set_global_optimize() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_global_sample_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_glycam_pdb_format() : core::io::StructFileReaderOptions
• set_GlyCorrection_values() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• set_GlyCorrection_values_for_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• set_glycosylation() : protocols::carbohydrates::SimpleGlycosylateMover
• set_glycosylation_weights() : protocols::carbohydrates::SimpleGlycosylateMover
• set_glycosylations() : protocols::carbohydrates::SimpleGlycosylateMover
• set_graft_design_options() : protocols::antibody::design::AntibodyDesignMover
• set_graft_h1() : protocols::antibody::GraftCDRLoopsProtocol
• set_graft_h2() : protocols::antibody::GraftCDRLoopsProtocol
• set_graft_h3() : protocols::antibody::GraftCDRLoopsProtocol
• set_graft_l1() : protocols::antibody::GraftCDRLoopsProtocol
• set_graft_l2() : protocols::antibody::GraftCDRLoopsProtocol
• set_graft_l3() : protocols::antibody::GraftCDRLoopsProtocol
• set_grid_param() : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• set_grid_spacing() : core::scoring::electron_density::ElectronDensityOptions
• set_group_discriminator() : protocols::simple_moves::GreenPacker
• set_group_ids() : protocols::simple_moves::UserDefinedGroupDiscriminator
• set_grouper() : protocols::match::output::MatchConsolidator
• set_grow_attempts_() : protocols::loops::loop_mover::IndependentLoopMover
• set_guarded_loops_not_in_charge() : protocols::loops::loop_mover::LoopMover
• set_h3_filter() : protocols::antibody::RefineOneCDRLoop
• set_h3_stem_graft() : protocols::antibody::GraftCDRLoopsProtocol
• set_H3Filter() : protocols::antibody::AntibodyModelerProtocol
• set_H3Filter_Tolerance() : protocols::antibody::AntibodyModelerProtocol
• set_half_width() : core::scoring::func::LinearPenaltyFunction
• set_handedness_score_flag() : core::scoring::SecondaryStructureWeights
• set_hardsphere_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_harmonic_constant_map() : protocols::normalmode::NormalMode
• set_harmonic_constants() : protocols::normalmode::NormalMode , protocols::normalmode::NormalModeRelaxMover
• set_has_silent_in() : protocols::jd2::archive::Batch
• set_hash_euclidean_bin_width() : protocols::match::Matcher , protocols::match::MatcherTask
• set_hash_euclidean_bin_widths() : protocols::match::Matcher
• set_hash_euler_bin_width() : protocols::match::Matcher , protocols::match::MatcherTask
• set_hash_euler_bin_widths() : protocols::match::Matcher
• set_hbond_options() : core::scoring::hbonds::HBondSet
• set_heat_after_cycles() : protocols::moves::MonteCarlo
• set_helicalMoveStepsize() : protocols::rbsegment_relax::RBSegmentRelax
• set_helix() : protocols::nonlocal::HelixRotate
• set_helix_index() : protocols::helical_bundle::PerturbBundleOptions
• set_helix_length() : protocols::helical_bundle::MakeBundleHelix
• set_helix_params_from_tag() : protocols::helical_bundle::MakeBundle
• set_helix_to_copy() : protocols::helical_bundle::PerturbBundleOptions
• set_hh_angle() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hh_angle_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hh_angle_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_highres_score_func() : protocols::antibody::H3RefineCCD , protocols::antibody_legacy::CDRH3Modeler
• set_highres_scorefxn() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• set_hightemp() : core::pack::annealer::SimAnnealerBase
• set_highval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• set_hires_scorefxn() : protocols::farna::RNA_FragmentMonteCarlo
• set_history_size() : protocols::pack_daemon::MultistateFitnessFunction
• set_hit_cacher() : protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameSequenceGrouper
• set_hpairset() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_hs_angle() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hs_angle_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hs_angle_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hs_atr_dist() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hs_atr_dist_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hs_atr_dist_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hsheet_repl_dist() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_hydrate() : protocols::magnesium::MgScanner
• set_icodes() : core::pose::PDBInfo
• set_icoor() : core::chemical::ResidueType
• set_icoor_private() : core::chemical::ResidueType
• set_id() : core::optimization::DOF_Node , protocols::denovo_design::components::NamedMover , protocols::denovo_design::connection::Connection , protocols::frag_picker::scores::FragmentScoringMethod , protocols::jd2::archive::Batch , protocols::moves::ConstraintGenerator , protocols::optimize_weights::OptEVariableExpression , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerSized
• set_ideal_helices() : protocols::forge::remodel::RemodelLoopMover
• set_ideal_xyz() : core::chemical::ResidueType
• set_idealize_conformers() : protocols::match::downstream::LigandConformerBuilder
• set_idealize_coord() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_idealize_h3_stems() : protocols::antibody::ModelCDRH3
• set_idealize_h3_stems_before_modeling() : protocols::antibody::AntibodyModelerProtocol
• set_idealize_insert() : protocols::antibody::AntibodyCDRGrafter
• set_idealize_loop_first() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_idealize_torsions() : protocols::carbohydrates::LinkageConformerMover
• set_idealized_abego() : protocols::denovo_design::connection::Connection
• set_ident_string() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• set_IGEdgeReweights() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• set_ignore_assignments() : protocols::noesy_assign::PeakFileFormat_Base
• set_ignore_cmdline_for_build_points() : protocols::match::MatcherTask
• set_ignore_default_docking_task() : protocols::docking::DockingProtocol
• set_ignore_default_task() : protocols::docking::DockingHighRes
• set_ignore_FARFAR_no_auto_bulge_parent_tag() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_ignore_FARFAR_no_auto_bulge_tag() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_ignore_negative_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• set_ignore_pikaa_natro() : protocols::flxbb::LayerDesignOperation
• set_ignore_pose_datacache() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_ignore_pose_profile_length_mismatch() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• set_ignore_secstruct() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_ignore_sugars() : core::io::StructFileRepOptions
• set_ignore_unconnected_upper() : core::select::residue_selector::PhiSelector
• set_ignore_unmatched_virtual_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_ignore_unrecognized_res() : core::io::StructFileRepOptions , protocols::rotamer_recovery::RotamerRecovery
• set_ignore_waters() : core::io::StructFileRepOptions
• set_ignore_zero_occupancy() : core::io::StructFileRepOptions
• set_implicit_hydrogen_included_radii_set() : core::scoring::sasa::SasaCalc
• set_in_range() : core::scoring::bin_transitions::BinTransitionData
• set_include_adjacent_residues() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• set_include_backbone_atoms() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• set_include_background_energies() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• set_include_carbon_sulfer_only_in_hydrophobic_calc() : core::scoring::sasa::SasaCalc
• set_include_cdr4_in_optimization() : protocols::antibody::AntibodyCDRGrafter
• set_include_default_linear_chainbreak() : protocols::farna::movers::RNA_Minimizer
• set_include_hydrogens_explicitly() : core::scoring::sasa::SasaCalc
• set_include_native_restype() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_include_native_type() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• set_include_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• set_include_probe_radius_in_atom_radii() : core::scoring::sasa::SasaCalc
• set_include_probe_radius_in_calc() : core::scoring::sasa::SasaMethod
• set_include_terminal_loops() : core::select::residue_selector::SecondaryStructureSelector
• set_increase_cycles() : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• set_index() : core::select::residue_selector::ResidueIndexSelector
• set_index_and_owner() : core::graph::UEVertex< V, E >
• set_info() : protocols::noesy_assign::CrossPeak
• set_inherit_scorefxn_temperature() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• set_init() : protocols::stepwise::sampler::StepWiseSamplerBase
• set_init_from_pose() : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_init_states() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_initial_decoy_stddev() : protocols::optimize_weights::PNatStructureOptEData
• set_initial_guesses() : protocols::helical_bundle::FitSimpleHelix
• set_initial_pose() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged , protocols::vip::VIP_Mover
• set_initial_values() : protocols::qsar::qsarOptFunc
• set_inner_cycles() : protocols::antibody::design::AntibodyDesignMover , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol
• set_inner_loop_cycles() : protocols::surface_docking::CentroidRelaxMover
• set_inp_chi() : protocols::make_rot_lib::RotData
• set_input_code() : protocols::sparta::ANN
• set_input_pose() : protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::TrialMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• set_input_pose_is_fa() : protocols::abinitio::KinematicTaskControl
• set_input_res() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_input_res_vectors() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_input_scan_res() : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• set_input_streams() : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler
• set_input_tags() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• set_insert_region() : protocols::grafting::GraftMoverBase
• set_insertion_prob() : protocols::jd2::archive::VarianceStatisticsArchive
• set_instruction_blueprint() : protocols::fldsgn::BluePrintBDR
• set_instruction_file() : protocols::antibody::design::AntibodyDesignMover
• set_instruction_file_path() : protocols::antibody::design::AntibodyDesignProtocol
• set_integration_test() : protocols::magnesium::MgScanner
• set_integration_test_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_intensity() : protocols::noesy_assign::Resonance
• set_inter_atr() : protocols::make_rot_lib::RotData
• set_inter_rep() : protocols::make_rot_lib::RotData
• set_interface_chains() : protocols::antibody::AntibodyFeatures , protocols::features::InterfaceFeatures
• set_interface_definition_task_operation() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• set_interface_dis() : protocols::antibody::design::AntibodyDesignMover
• set_interface_dist() : protocols::docking::InterfaceSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• set_interface_distance() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• set_interface_jump() : protocols::analysis::InterfaceAnalyzerMover
• set_interface_residue() : protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::ligand_options::Interface
• set_interface_sasa_filter() : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• set_interfaces() : core::conformation::symmetry::SymmData
• set_intermediate_structs() : protocols::jd2::archive::Batch
• set_internal_cycles() : protocols::stepwise::monte_carlo::mover::AddMover
• set_interval() : protocols::checkpoint::Timer
• set_interval_data_dump() : protocols::canonical_sampling::CanonicalSamplingMover
• set_interval_pose_dump() : protocols::canonical_sampling::CanonicalSamplingMover
• set_intra_atr() : protocols::make_rot_lib::RotData
• set_intra_rep() : protocols::make_rot_lib::RotData
• set_invert() : core::kinematics::Jump
• set_invert_helix() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_invert_task() : protocols::simple_moves::ConsensusDesignMover
• set_invrots_for_listnum() : protocols::toolbox::match_enzdes_util::InvrotCollector
• set_is_do_minimize() : protocols::analysis::PeptideDeriverFilter
• set_is_dump_cyclic_poses() : protocols::analysis::PeptideDeriverFilter
• set_is_dump_peptide_pose() : protocols::analysis::PeptideDeriverFilter
• set_is_dump_prepared_pose() : protocols::analysis::PeptideDeriverFilter
• set_is_dump_report_file() : protocols::analysis::PeptideDeriverFilter
• set_is_internal() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_is_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_is_prepend() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_is_prepend_map() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_is_properly_initialized() : protocols::simple_moves::ShakeStructureMover
• set_is_report_gzip() : protocols::analysis::PeptideDeriverFilter
• set_is_simple_full_length_job_params() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_is_skip_zero_isc() : protocols::analysis::PeptideDeriverFilter
• set_is_working_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_iteration() : protocols::vip::VIP_Mover
• set_iterations() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• set_job_data() : core::chemical::sdf::MolWriter
• set_job_id() : protocols::trajectory::DbTrajectoryReader
• set_job_inputter() : protocols::jd2::JobDistributor , protocols::jd2::JobsContainer
• set_job_outputter() : protocols::jd2::JobDistributor
• set_job_queen() : protocols::jd3::JobDistributor
• set_jump() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::fragment::DownJumpSRFD , core::kinematics::AtomTree , core::kinematics::MoveMap , core::pose::Pose , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpUpstreamSelector , protocols::denovo_design::components::StructureData , protocols::environment::ProtectedConformation
• set_jump_atom() : protocols::topology_broker::claims::JumpClaim
• set_jump_atom_stub_id() : core::conformation::Conformation , core::kinematics::AtomTree
• set_jump_atoms() : core::kinematics::FoldTree
• set_jump_change_frequency() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_jump_def() : protocols::topology_broker::FragmentJumpClaimer
• set_jump_library_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_jump_mover() : protocols::abinitio::KinematicControl
• set_jump_name() : core::conformation::symmetry::SymmetryInfo
• set_jump_now() : core::kinematics::AtomTree
• set_jump_point_pair_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_jump_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_jump_sample() : protocols::jumping::JumpSetup
• set_jumpAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• set_jumps_manually : protocols::seeded_abinitio::SeedFoldTree
• set_just_min_after_mutation_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_just_polar_hydrogens() : protocols::simple_moves::ConstrainToIdealMover
• set_just_rna_backbone() : protocols::simple_moves::ConstrainToIdealMover
• set_Kappa() : protocols::md::MDBase
• set_keep_base_fixed() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• set_keep_covalent() : protocols::enzdes::AddOrRemoveMatchCsts
• set_keep_input_foldtree() : protocols::forge::remodel::RemodelLoopMover
• set_keep_input_protonation_state() : core::io::StructFileRepOptions
• set_keep_jumps_from_input_pose() : protocols::topology_broker::FragmentJumpClaimer
• set_keep_pose_in_memory() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_keep_task_allowed_aas() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_keep_top_designs() : protocols::antibody::design::AntibodyDesignMover
• set_kic_modeler_if_relevant() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_kic_mover() : protocols::denovo_design::connection::BridgeTomponents
• set_kin_writer() : protocols::match::output::WriteKinemageOutputter
• set_kinemage_file() : protocols::match::output::WriteUpstreamHitKinemage
• set_kinemage_file_name() : protocols::match::output::WriteUpstreamCoordinateKinemage
• set_kinematic_defaults() : protocols::protein_interface_design::movers::PlaceOnLoop
• set_kinematics() : protocols::abinitio::Protocol
• set_kinmover() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• set_kt() : protocols::carbohydrates::GlycanRelaxMover
• set_kT() : protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_label() : core::select::residue_selector::ResiduePDBInfoHasLabelSelector , protocols::noesy_assign::CrossPeakInfo , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::FragmentContainer , protocols::topology_broker::TopologyClaimer
• 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_last_accepted() : protocols::canonical_sampling::MetropolisHastingsMover
• set_last_accepted_pose() : protocols::moves::MonteCarlo
• set_last_accepted_score() : protocols::moves::MonteCarlo
• set_last_apply_failed() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundleHelix
• set_last_considered_backbone_sub_valid() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_last_move() : protocols::canonical_sampling::MetropolisHastingsMover
• set_last_move_status() : protocols::moves::Mover
• set_layer_mode() : protocols::flxbb::FlxbbDesign
• set_layer_operation() : protocols::flxbb::LayerDesignOperation
• set_layer_residues() : protocols::flxbb::LayerDesignOperation
• set_layer_specification() : protocols::flxbb::LayerDesignOperation
• set_layers() : core::select::residue_selector::LayerSelector
• set_legacy_mode() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• set_length() : core::scoring::loop_graph::LoopScoreInfo
• set_lengths() : protocols::denovo_design::connection::Connection
• set_lib_chi_val() : protocols::make_rot_lib::RotData
• set_ligand() : protocols::enzdes::PredesignPerturbMover
• set_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• set_ligand_atom_name() : protocols::metal_interface::MetalSiteResidue
• set_ligand_atom_xyz() : protocols::metal_interface::MetalSiteResidue
• set_ligand_jump_id() : protocols::simple_moves::CoupledMover
• set_ligand_resnum() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• set_ligand_rings() : protocols::qsar::scoring_grid::AtrGrid
• set_ligand_weight() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• set_ligres() : protocols::match::MatcherMover
• set_limit() : protocols::simple_moves::symmetry::SetupNCSMover
• set_limit_for_rotamer_combo() : protocols::match::output::LimitHitsPerRotamerFilter
• set_limit_only_to_length() : protocols::antibody::task_operations::AddCDRProfileSetsOperation
• set_line_color() : protocols::match::Bool3DGridKinemageWriter
• set_line_continuation() : core::io::HeaderInformation
• set_linear_chainbreak_weight() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_linecount_offset() : protocols::loops::JSONFormattedLoopsFileReader , protocols::loops::PoseNumberedLoopFileReader
• set_links() : core::pack::task::operation::SetRotamerLinks
• set_linmin_only() : protocols::hybridization::CartesianHybridize
• set_lj_atr_weight() : protocols::match::output::MatchCollisionFilter
• set_lj_cutoff() : protocols::match::output::MatchCollisionFilter
• set_lj_ramp_cycles() : protocols::relax::ClassicRelax
• set_lj_ramp_inner_cycles() : protocols::relax::ClassicRelax
• set_lj_rep_weight() : protocols::match::output::MatchCollisionFilter
• set_lj_sol_weight() : protocols::match::output::MatchCollisionFilter
• set_ljrepulsion_weight() : protocols::surface_docking::FullatomRelaxMover
• set_local_positions() : protocols::environment::claims::EnvLabelSelector
• set_local_redock_only() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_local_refine() : protocols::symmetric_docking::SymDockProtocol
• set_localstrandpair_penalty() : core::scoring::SecondaryStructureWeights
• set_location_in_parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• set_long_range_container() : core::scoring::Energies
• set_loop() : protocols::kinematic_closure::BalancedKicMover , protocols::loop_modeling::LoopMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_loop_ang() : protocols::forge::remodel::ResidueVicinityInfo
• set_loop_begin_and_end() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_loop_cluster_radius() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_loop_combine_rate_() : protocols::loops::loop_mover::IndependentLoopMover
• set_loop_dih() : protocols::forge::remodel::ResidueVicinityInfo
• set_loop_file_name_and_reset() : protocols::loops::Loops
• set_loop_info() : protocols::dna::DesignProteinBackboneAroundDNA
• set_loop_lower() : protocols::denovo_design::connection::Connection
• set_loop_mover() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• set_loop_segments() : protocols::relax::AtomCoordinateCstMover
• set_loop_start() : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• set_loop_stop() : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• set_loop_upper() : protocols::denovo_design::connection::Connection
• set_loopres_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• set_loopres_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• set_loopres_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• set_looprlx_allow_move_map() : protocols::LoopRebuild
• set_loops() : protocols::grafting::AnchoredGraftMover , protocols::loop_modeling::LoopMover , protocols::toolbox::task_operations::RestrictToLoops
• set_loops_and_anchor() : protocols::anchored_design::AnchorMoversData
• set_loops_from_file() : protocols::toolbox::task_operations::RestrictToLoops
• set_loops_from_pose_observer_cache() : protocols::loops::loop_mover::LoopMover
• set_loops_pointer() : protocols::loops::GuardedLoopsFromFile
• set_loose_rep_cutoff() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• set_lores() : protocols::stepwise::options::StepWiseBasicOptions
• set_lores_scorefxn() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_DeNovoProtocolOptions
• set_low_energy_ring_conformers() : core::chemical::ResidueType
• set_low_memory_mode() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_low_res_protocol_only() : protocols::docking::DockingProtocol
• set_lower_connect_atom() : core::chemical::ResidueType
• set_lower_overlap() : protocols::denovo_design::connection::Connection
• set_lower_residues() : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• set_lower_segment() : protocols::denovo_design::components::Segment
• set_lower_segment_id() : protocols::denovo_design::connection::Connection
• set_lower_threshold() : protocols::filters::IfThenFilter
• set_lower_value() : protocols::helical_bundle::PerturbBundleOptions
• set_lowest_energy_ring_conformer() : core::chemical::ResidueType
• set_lowest_score_pose() : protocols::moves::MonteCarlo
• set_lowres_score_func() : protocols::antibody::H3PerturbCCD , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• set_lowres_scorefxn() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• set_lowtemp() : core::pack::annealer::SimAnnealerBase
• set_lowval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• set_lt_dih() : protocols::forge::remodel::ResidueVicinityInfo
• set_magnitude() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• set_magnitude_rotation() : protocols::rigid::RigidBodyMotionMover
• set_magnitude_translation() : protocols::rigid::RigidBodyMotionMover
• set_mainchain_atoms() : core::chemical::ResidueType
• set_mainchain_torsions() : core::io::silent::RNA_SilentStruct , protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• set_major_helix_params() : protocols::helical_bundle::MakeBundleHelix
• set_make_movie() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_manager() : protocols::abinitio::IterativeAbrelax , protocols::jd2::archive::AbstractArchiveBase
• set_map_cst_from_centroid_to_fa() : protocols::abinitio::ResolutionSwitcher
• set_map_type() : core::scoring::cryst::PhenixInterface
• set_mapfile_activated() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_mapreso() : core::scoring::electron_density::ElectronDensityOptions
• set_master() : protocols::match::Bool3DGridKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• set_master_packer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• set_match_algorithm() : protocols::match::output::WriteUpstreamCoordinateKinemage
• set_match_positions() : protocols::match::MatcherMover
• set_match_rt_limit() : protocols::denovo_design::DisulfidizeMover
• set_match_score_writer() : protocols::match::output::MatchProcessor
• set_matrix_entry() : core::scoring::bin_transitions::BinTransitionData
• set_max_allowed_conserved_pos_mutations() : protocols::simple_filters::ConservedPosMutationFilter
• set_max_angle_disp_4() : protocols::backrub::BackrubMover
• set_max_angle_disp_7() : protocols::backrub::BackrubMover
• set_max_angle_disp_slope() : protocols::backrub::BackrubMover
• set_max_atoms() : protocols::backrub::BackrubMover
• set_max_attempts() : protocols::loop_modeling::LoopBuilder
• set_max_bbrms() : protocols::loophash::LoopHashSampler
• set_max_chi_considered() : protocols::rotamer_recovery::RRComparerChiDiff
• set_max_context_neighbor_cutoff() : core::scoring::Energies
• set_max_decoys() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_max_distance() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_max_disulf_score() : protocols::denovo_design::DisulfidizeMover
• set_max_frag_length() : core::fragment::FragSet
• set_max_gaplength_to_model() : protocols::hybridization::MRMover
• set_max_generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_max_insertion() : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• set_max_kic_build_attempts() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• set_max_lib_size() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• set_max_missing_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_max_nstruct() : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashSampler
• set_max_ntries() : protocols::stepwise::StepWiseSampleAndScreen
• set_max_pop_size() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_max_pos() : core::fragment::FragSet
• set_max_radius() : protocols::loophash::LoopHashSampler
• set_max_range() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• set_max_ref_lib_size() : protocols::mpi_refinement::MPI_Refinement
• set_max_registry_shift() : protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize
• set_max_repeats() : protocols::symmetric_docking::SymDockProtocol
• set_max_rms() : protocols::loophash::LoopHashSampler
• set_max_rot_bumpenergy() : core::pack::rotamer_set::BumpSelector
• set_max_sample_iterations() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• set_max_samples() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_max_seq_sep() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::constraints_additional::MaxSeqSepConstraintSet
• set_max_small_angle() : protocols::simple_moves::a3b_hbs::A3BHbsRandomSmallMover , protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• set_max_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_max_struct() : protocols::loophash::LoopHashSampler , protocols::simple_moves::CombinePoseMover
• set_max_struct_per_radius() : protocols::loophash::LoopHashSampler
• set_max_surface_deltaE() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• set_max_tries() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• set_max_tries_multiplier_for_ccd() : protocols::stepwise::options::StepWiseBasicOptions
• set_max_try() : protocols::simple_moves::CombinePoseMover
• set_maxfrac() : protocols::mpi_refinement::WorkUnit_CombinePose
• set_maxfrac_crossover() : protocols::simple_moves::CombinePoseMover
• set_maxscale() : protocols::mpi_refinement::WorkUnit_NormalMode
• set_maxtrials() : protocols::simple_moves::GenericMonteCarloMover
• set_mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::moves::TrialMover , protocols::relax::ClassicRelax
• set_MC() : protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest
• set_mc_accepted() : protocols::moves::MonteCarlo
• set_mc_scorefunction() : protocols::hybridization::CartesianSampler
• set_mc_temp() : protocols::simple_moves::ShakeStructureMover
• set_mc_temperature() : protocols::simple_moves::ShakeStructureMover
• set_MCA() : protocols::pack_daemon::DenseIGRepacker
• set_mcfi() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• set_mean() : protocols::ddg::ddGMover
• 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_limit() : protocols::wum::WorkUnitQueue
• 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_metropolis_hastings_mover() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• set_mg_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• set_mg_coord_cst_dist() : protocols::magnesium::MgMinimizer
• set_mg_res() : protocols::magnesium::MgMinimizer
• set_middle_pack_min() : protocols::antibody::AntibodyModelerProtocol
• set_min() : protocols::ddg::ddGMover
• set_min_allowed_score() : protocols::frag_picker::scores::FragmentScoringMethod
• set_min_atoms() : protocols::backrub::BackrubMover
• set_min_bb() : protocols::enzdes::EnzRepackMinimize
• set_min_bbrms() : protocols::loophash::LoopHashSampler
• set_min_chi() : protocols::make_rot_lib::RotData
• set_min_cst() : protocols::ddg::ddGMover
• set_min_eps() : protocols::make_rot_lib::RotData
• set_min_frag_length() : protocols::simple_moves::ClassicFragmentMover
• set_min_lig() : protocols::enzdes::EnzRepackMinimize
• set_min_loop() : protocols::denovo_design::DisulfidizeMover
• set_min_max_angles() : protocols::rigid::RollMover
• set_min_move() : protocols::abinitio::FoldConstraints
• set_min_num_south_sugar_filter() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_min_omg() : protocols::make_rot_lib::RotData
• set_min_options() : protocols::loop_modeling::refiners::MinimizationRefiner
• set_min_overlap() : protocols::simple_moves::ClassicFragmentMover
• set_min_pos() : core::fragment::FragSet
• set_min_rb() : protocols::enzdes::EnzRepackMinimize
• set_min_rms() : protocols::loophash::LoopHashSampler
• set_min_sc() : protocols::enzdes::EnzRepackMinimize
• set_min_scorefunction() : protocols::hybridization::CartesianHybridize , protocols::simple_moves::ShakeStructureMover
• set_min_solution_count() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_min_tolerance() : protocols::docking::DockMinMover , protocols::helical_bundle::FitSimpleHelix , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• set_min_type() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::farna::movers::RNA_Minimizer , protocols::helical_bundle::FitSimpleHelix , protocols::relax::CentroidRelax , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes
• set_min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
• set_minfrac() : protocols::mpi_refinement::WorkUnit_CombinePose
• set_minfrac_crossover() : protocols::simple_moves::CombinePoseMover
• set_minimization_graph() : core::scoring::Energies
• set_minimization_score_function() : protocols::ddg::ddGMover
• set_minimize() : protocols::magnesium::MgScanner , protocols::simple_moves::CombinePoseMover
• set_minimize_after_delete() : protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_minimize_all() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• set_minimize_and_score_native_pose() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_minimize_and_score_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_minimize_at_end() : protocols::hybridization::FoldTreeHybridize
• set_minimize_bps() : protocols::farna::options::RNA_MinimizerOptions
• set_minimize_during_scoring() : protocols::magnesium::MgScanner
• set_minimize_mg_coord_constraint_distance() : protocols::magnesium::MgScanner
• set_minimize_options() : protocols::enzdes::EnzdesBaseProtocol
• set_minimize_res() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• set_minimize_rounds() : protocols::farna::options::RNA_MinimizerOptions
• set_minimize_scorefxn() : protocols::magnesium::MgMinimizer
• set_minimize_sf() : protocols::hybridization::FoldTreeHybridize
• set_minimize_single_res() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• set_minimize_single_res_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_minimize_structure() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_minimize_with_cst() : protocols::simple_moves::ShakeStructureMover
• set_minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• set_minimizer_rename_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_minimizer_use_coordinate_constraints() : protocols::farna::options::RNA_MinimizerOptions
• set_minimum_peak_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• set_minmover() : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• set_minoption() : protocols::normalmode::NormalModeRelaxMover
• set_minor_helix_params() : protocols::helical_bundle::MakeBundleHelix
• set_minor_helix_params_from_file() : protocols::helical_bundle::MakeBundleHelix
• set_minor_helix_params_from_tag() : protocols::helical_bundle::MakeBundle
• set_minorhelix_defaults_from_tag() : protocols::helical_bundle::MakeBundle
• set_mintolerance() : protocols::cyclic_peptide::TryDisulfPermutations
• set_mintype() : protocols::cyclic_peptide::TryDisulfPermutations , protocols::grafting::AnchoredGraftMover
• set_mirror_z() : core::conformation::symmetry::SymmetryTransform , core::conformation::symmetry::VirtualCoordinate
• set_missing_dens_as_jump() : core::io::StructFileRepOptions
• set_mm_atom_type() : core::chemical::ResidueType
• set_mode() : protocols::normalmode::NormalModeRelaxMover
• set_model_and_remove_capping_residues() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• set_model_tag() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• set_ModelH3() : protocols::antibody::AntibodyModelerProtocol
• set_modes() : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• set_monte_carlo() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController
• set_monte_carlo_cycles() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• set_motifs() : protocols::denovo_design::connection::Connection
• set_movable_group() : protocols::denovo_design::components::StructureData
• set_movable_jumps() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::InterfaceTaskOperation
• set_move() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• set_move_element() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• set_move_first_rigid_body() : protocols::farna::options::RNA_BasicOptions
• set_move_jump_points_away() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• set_move_jumps_between_chains() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_move_map() : protocols::antibody::CDRsMinPackMin , protocols::antibody::LHRepulsiveRamp , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::symmetric_docking::SymDockingHiRes
• set_move_takeoff_torsions() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• set_move_type() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• set_moveable_jumps() : protocols::docking::DockingHighResFilter
• set_movemap() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::anchored_design::AnchorMoversData , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::LinkageConformerMover , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FlxbbDesign , protocols::jd2::parser::BluePrint , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::CartesianMD , protocols::md::MDBase , protocols::moves::MoveMapMover , protocols::moves::NullMover , protocols::normalmode::NormalModeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• set_movemap_from_kic_segment() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_movemap_smallmover() : protocols::backrub::BackrubProtocol
• set_movemaps() : protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover
• set_movement() : protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::RBSegmentMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::StrandTwistingMover
• set_mover() : protocols::abinitio::abscript::FragmentCM , protocols::flxbb::DesignTask , protocols::moves::FilterMover , protocols::moves::FilterReporterMover , protocols::moves::MoverApplyingMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• set_mover_cycles() : protocols::loop_modeling::LoopProtocol
• set_mover_tag() : protocols::topology_broker::FragmentClaimer
• set_mover_weight() : protocols::topology_broker::TopologyClaimer
• set_moverkey() : protocols::abinitio::abscript::FragmentJumpCM
• set_moves() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• set_moving_lattice() : protocols::cryst::MakeLayerMover
• set_moving_partition_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• set_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_moving_res_and_reset() : protocols::stepwise::modeler::StepWiseModeler
• set_moving_res_list() : protocols::stepwise::modeler::StepWiseModeler
• set_moving_residues() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_mpi_feedback() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• set_mulfactor() : protocols::mpi_refinement::StructAvrgMover
• set_multicomponent_info() : core::conformation::symmetry::SymmetryInfo
• set_multifunc() : protocols::optimize_weights::WrapperOptEMultifunc
• set_multiple_origin() : protocols::pockets::NonPlaidFingerprint
• set_must_switch_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
• set_mut_aa() : protocols::optimize_weights::DDGMutationOptEData
• set_mut_unfolded_energies_emap() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• set_mutate_gly() : protocols::denovo_design::DisulfidizeMover
• set_mutate_pro() : protocols::denovo_design::DisulfidizeMover
• set_mutate_to_glycine() : protocols::simple_moves::RepulsiveOnlyMover
• set_mutation_rate() : protocols::genetic_algorithm::EntityRandomizer
• set_mutation_sets() : protocols::toolbox::task_operations::MutationSetDesignOperation
• set_n_atom() : protocols::toolbox::DecoySetEvaluation
• set_n_bins() : core::scoring::bin_transitions::BinTransitionData
• set_n_chi_bins() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• set_n_downstream_to_output() : protocols::match::output::WriteUpstreamCoordinateKinemage
• set_n_geomcst() : protocols::match::output::WriteKinemageOutputter
• set_n_geometric_constraints() : protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameSequenceGrouper
• set_n_helices() : protocols::helical_bundle::parameters::BundleParametersSet
• set_n_mainchain_torsions_i() : core::scoring::bin_transitions::BinTransitionData
• set_n_mainchain_torsions_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_n_max_cluster() : protocols::toolbox::ClusterPhilStyle
• set_n_sample() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_n_samples_per_side_of_nrchi_bin() : protocols::match::upstream::SampleStrategyData
• set_n_samples_wi_sd_range() : protocols::match::upstream::SampleStrategyData
• set_n_to_output_per_group() : protocols::match::output::MatchConsolidator
• set_n_worker() : protocols::jd2::MPIFileBufJobDistributor
• set_name() : core::chemical::Patch , core::grid::CartGrid< T > , core::io::rna::RDAT , protocols::jd2::archive::AbstractArchiveBase , protocols::pockets::SmallMol
• set_name1() : core::chemical::ResidueTypeSelector
• set_names() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• set_names_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• set_natbias_helices_sheet_pot() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• set_natbias_hpairpot() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• set_natbias_spairpot() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• set_native() : protocols::abinitio::Templates , protocols::relax::RangeRelaxMover , protocols::rotamer_recovery::PerNativeRRReporterHuman
• set_native_aa() : protocols::optimize_weights::PNatAAOptEPositionData
• set_native_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_native_alignment_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_native_chi_periodicity() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_cst_set() : protocols::forge::remodel::RemodelGlobalFrame
• set_native_distance_viol() : protocols::noesy_assign::PeakAssignment
• set_native_edensity_score_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_native_flag() : protocols::match::upstream::ProteinUpstreamBuilder
• set_native_pose() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::TrialMover , protocols::relax::WorkUnit_BatchRelax , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• set_native_rotamer_chi() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_rotamer_index() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_sequence() : protocols::toolbox::task_operations::ConservativeDesignOperation
• set_native_spairset() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• set_native_task() : core::pack::task::operation::ReplicateTask
• set_native_topology() : protocols::abinitio::PairingStatistics
• set_native_virtual_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_nativeness_high() : protocols::optimize_weights::PNatStructureOptEData
• set_nativeness_low() : protocols::optimize_weights::PNatStructureOptEData
• 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_nc_layer_residues() : protocols::flxbb::LayerDesignOperation
• set_nchi() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_ncluster() : protocols::toolbox::KCluster
• set_ncopies() : core::fragment::FragmentIO
• set_ncycle() : protocols::flxbb::DesignTask
• set_ncycles() : protocols::cryst::DockLatticeMover , protocols::flxbb::FlxbbDesign , protocols::hybridization::CartesianSampler , protocols::rbsegment_relax::RBSegmentRelax
• set_ND_torsion_to_pose() : protocols::simple_moves::bb_sampler::BBDihedralSamplerND
• set_neighbor_count() : protocols::optimize_weights::PNatAAOptEPositionData
• set_neighbor_dis() : protocols::antibody::design::AntibodyDesignMover
• set_neighbor_distance() : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::simple_moves::SimpleThreadingMover
• set_neighborhood_parameters() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• set_network_anchoring() : protocols::noesy_assign::PeakAssignment
• set_network_anchoring_per_residue() : protocols::noesy_assign::PeakAssignment
• set_network_state() : core::pack::interaction_graph::AnnealableGraphBase , 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::MultiplexedAnnealableGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• set_new_chain_order() : core::io::StructFileReaderOptions
• set_new_conformation() : core::pose::Pose
• set_new_energies_object() : core::pose::Pose
• set_new_move_selector() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_new_rots() : protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• set_new_topology() : core::kinematics::AtomTree
• set_new_upper_bounds() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• set_next() : core::graph::NegSpaceElement< T >
• set_next_angle() : protocols::backrub::BackrubMover
• set_next_segment_id() : protocols::backrub::BackrubMover
• set_next_size() : boost::unordered_object_pool< T, UserAllocator >
• set_nfrags() : protocols::hybridization::CartesianSampler
• set_nhits_per_match() : protocols::match::HitHasher
• set_nminsteps() : protocols::hybridization::CartesianSampler
• set_nmodes() : protocols::mpi_refinement::WorkUnit_NormalMode
• set_nmoves() : protocols::relax::RangeRelaxMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• set_nmtype() : protocols::mpi_refinement::WorkUnit_NormalMode
• set_nneighbors() : core::scoring::hbonds::HBondResidueMinData
• set_no_chainend_ter() : core::io::StructFileRepOptions
• set_no_design_cys() : protocols::enzdes::DetectProteinLigandInterface
• set_no_filters() : protocols::docking::DockingProtocol
• set_no_frags() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchorMoversData
• set_no_global_frame() : protocols::hybridization::CartesianHybridize
• set_no_longer_perturbed() : core::pack::interaction_graph::FASTERNode
• set_no_optH() : core::import_pose::ImportPoseOptions
• set_no_output_cen() : core::io::StructFileRepOptions
• set_no_stem_copy() : protocols::antibody::GraftOneCDRLoop
• set_node_considering_alt_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_node_state_to_zero() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_nodes_alt_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_nodes_alt_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_nodes_considering_bb_move() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_nodes_cur_info() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_nodes_cur_state() : protocols::flexpack::interaction_graph::FlexbbEdge
• set_noesy_assign_float_cycle() : protocols::abinitio::IterativeBase
• set_non_main_chain_sugar_coords() : core::io::silent::RNA_SilentStruct
• set_non_standard_residue_map() : core::pose::full_model_info::FullModelParameters
• set_noncanonical_connection() : core::conformation::Conformation
• set_nonideal() : core::pack::RTMin , core::pack::scmin::SCMinMinimizerMap , protocols::loophash::LoopHashSampler , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin , protocols::simple_moves::CombinePoseMover
• set_nonpivot_bb_torsion_id() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_nonpivot_res_to_sweep() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_nonpivot_torsion_sampling() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• 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_norepack1() : protocols::docking::DockTaskFactory
• set_norepack2() : protocols::docking::DockTaskFactory
• set_normal() : core::scoring::MembraneEmbed , protocols::membrane::geometry::EmbeddingDef
• set_normalization_function() : protocols::qsar::scoring_grid::GridManager
• set_normalize_decoy_stddev() : protocols::optimize_weights::PNatStructureOptEData
• set_normalize_to_thk() : core::io::StructFileRepOptions
• set_not_to_quench() : core::pack::annealer::SimAnnealerBase
• set_nr_fragments() : protocols::loops::loop_closure::ccd::LoopClosure
• set_nrchi_lower_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_periodicity() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• set_nrchi_prob_minimum_for_extra_samples() : protocols::match::upstream::SampleStrategyData
• set_nrchi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_sample() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrchi_upper_boundary() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_nrepeat() : protocols::mpi_refinement::WorkUnit_Relax
• set_nres() : core::scoring::electron_density::ElectronDensity , protocols::helical_bundle::BackboneGridSampler
• set_nres_mono() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy
• set_nres_subunit() : core::conformation::symmetry::SymmetryInfo
• set_nresidues() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• set_nrounds() : protocols::simple_moves::ShakeStructureMover
• set_nseq() : core::scoring::TMscoreStore
• set_nstep() : protocols::md::MDBase
• set_nsteps() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• set_nstruct() : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::jd2::archive::ArchiveBase , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_MD
• set_nstruct_centroid() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_nstruct_mode() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_nstruct_repeats() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_nterm_included() : protocols::denovo_design::components::Segment
• set_ntrial() : protocols::flxbb::FilterStructs
• set_ntrials() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• set_ntries_before_giving_up() : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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_bb_for_node() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_num_bbs() : protocols::make_rot_lib::RotData
• set_num_chi() : protocols::make_rot_lib::RotData
• set_num_clusters() : protocols::make_rot_lib::RotData
• set_num_cycles() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_num_decoys_used_in_calculations() : protocols::ddg::ddGMover
• set_num_distinct_backbones() : protocols::flexpack::interaction_graph::FlexbbNode
• set_num_entities() : protocols::pack_daemon::EntityCorrespondence
• set_num_entity_elements() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• set_num_filter_tries() : protocols::antibody::RefineOneCDRLoop
• set_num_flexsegs() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_num_geometric_constraints() : protocols::match::output::UpstreamDownstreamCollisionFilter
• 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
• set_num_npd_properties() : protocols::pack_daemon::MPIMultistateFitnessFunction
• set_num_pack_daemons() : protocols::pack_daemon::MPIMultistateFitnessFunction
• set_num_packs() : protocols::multistate_design::MultiStatePacker
• set_num_pose_kept() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• set_num_pose_minimize() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions
• set_num_random_samples() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::StepWiseSampleAndScreen
• set_num_residues_in_protein() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_num_restypes() : protocols::match::downstream::TargetRotamerCoords
• set_num_sa() : protocols::pack_daemon::FASTER_IG_Repacker
• set_num_sa_trajectories() : core::pack::annealer::FASTERAnnealer
• set_num_states_for_node() : core::pack::interaction_graph::InteractionGraphBase
• set_num_states_per_backbone() : protocols::flexpack::interaction_graph::FlexbbNode
• set_num_states_per_backbone_for_node() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_num_target_rotamers() : protocols::match::downstream::TargetRotamerCoords
• set_num_to_propagate() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_num_trials() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• set_num_vertices() : core::graph::UpperEdgeGraph< V, E >
• set_number_of_energy_sum_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• set_number_of_moves() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• set_numbering() : core::pose::PDBInfo
• set_numbering_scheme() : protocols::antibody::clusters::CDRClusterFeatures
• set_nus() : core::kinematics::MoveMap
• set_o2prime_legacy_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_obey_ENDMDL() : core::io::StructFileReaderOptions
• 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_occupied_space_bounding_box() : protocols::match::Matcher , protocols::match::MatcherTask
• set_occupied_space_hash() : protocols::match::downstream::DownstreamBuilder
• set_of_rotamer_sets_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• set_offset() : core::id::SequenceMapping , core::io::rna::RDAT
• set_ok_to_increment() : protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::StepWiseSampleAndScreen
• set_omega() : core::pose::Pose , protocols::denovo_design::components::StructureData
• set_omega0() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_omega0_copies_pitch_instead() : protocols::helical_bundle::PerturbBundleOptions
• set_omega1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_omg() : protocols::make_rot_lib::RotData
• 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_only_enumerate_non_match_redundant_ligand_rotamers() : protocols::match::MatcherTask
• set_only_stage4() : protocols::abinitio::MembraneAbinitio
• set_optimize_cdrs() : protocols::antibody::AntibodyCDRGrafter
• set_optimize_cyclic_threshold() : protocols::analysis::PeptideDeriverFilter
• set_optimize_memory_usage() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_options() : protocols::farna::movers::RNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::wum::WorkUnitBase
• set_options_from_cmdline() : protocols::noesy_assign::PeakAssignmentParameters
• set_OrbH_features_data() : protocols::features::OrbitalsFeatures
• set_orbital_icoor_id() : core::chemical::ResidueType
• set_orbital_type_and_bond() : core::chemical::orbitals::AssignOrbitals
• set_orbital_xyz() : core::conformation::Residue
• set_OrbOrb_features_data() : protocols::features::OrbitalsFeatures
• set_order_by_energy() : core::import_pose::pose_stream::SilentFilePoseInputStream
• set_orientation() : core::pose::rna::BasePair , core::pose::rna::BaseStack
• set_origin() : protocols::pockets::NonPlaidFingerprint
• set_origin_away_from_eggshell() : protocols::pockets::NonPlaidFingerprint
• set_origin_away_from_eggshell_plane() : protocols::pockets::NonPlaidFingerprint
• set_origin_away_from_protein_center() : protocols::pockets::NonPlaidFingerprint
• set_origin_from_option_() : protocols::pockets::NonPlaidFingerprint
• set_origin_from_residue() : protocols::pockets::NonPlaidFingerprint
• set_original_pose() : protocols::loop_modeling::utilities::PrepareForFullatom
• set_original_scaffold_build_points() : protocols::match::Matcher , protocols::match::MatcherTask
• set_original_scaffold_build_points_for_constraint() : protocols::match::Matcher
• set_original_scaffold_build_points_for_geometric_constraint() : protocols::match::MatcherTask
• set_other_defaults_from_tag() : protocols::helical_bundle::MakeBundle
• set_other_helix_params_from_tag() : protocols::helical_bundle::MakeBundle
• set_other_pose_list() : core::pose::full_model_info::FullModelInfo
• set_out() : protocols::moves::FilterReporterMover
• set_out_file_tag() : protocols::farna::RNA_FragmentMonteCarlo
• set_out_path() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• set_outer_cycles() : protocols::antibody::design::AntibodyDesignMover , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol
• set_outer_loop_cycles() : protocols::surface_docking::CentroidRelaxMover
• set_outlier_use() : protocols::antibody::AntibodyDatabaseManager
• set_output() : protocols::match::output::MatchScoreWriter
• set_output_cluster_size() : protocols::stepwise::options::StepWiseBasicOptions
• set_output_extra_RMSDs() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_output_file_name() : protocols::jobdist::BasicJob
• set_output_filename() : protocols::match::output::MatchScoreWriter , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_output_filters() : protocols::farna::options::RNA_DeNovoProtocolOptions
• set_output_level() : protocols::rotamer_recovery::RRReporterSQLite
• set_output_lores_silent_file() : protocols::farna::options::RNA_DeNovoProtocolOptions
• set_output_minimized_pose_list() : protocols::stepwise::options::StepWiseBasicOptions
• set_output_name() : protocols::canonical_sampling::MetropolisHastingsMover
• set_output_pdb() : protocols::magnesium::MgMonteCarlo , protocols::magnesium::MgScanner , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• set_output_period() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_output_prefix() : protocols::contact_map::ContactMap
• set_output_torsions() : core::io::StructFileRepOptions
• set_output_virtual() : core::io::StructFileRepOptions
• set_output_virtual_zero_occ() : core::io::StructFileRepOptions
• set_output_writer() : protocols::match::output::MatchProcessor
• set_overall_aa_probabilities() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_overall_cstfilter_weight() : protocols::abinitio::IterativeBase
• set_overhang() : protocols::antibody::AntibodyCDRGrafter
• set_overlap() : core::select::residue_selector::SecondaryStructureSelector , protocols::denovo_design::connection::Connection , protocols::hybridization::CartesianSampler
• set_owner() : core::scoring::Energies , protocols::environment::claims::EnvClaim , protocols::flexpack::rotamer_set::FlexbbRotamerSet
• set_pack() : protocols::scoring::Interface
• set_pack_all_side_chains() : protocols::stepwise::modeler::packer::StepWisePacker
• set_pack_input() : protocols::analysis::InterfaceAnalyzerMover
• set_pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• set_pack_neighbors() : protocols::simple_moves::SimpleThreadingMover
• set_pack_o2prime_hydrogens() : protocols::stepwise::modeler::packer::StepWisePacker
• set_pack_rounds() : protocols::simple_moves::SimpleThreadingMover
• set_pack_score_func() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• set_pack_scorefunction() : protocols::hybridization::CartesianHybridize
• set_pack_separated() : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• set_pack_shell() : protocols::antibody::design::MutateFrameworkForCluster
• set_pack_together() : protocols::features::InterfaceFeatures
• set_pack_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_packer() : protocols::docking::DockingEnsemble
• set_packer_default() : protocols::antibody_legacy::GraftMover
• 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 , protocols::simple_moves::CoupledMover
• set_packertask() : protocols::flxbb::DesignTask
• set_packerTasks_target_and_seeds() : protocols::seeded_abinitio::SeedSetupMover
• set_packonly_after_graft() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol
• set_pair_and_func_map() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• set_pair_overlap_tolerance() : protocols::match::BumpGrid
• set_pairings_file() : protocols::hybridization::FoldTreeHybridize
• set_parallel_weight() : core::scoring::SecondaryStructureWeights
• set_param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• set_param_from_options() : protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• set_param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• 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_parameters() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::fldsgn::potentials::SetAACompositionPotential
• set_parameters_index() : protocols::helical_bundle::PerturbBundleHelix
• set_parameters_set_index() : protocols::helical_bundle::PerturbBundleHelix
• set_params() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_params_angle_pot() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_params_distance_pot() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_paratope_cdrs() : protocols::antibody::design::AntibodyDesignMover
• set_parent() : core::optimization::DOF_Node , protocols::pockets::SmallMol
• set_parent_full_model_parameters() : core::pose::full_model_info::FullModelParameters
• set_parent_id() : protocols::denovo_design::components::NamedMover
• set_parin_favorite_output() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_partition_definition() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_partner() : protocols::sewing::Assembly
• set_partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_PBP_clustering_at_chain_closure() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_pdb_comments() : core::io::StructFileRepOptions
• set_pdb_numbering() : protocols::antibody::clusters::CDRCluster
• set_pdb_output() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_pdb_parents() : core::io::StructFileRepOptions
• set_pdb_prefix() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_pdb_source() : protocols::features::strand_assembly::StrandFragment
• set_peak_id() : protocols::noesy_assign::CrossPeak
• set_penalty() : core::scoring::MembraneEmbed
• set_pep_lengths() : protocols::analysis::PeptideDeriverFilter
• set_peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags , protocols::simple_moves::DisulfideInsertionMover
• set_per_chain_renumbering() : core::io::StructFileRepOptions
• set_per_residue_controls() : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• set_perform_filters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_perform_minimizer_run() : protocols::farna::movers::RNA_Minimizer
• set_perform_score_diff_cut() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_perform_VDW_rep_screen() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_performs_orientation() : protocols::denovo_design::connection::Connection
• set_permitted_overlap() : protocols::match::MatcherTask
• set_perturb_CCD_off() : protocols::anchored_design::AnchoredPerturbMover
• set_perturb_cycles() : protocols::anchored_design::AnchoredPerturbMover
• set_perturb_KIC_off() : protocols::anchored_design::AnchoredPerturbMover
• set_perturb_show() : protocols::anchored_design::AnchoredPerturbMover
• set_perturb_temp() : protocols::anchored_design::AnchoredPerturbMover
• set_perturb_type() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::ModelCDRH3
• set_perturbable() : protocols::helical_bundle::PerturbBundleOptions
• set_perturbation_magnitude() : protocols::helical_bundle::PerturbBundleOptions
• set_perturbation_type() : protocols::helical_bundle::PerturbBundleOptions
• set_perturbed_state() : core::pack::interaction_graph::FASTERNode
• set_perturber() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_perturber_attach_boinc_ghost_observer() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_perturber_bin() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_perturber_custom_rama_table() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_perturber_effect() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• set_perturber_iterations() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_perturber_must_switch_bins() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_pH() : core::scoring::methods::pHEnergy
• set_phi() : core::pose::Pose , protocols::denovo_design::components::StructureData , protocols::make_rot_lib::RotData , protocols::simple_moves::a3b_hbs::A3BHbsMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• set_phosphate() : protocols::toolbox::AtomLevelDomainMap
• set_phosphate_domain() : protocols::toolbox::AtomLevelDomainMap
• set_phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• set_physical_pose_clash_dist_cutoff() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• set_picked_positions() : protocols::frag_picker::FragmentPicker
• set_picking_rounds() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::toolbox::task_operations::MutationSetDesignOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_piece() : protocols::grafting::GraftMoverBase
• set_pivot_atoms() : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::generalized_kinematic_closure::GeneralizedKIC
• set_pivot_picker() : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• set_pivot_residues() : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover
• set_pivots() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_placeholder() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• set_plaintext() : protocols::sparta::GDB
• set_point() : protocols::qsar::scoring_grid::SingleGrid
• set_polar_charge_cutoff() : core::scoring::sasa::SasaCalc
• set_polymeric_connection() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• set_pool_name() : protocols::frag_picker::FragmentCandidate
• set_poolrmsd() : protocols::canonical_sampling::CanonicalSamplingMover
• set_population_weight() : protocols::cluster::ClusterBase
• 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_pos_list() : protocols::idealize::IdealizeMover
• 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 , protocols::denovo_design::components::StructureData , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::jd2::InnerJob , protocols::pack_daemon::EntityCorrespondence
• set_pose_after_closure() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• set_pose_and_task() : protocols::pack_daemon::PackDaemon
• set_pose_from_broker() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• set_pose_info() : protocols::analysis::InterfaceAnalyzerMover
• set_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::StepWiseConnectionSampler
• set_pose_no_initialize() : core::pack::interaction_graph::SimpleInteractionGraph
• set_pose_secstruct() : core::select::residue_selector::SecondaryStructureSelector
• set_pose_start() : protocols::denovo_design::components::Segment
• set_pose_tag() : protocols::simple_moves::CombinePoseMover
• set_pose_torsions() : protocols::topology_broker::TMHTopologySamplerClaimer
• set_poses() : protocols::moves::VectorPoseMover
• set_position() : core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity , protocols::carbohydrates::SimpleGlycosylateMover , protocols::optimize_weights::PNatAAOptEPositionData
• set_position_for_missing_res() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• set_position_for_missing_res_in_parameter_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• set_position_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• set_positions() : protocols::carbohydrates::SimpleGlycosylateMover , protocols::simple_filters::ScoreCutoffFilter
• set_positions_from_movemap() : protocols::carbohydrates::SimpleGlycosylateMover
• set_pr_idx() : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• set_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• set_pre_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• set_preapply() : protocols::simple_moves::GenericMonteCarloMover
• set_precision() : protocols::frag_picker::scores::FragmentScoreManager , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• set_precomputed_library_mover() : protocols::stepwise::modeler::StepWiseModeler
• set_predicted_report_to_db() : protocols::rotamer_recovery::RRReporterSQLite
• set_prefix() : protocols::match::output::PDBWriter
• set_premin() : protocols::md::MDBase
• set_preminimize() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_prepack() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_prepack_only() : protocols::docking::DockTaskFactory
• set_presample_added_residue() : protocols::stepwise::monte_carlo::mover::AddMover
• set_presample_by_swa() : protocols::stepwise::monte_carlo::mover::AddMover
• set_prescoring_filter() : protocols::helical_bundle::BackboneGridSampler
• set_prescoring_mover() : protocols::helical_bundle::BackboneGridSampler
• set_preselection_filter() : protocols::helical_bundle::BundleGridSampler
• set_preselection_mover() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• set_preserve_atom_coords() : protocols::simple_moves::MutateResidue
• set_preserve_crystinfo() : core::io::StructFileRepOptions
• set_preserve_detailed_balance() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , protocols::rigid::RigidBodyMover , protocols::rigid::UniformRigidBodyMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• set_preserve_header() : core::io::StructFileRepOptions
• set_preserve_whole_input_tag() : protocols::jobdist::BasicJob
• set_previous_mover() : protocols::rosetta_scripts::MultiplePoseMover
• set_primary_strategy() : protocols::antibody::task_operations::AddCDRProfilesOperation
• set_priority() : protocols::topology_broker::SequenceClaimer
• set_prob() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::dunbrack::DunbrackRotamerSampleData
• set_prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• set_prob_sd_sampling() : protocols::carbohydrates::LinkageConformerMover
• set_prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• set_prob_withinrot() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• set_probability() : protocols::make_rot_lib::RotData
• set_probability_data_cutoff() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_probe_atom_type() : protocols::qsar::scoring_grid::SolvationGrid
• set_probe_radius() : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• set_proc_id() : protocols::jobdist::BaseJobDistributor
• set_ProCorrection_values() : core::pack::interaction_graph::OnTheFlyEdge , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• set_ProCorrection_values_for_edge() : core::pack::interaction_graph::OnTheFlyInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• set_profile() : protocols::simple_moves::FavorSequenceProfile
• set_profile_wgt() : protocols::simple_moves::SequenceProfileMover
• set_project_pref_max_cpu_run_time() : protocols::boinc::Boinc
• set_project_pref_max_gfx_cpu() : protocols::boinc::Boinc
• set_project_pref_max_gfx_fps() : protocols::boinc::Boinc
• set_properties() : core::chemical::ResidueType
• set_property() : core::chemical::Atom , core::chemical::AtomProperties , core::chemical::AtomType , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::orbitals::OrbitalType , core::chemical::ResidueProperties , core::chemical::ResidueTypeSelector
• set_protein_esp_to_zero() : protocols::pockets::ElectrostaticpotentialGrid
• set_protein_prepack() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_protein_rings() : protocols::qsar::scoring_grid::AtrGrid
• set_protocol() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_protocol_info() : protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite
• set_proton() : protocols::noesy_assign::CrossPeakInfo
• set_proton_chi() : core::chemical::ResidueType
• set_protonated_H1_adenosine_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_pseudobonds_to_residue() : core::conformation::Residue
• set_psi() : core::pose::Pose , protocols::denovo_design::components::StructureData , protocols::make_rot_lib::RotData , protocols::simple_moves::a3b_hbs::A3BHbsMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• set_pssm_probabilities() : protocols::optimize_weights::PSSMOptEPositionData
• set_pucker_flip_rate() : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_pucker_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• set_PyMol_model_name() : protocols::moves::PyMolMover
• set_qsar_map() : protocols::qsar::scoring_grid::GridManager
• set_query_profile() : protocols::frag_picker::FragmentPicker
• set_query_seq() : protocols::frag_picker::FragmentPicker
• set_quick_alignment() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_quota_score() : protocols::frag_picker::scores::FragmentScoreMap
• set_r0() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_r1() : protocols::helical_bundle::parameters::BundleParameters
• set_r1_guesses() : protocols::helical_bundle::FitSimpleHelix
• set_radial_disp_ranges() : protocols::matdes::SymDofMoverSampler
• set_radial_disps() : protocols::matdes::SymDofMoverSampler
• set_radii_set() : core::scoring::sasa::SasaMethod
• set_radius() : protocols::toolbox::ClusterPhilStyle
• set_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_rama_cutoff_energy() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• set_rama_table_type_by_res() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• set_rama_term_ramping() : protocols::loop_modeling::LoopProtocol
• set_ramp_fa_rep() : protocols::simple_moves::ShakeStructureMover
• set_ramp_rama() : protocols::relax::CentroidRelax
• set_ramp_vdw() : protocols::relax::CentroidRelax
• set_rand() : protocols::genetic_algorithm::GeneticAlgorithmBase
• set_random() : protocols::mpi_refinement::Scheduler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• set_random_confomer() : protocols::docking::ConformerSwitchMover
• set_random_loop_flag() : protocols::LoopRebuild
• set_random_membrane_flip_angle() : protocols::membrane::FlipMover
• set_random_membrane_tilt_angle() : protocols::membrane::TiltMover
• set_random_mode() : protocols::normalmode::NormalModeRelaxMover
• set_random_order_() : protocols::loops::loop_mover::IndependentLoopMover
• set_random_sheets() : protocols::hybridization::FoldTreeHybridize
• set_randomize() : protocols::rbsegment_relax::RBSegmentRelax
• set_randomize1() : protocols::docking::DockingInitialPerturbation
• set_randomize2() : protocols::docking::DockingInitialPerturbation
• set_randomize_input_sequence() : protocols::anchored_design::AnchoredDesignMover
• set_randomize_missing_coords() : core::io::StructFileRepOptions
• set_randomize_resnum() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• set_range() : protocols::helical_bundle::FitSimpleHelix , protocols::membrane::FlipMover
• 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_rb_min_post_graft() : protocols::antibody::design::AntibodyDesignMover
• set_rcgs() : protocols::fldsgn::BluePrintBDR
• 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::StructFileReaderOptions
• set_read_pdb_header() : core::io::StructFileReaderOptions
• set_rebuild_bulge_mode() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• set_receptor_constraints() : protocols::flexpep_docking::FlexPepDockingProtocol
• set_reconstruct() : protocols::mpi_refinement::WorkUnit_PartialAbinitio
• set_record_source() : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• set_record_statistics() : protocols::backrub::BackrubSidechainMover
• set_recover_low() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_recover_sidechains_filename() : protocols::docking::DockingProtocol
• set_recovery_threshold() : protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins
• set_redesign_loop() : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_reference_atom() : protocols::helical_bundle::FitSimpleHelix
• set_reference_energy() : core::pack::rotamers::SingleLigandRotamerLibrary
• set_reference_pose() : protocols::dna::RestrictDesignToProteinDNAInterface , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::simple_moves::SuperimposeMover
• set_reference_pose_name() : protocols::simple_moves::StorePoseSnapshot
• set_reference_residue() : protocols::helical_bundle::FitSimpleHelix
• set_reference_round_task_factory() : protocols::simple_moves::GreenPacker
• set_reference_xyz() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• set_refinable_lattice() : protocols::cryst::MakeLatticeMover
• set_refine_CCD_off() : protocols::anchored_design::AnchoredRefineMover
• set_refine_cycles() : protocols::anchored_design::AnchoredRefineMover
• set_refine_h3() : protocols::antibody::AntibodyModelerProtocol
• set_refine_input_loop() : protocols::antibody::RefineOneCDRLoopCentroid
• set_refine_KIC_off() : protocols::anchored_design::AnchoredRefineMover
• set_refine_mode() : protocols::antibody::RefineOneCDRLoop
• set_refine_only() : protocols::anchored_design::AnchoredDesignMover
• set_refine_pose() : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::RNA_FragmentMonteCarlo
• set_refine_pose_list() : protocols::farna::RNA_DeNovoProtocol
• set_refine_repack_cycles() : protocols::anchored_design::AnchoredRefineMover
• set_refine_temp() : protocols::anchored_design::AnchoredRefineMover
• set_refine_type() : protocols::antibody::AntibodyModelerProtocol
• set_refstruct() : protocols::relax::AtomCoordinateCstMover
• set_region() : protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• set_regions_from_flexibility() : protocols::grafting::AnchoredGraftMover
• set_regions_from_movemap() : protocols::grafting::AnchoredGraftMover
• set_registry_shift() : protocols::hybridization::InsertChunkMover
• set_reinitialize_CCD_torsions() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• set_relative() : protocols::environment::claims::XYZClaim
• set_relax_schedule() : protocols::mpi_refinement::WorkUnit_Relax
• set_relax_structure() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_relaxmode() : protocols::normalmode::NormalModeRelaxMover
• set_relaxtype() : protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_Relax
• set_relevant_atom_ids() : protocols::match::output::SameSequenceAndDSPositionGrouper
• set_relevant_residues() : protocols::features::ReportToDB
• set_relevant_residues_mode() : protocols::features::FeaturesReporter , protocols::features::ReportToDB
• set_relevant_residues_task_factory() : protocols::features::ReportToDB
• set_remember_unrecognized_res() : core::io::StructFileRepOptions
• set_remember_unrecognized_water() : core::io::StructFileRepOptions
• set_removable() : protocols::simple_moves::VirtualRootMover
• set_remove() : protocols::simple_moves::VirtualRootMover
• set_remove_any_set_forced_cluster() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_remove_cterminus_variant() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_remove_nterminus_variant() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_rename_tags() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_renumber_pdb() : core::io::StructFileRepOptions
• set_rep_cutoff() : protocols::moves::SimulatedTempering
• set_repack() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_repack_list() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• set_repack_period() : protocols::loop_modeling::refiners::RepackingRefiner
• set_repack_shell() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• set_repeat_tail_length() : protocols::forge::remodel::RemodelLoopMover
• set_repeating_unit_offset() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_repeats() : protocols::simple_moves::bin_transitions::PerturbByBins
• set_replacement_resid() : protocols::match::output::PoseInserter
• set_repldist_params_helix_sheet() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_report_format() : protocols::analysis::PeptideDeriverFilter
• set_report_scorecomp() : protocols::md::MDBase
• set_report_sequence() : protocols::helical_bundle::BundleReporterFilter
• set_reporting() : protocols::docking::DockingProtocol
• set_reportstep() : protocols::md::MDBase
• set_representative_target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget
• set_repulsive_term_ramping() : protocols::loop_modeling::LoopProtocol
• set_require_mm_bend() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• set_required_atoms() : protocols::match::downstream::TargetRotamerCoords
• set_required_connections_for_residue() : protocols::simple_filters::PackerNeighborGraphFilter
• set_res1() : core::pose::rna::BasePair , core::pose::rna::BaseStack , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• set_res1_data() : core::scoring::hbonds::HBondResPairMinData
• set_res2() : core::pose::rna::BasePair , core::pose::rna::BaseStack , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• 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_res_name() : protocols::simple_moves::MutateResidue
• set_rescoords() : core::pack::scmin::ResidueAtomTreeCollection
• set_rescore_only() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• set_reserve_size() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• set_reset_filters() : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter
• set_reset_mode() : protocols::cyclic_peptide::PeptideStubMover , protocols::helical_bundle::BundleGridSampler
• set_reset_pose() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix
• set_resfile() : protocols::flxbb::DesignTask , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• set_resfile_1() : protocols::anchored_design::AnchorMoversData
• set_resfile_2() : protocols::anchored_design::AnchorMoversData
• set_resid() : core::pack::rotamer_set::RotamerSet , protocols::filters::CompoundFilter , protocols::moves::ResId , protocols::rosetta_scripts::ParsedProtocol
• 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_base2_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• set_residue_base_atoms() : protocols::forge::remodel::ResidueVicinityInfo
• set_residue_name() : protocols::helical_bundle::MakeBundleHelix
• set_residue_name3() : core::select::residue_selector::ResidueNameSelector
• set_residue_names() : core::select::residue_selector::ResidueNameSelector
• set_residue_numbers() : core::io::silent::SilentStruct
• set_residue_range() : protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• set_residue_range_not_surface() : core::scoring::solid_surface::SurfaceEnergies
• set_residue_selection_big_frags() : protocols::hybridization::hConvergenceCheck
• set_residue_selection_small_frags() : protocols::hybridization::hConvergenceCheck
• set_residue_selector() : core::select::residue_selector::NotResidueSelector , protocols::grafting::simple_movers::DeleteRegionMover , protocols::simple_moves::BackboneMover
• set_residue_type() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::upstream::BuildSet
• set_residue_type_set() : core::import_pose::ImportPoseOptions
• set_residues() : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• 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::StructFileRepOptions
• set_residues_per_repeat() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_resinfo() : core::pose::PDBInfo
• set_resname() : protocols::helical_bundle::BackboneGridSampler , protocols::metal_interface::MetalSiteResidue
• set_resnum() : core::pack::task::operation::AppendResidueRotamerSet , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• set_resnum_alias() : protocols::denovo_design::components::StructureData
• set_resolution() : protocols::qsar::scoring_grid::GridManager
• set_resonances() : protocols::noesy_assign::CrossPeak
• set_restore_csts() : protocols::hybridization::CartesianSampler
• set_restrict_only_design_to_loops() : protocols::toolbox::task_operations::RestrictToLoops
• set_restrict_partners_to_chains() : protocols::analysis::PeptideDeriverFilter
• set_restrict_receptors_to_chains() : protocols::analysis::PeptideDeriverFilter
• set_restrict_restypes() : protocols::flxbb::LayerDesignOperation
• set_restrictions_aa() : protocols::toolbox::task_operations::DsspDesignOperation
• set_restrictions_append() : protocols::toolbox::task_operations::DsspDesignOperation
• set_restrictions_exclude() : protocols::toolbox::task_operations::DsspDesignOperation
• set_restype() : protocols::match::downstream::TargetRotamerCoords , protocols::match::output::SingleDownstreamResidueWriter
• set_restype_index() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• set_return_single_random_match() : protocols::match::MatcherMover
• set_rho_to_zero() : protocols::pockets::NonPlaidFingerprint
• set_rigid_body_confs() : protocols::enzdes::ModifyStoredRBConfs , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
• set_rigid_body_confs_for_lig() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• set_rigid_body_confs_for_seqpos() : protocols::enzdes::ModifyStoredRBConfs
• set_rigid_body_mover() : protocols::simple_moves::CoupledMover
• set_ring() : protocols::qsar::scoring_grid::SingleGrid
• set_ring_conformation() : core::pose::Pose
• set_rm_virt_phosphate() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_rms_cutoff() : protocols::hybridization::CartesianSampler
• set_rms_group_cutoff() : protocols::match::output::SameSequenceAndDSPositionGrouper
• set_rms_offset() : protocols::helical_bundle::FitSimpleHelix
• set_rmsd() : protocols::anchored_design::AnchoredDesignMover
• set_rmsd_cutoff() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• set_RMSD_only_this() : protocols::anchored_design::AnchoredDesignMover
• set_rmsd_screen() : protocols::stepwise::options::StepWiseBasicOptions
• set_rmsd_target_tolerance() : protocols::simple_moves::ShakeStructureMover
• set_rmsd_unique_cutoff() : protocols::match::downstream::LigandConformerBuilder
• set_rmsdcut() : protocols::simple_moves::CombinePoseMover
• set_rna_base_pair_handler() : protocols::farna::RNA_FragmentMonteCarlo
• set_rna_data_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_rna_de_novo_pose_setup() : protocols::farna::RNA_FragmentMonteCarlo
• set_rna_legacy_output_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_rna_pairing_list() : protocols::farna::movers::RNA_JumpMover
• set_rna_params_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_root() : protocols::jumping::ResiduePairJumpSetup
• set_root_at_first_rigid_body() : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::setup::RNA_DeNovoPoseSetup
• set_root_atom() : core::scoring::methods::GoapRsdType
• set_root_partition_res() : protocols::stepwise::modeler::align::StepWisePoseAligner
• set_rosetta_scripts_tag() : protocols::rosetta_scripts::MultiplePoseMover
• set_rot_mag() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::cryst::DockLatticeMover
• set_rot_magnitude() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle
• set_rotamer() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , protocols::flexpack::interaction_graph::OTFFlexbbNode
• 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_rotamer_well_counts() : protocols::optimize_weights::PNatRotOptEPositionData
• set_rotamers() : 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_magnitude() : protocols::simple_moves::CoupledMover
• set_rotation_matrix() : core::conformation::symmetry::SymmData
• set_rotation_std_dev() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• set_rottrial() : protocols::relax::ClassicRelax
• set_rottrials_from_kic_segment() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_rotwell() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_rounds() : protocols::carbohydrates::GlycanRelaxMover , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::relax::CentroidRelax
• set_rsd_id() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• set_rsd_neighbor_denominator() : core::select::util::SelectResiduesByLayer
• set_rsd_set() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• set_rsd_type_set() : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_rsd_wdw_to_assign_prob() : protocols::hybridization::FragmentBiasAssigner
• set_rsr_update_step() : protocols::md::MDBase
• set_rt_min() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol
• set_rtmin() : protocols::docking::DockMCMCycle
• set_run_relax() : protocols::antibody::design::AntibodyDesignProtocol
• set_run_snugdock() : protocols::antibody::design::AntibodyDesignProtocol
• set_run_start() : protocols::wum::WorkUnitBase
• set_run_stop() : protocols::wum::WorkUnitBase
• set_rv_infos() : protocols::forge::remodel::ResidueVicinityRCG
• set_sa_length_scale() : core::pack::annealer::FASTERAnnealer
• set_sa_scale() : protocols::pack_daemon::FASTER_IG_Repacker
• set_sample_bb() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_sample_beta() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• set_sample_both_sugar_base_rotamer() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_sample_five_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• set_sample_index() : protocols::toolbox::task_operations::MutationSetDesignOperation
• set_sample_level() : protocols::match::upstream::SampleStrategyData
• set_sample_lower_nucleoside() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_sample_near_a_form() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_sample_nonpivot_torsions() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_sample_nucleoside() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• set_sample_nucleoside_lower() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_sample_nucleoside_upper() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_sample_ONLY_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sample_range_large() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_sample_range_small() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• set_sample_rna_chi() : core::pack::task::rna::RNA_ResidueLevelTask
• set_sample_startegy_for_constraint() : protocols::match::Matcher
• set_sample_strategy_for_chi() : protocols::match::upstream::BuildSet
• set_sample_three_prime_phosphate() : core::pack::task::rna::RNA_ResidueLevelTask
• set_sample_type() : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• set_sample_upper_nucleoside() : protocols::stepwise::sampler::rna::RNA_MC_Suite
• set_sample_zero_probs_at() : protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation
• set_sampler() : protocols::match::upstream::ProteinUpstreamBuilder , protocols::simple_moves::BBDihedralSamplerMover
• set_sampler_ : protocols::matdes::SymDofMover
• set_sampler_assert_no_virt_sugar_sampling() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sampler_extra_beta_rotamer() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sampler_extra_epsilon_rotamer() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sampler_include_torsion_value_in_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sampler_max_centroid_distance() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_sampler_num_pose_kept() : protocols::stepwise::options::StepWiseBasicOptions
• set_sampler_perform_phosphate_pack() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_sampler_silent_file() : protocols::stepwise::options::StepWiseBasicOptions
• set_sampler_try_sugar_instantiation() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_sampler_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_samples() : protocols::helical_bundle::PerturbBundleOptions
• set_sampletype() : protocols::simple_moves::GenericMonteCarloMover
• set_sampling_fold_tree() : protocols::abinitio::KinematicControl
• set_sampling_temperature() : protocols::simple_moves::sidechain_moves::SidechainMover
• set_sasa_cutoff() : protocols::simple_moves::ConsensusDesignMover
• set_save_times() : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_sc_min() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::simple_moves::ShakeStructureMover , protocols::symmetric_docking::SymDockProtocol
• set_sc_neighbor_angle_exponent() : protocols::flxbb::LayerDesignOperation
• set_sc_neighbor_angle_shift_factor() : protocols::flxbb::LayerDesignOperation
• set_sc_neighbor_denominator() : core::select::residue_selector::LayerSelector , protocols::flxbb::LayerDesignOperation
• set_sc_neighbor_dist_exponent() : protocols::flxbb::LayerDesignOperation
• set_sc_neighbor_dist_midpoint() : core::select::residue_selector::LayerSelector , protocols::flxbb::LayerDesignOperation
• set_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• set_scaffold_status() : protocols::hotspot_hashing::HotspotStub
• set_scaling() : protocols::simple_moves::FavorSequenceProfile
• set_scmin() : protocols::docking::DockMCMCycle
• set_score() : core::fragment::FragData , core::optimization::Particle , core::scoring::motif::XformScore
• set_score_component() : protocols::frag_picker::scores::FragmentScoreMap
• set_score_cut() : protocols::magnesium::MgScanner
• set_score_cut_PDB() : protocols::magnesium::MgScanner
• set_score_cutoff() : protocols::docking::DockingHighResFilter
• set_score_diff_cut() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_score_file() : protocols::simple_moves::ScoreMover
• set_score_function() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::cluster::GatherPosesMover , protocols::farna::movers::RNA_Minimizer , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::PackDaemon , protocols::relax::CentroidRelax , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• set_score_fxn() : core::pack::task::residue_selector::ClashBasedRepackShellSelector , protocols::simple_moves::CoupledMover
• set_score_margin() : protocols::docking::DockingHighResFilter
• 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_sphere_for_atom() : protocols::qsar::scoring_grid::SingleGrid
• set_score_threshold() : protocols::hybridization::FragmentBiasAssigner
• set_score_type() : protocols::helical_bundle::BundleReporterFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_moves::ConstrainToIdealMover
• set_score_type_threshold() : protocols::helical_bundle::BundleReporterFilter
• set_score_types() : core::scoring::methods::EnergyMethod
• set_score_weight() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• set_scorefunction() : core::pack::interaction_graph::SimpleInteractionGraph , protocols::analysis::InterfaceAnalyzerMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::GeneralAntibodyModeler , protocols::backrub::BackrubProtocol , protocols::canonical_sampling::CanonicalSamplingMover , protocols::carbohydrates::GlycanRelaxMover , protocols::cryst::DockLatticeMover , protocols::docking::DockingHighResFilter , protocols::features::DatabaseJobInputter , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::ncbb::SecStructMinimizeMover , protocols::relax::RangeRelaxMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::GreenPacker , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• set_scorefunction_min() : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::GeneralAntibodyModeler
• set_scorefxn() : protocols::abinitio::ResolutionSwitcher , protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::DisulfidizeMover , protocols::docking::DockingHighRes , protocols::docking::DockingLowRes , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::RepackWithoutLigandFilter , protocols::features::InterfaceFeatures , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::DesignTask , protocols::helical_bundle::BundleReporterFilter , protocols::jd2::archive::EvaluatedArchive , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::magnesium::MgScanner , protocols::multistate_design::MultiStateFitnessFunction , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::movers::TryRotamers , protocols::relax::RelaxProtocolBase , protocols::simple_filters::ScoreTypeFilter , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::SimpleThreadingMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• set_scorefxn_deriver() : protocols::analysis::PeptideDeriverFilter
• set_scorefxn_design() : protocols::flxbb::FlxbbDesign
• set_scorefxn_info() : core::scoring::Energies
• set_scorefxn_low() : protocols::antibody::AntibodyCDRGrafter
• set_scorefxn_min() : protocols::antibody::design::AntibodyDesignProtocol
• set_scorefxn_minimize() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• set_scorefxn_obj() : protocols::md::MDBase
• set_scorefxn_pack() : protocols::antibody::AntibodyCDRGrafter , protocols::docking::DockingHighRes
• set_scorefxn_relax() : protocols::flxbb::FlxbbDesign
• set_scorefxn_repack() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• set_scoretype() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_Relax
• set_scoretypes() : core::scoring::etable::EtableEvaluator
• set_screen_all() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• set_script_from_lines() : protocols::relax::FastRelax
• set_script_to_batchrelax_default() : protocols::relax::FastRelax
• set_sd() : protocols::simple_moves::symmetry::SetupNCSMover
• 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_sd_range() : protocols::match::upstream::SampleStrategyData
• set_seal_foldtree() : protocols::forge::remodel::RemodelLoopMover
• set_second_cycle() : protocols::docking::DockMCMProtocol
• set_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• set_secondary_structure() : protocols::star::Extender , protocols::surface_docking::SurfaceDockingProtocol
• set_secstruct() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::SecstructSRFD , core::io::silent::RNA_SilentStruct , core::pose::Pose , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::environment::ProtectedConformation , protocols::farna::secstruct::RNA_SecStructInfo , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::SheetConstraintGenerator , protocols::frags::TorsionFragment , protocols::jumping::JumpSelector , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_secstruct_from_blueprint() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• set_segdef() : protocols::mpi_refinement::WorkUnit_bbGauss
• set_segment() : protocols::rbsegment_relax::RBSegmentMover
• set_segment_IDs() : core::io::silent::SilentStruct
• set_segment_ids() : core::pose::PDBInfo
• set_segment_names() : protocols::denovo_design::components::NamedMover
• set_segment_size() : protocols::forge::remodel::RemodelGlobalFrame
• set_segment_stage() : protocols::forge::remodel::RemodelLoopMover
• set_select_designable() : protocols::residue_selectors::TaskSelector
• set_select_fixed() : protocols::residue_selectors::TaskSelector
• set_select_packable() : protocols::residue_selectors::TaskSelector
• set_select_positive_phi() : core::select::residue_selector::PhiSelector
• set_selected_ss() : core::select::residue_selector::SecondaryStructureSelector
• set_selection_low() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• set_selectmode() : protocols::md::MDBase
• set_selector() : core::chemical::Patch , core::chemical::PatchCase , core::scoring::aa_composition_energy::AACompositionConstraint , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::constraints::CoordinateConstraintGenerator , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_selector_kbt() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_selector_scorefunction() : protocols::generalized_kinematic_closure::GeneralizedKIC
• set_selector_scorefxn() : protocols::denovo_design::connection::BridgeTomponents
• set_selector_type() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• set_semi_energy_dist() : protocols::make_rot_lib::RotData
• set_semi_prob_dist() : protocols::make_rot_lib::RotData
• set_separate_prt_ligand() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• set_seq_design_options() : protocols::antibody::design::AntibodyDesignMover
• set_seq_recovery_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• set_seq_sep_ramping() : protocols::abinitio::abscript::AbscriptStageMover
• set_seq_sep_scale() : core::scoring::SecondaryStructureWeights
• set_seq_sep_stage1() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• set_seq_sep_stage3() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• set_seqfrags_only() : protocols::hybridization::CartesianHybridize
• set_seqmap() : protocols::forge::remodel::RemodelConstraintGenerator
• set_seqpos() : core::io::rna::RDAT , protocols::metal_interface::MetalSiteResidue
• set_seqprof() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• set_sequence() : core::fragment::FragData , core::fragment::SingleResidueFragData , core::io::rna::RDAT , core::io::silent::SimpleSequenceData , protocols::antibody::design::NativeAntibodySeq , protocols::frags::TorsionFragment , protocols::noesy_assign::FragsToAtomDist , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::SimpleThreadingMover , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache , protocols::topology_broker::SequenceClaimer
• set_sequence_coupling() : protocols::constraints_additional::SequenceCouplingConstraint
• set_sequence_profile() : core::scoring::constraints::SequenceProfileConstraint
• set_sequences() : core::io::rna::RDAT
• set_sequential_distribution() : protocols::jd2::MPIWorkPoolJobDistributor
• set_set1_selector() : protocols::denovo_design::DisulfidizeMover
• set_set2_selector() : protocols::denovo_design::DisulfidizeMover
• set_set_up_metal_bonds() : core::import_pose::ImportPoseOptions
• set_sf() : protocols::analysis::LoopAnalyzerMover
• set_sfxn() : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::flexpack::FlexPacker , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_sfxn_cycles() : protocols::loop_modeling::LoopProtocol
• set_shadowing_atom() : core::chemical::ResidueType
• set_shared_silent_data() : core::io::silent::SilentFileData
• set_sharpen_b() : core::scoring::cryst::PhenixInterface
• set_sheet() : protocols::nonlocal::SheetTranslate
• set_sheet_number() : protocols::fldsgn::topology::SheetSet
• set_sheets() : protocols::hybridization::FoldTreeHybridize
• set_short_backrub_mover() : protocols::simple_moves::CoupledMover
• set_show_all_fixes() : core::io::StructFileRepOptions
• set_show_extended() : protocols::anchored_design::AnchoredDesignMover
• set_show_viol_level() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• set_shrink_factor() : protocols::match::Bool3DGridKinemageWriter
• set_sidechain() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• set_silent_file() : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::magnesium::MgScanner , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::options::StepWiseBasicOptions
• set_silent_file_data() : core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• set_silent_file_name() : protocols::jd2::SilentFileJobOutputter
• set_silent_file_out() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• set_silent_files_in() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_silent_struct_type() : core::io::silent::SilentFileOptions
• set_silentout_file_name() : protocols::abinitio::Protocol
• set_sim() : protocols::cluster::APCluster
• set_sim_anneal() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_simple_append_map() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_simple_rmsd_cutoff_relax() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_single_resnum() : protocols::carbohydrates::LinkageConformerMover , protocols::simple_moves::BBDihedralSamplerMover
• set_size() : core::scoring::Energies , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::pockets::SmallMol
• set_size_and_nbb() : protocols::frags::TorsionFragment
• set_skip_bulge_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_skip_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_skip_completely_buried_positions() : protocols::match::Bool3DGridKinemageWriter
• set_skip_complicated_stuff() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• set_skip_connect_info() : core::io::StructFileRepOptions
• set_skip_coord_constraints() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_skip_deletions() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_skip_long_min() : protocols::hybridization::CartesianHybridize
• set_skip_low_temp_phase() : protocols::simple_moves::ShakeStructureMover
• set_skip_lr() : protocols::rbsegment_relax::RBSegmentRelax
• set_skip_minimize() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• set_skip_o2prime_trials() : protocols::farna::options::RNA_MinimizerOptions
• set_skip_preminimize() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_skip_redundant() : protocols::topology_broker::ConstraintClaimer
• set_skip_reporting() : protocols::analysis::InterfaceAnalyzerMover
• set_skip_ring_closure() : core::scoring::methods::ProClosureEnergy
• set_skip_ring_closure_from_flags() : core::scoring::methods::ProClosureEnergy
• set_skip_same_pucker() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• set_skip_sampling() : protocols::grafting::AnchoredGraftMover
• set_skip_set_reasonable_fold_tree() : core::import_pose::ImportPoseOptions
• set_skip_stage1() : protocols::abinitio::ClassicAbinitio
• set_skip_stage2() : protocols::abinitio::ClassicAbinitio
• set_SlaveCanOpenFile() : protocols::jd2::MpiFileBuffer
• set_slice_res() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• set_slice_res_list() : core::pose::full_model_info::FullModelParameters
• set_slide_axis() : protocols::surface_docking::SurfaceParameters
• set_slide_criteria() : protocols::simple_moves::symmetry::SymmetrySlider
• set_slide_info() : core::conformation::symmetry::SymmData
• set_slide_order() : core::conformation::symmetry::SymSlideInfo
• set_slide_threshold() : protocols::simple_moves::symmetry::SymmetrySlider
• 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_small_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_small_fragments() : protocols::hybridization::MRMover
• set_smallmovesize() : protocols::surface_docking::FullatomRelaxMover
• set_snugdock_foldtree() : protocols::antibody_legacy::AntibodyModeler
• set_SnugFit() : protocols::antibody::AntibodyModelerProtocol
• set_snugfit() : protocols::antibody::RefineOneCDRLoopCentroid
• set_solution_picker() : protocols::kinematic_closure::KicMover
• set_solvation() : protocols::make_rot_lib::RotData
• set_spacegroup() : protocols::cryst::Spacegroup
• 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_special_edges() : protocols::sewing::SewGraph
• set_sphere() : protocols::qsar::scoring_grid::SingleGrid
• set_spin() : protocols::docking::DockingInitialPerturbation
• set_ss_cutoff() : core::scoring::SecondaryStructureWeights
• set_ss_from_str() : protocols::frag_picker::VallResidue
• set_ss_lowstrand() : core::scoring::SecondaryStructureWeights
• set_ssid() : protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• set_SSorient() : protocols::fldsgn::topology::SS_Info2
• set_stage() : protocols::abinitio::IterativeBase
• set_stage1_1_cycles() : protocols::hybridization::FoldTreeHybridize
• set_stage1_2_cycles() : protocols::hybridization::FoldTreeHybridize
• set_stage1_3_cycles() : protocols::hybridization::FoldTreeHybridize
• set_stage1_4_cycles() : protocols::hybridization::FoldTreeHybridize
• set_stage1_increase_cycles() : protocols::hybridization::HybridizeProtocol
• set_stage1_scorefxn() : protocols::hybridization::HybridizeProtocol
• set_stage2_cycles() : protocols::relax::ClassicRelax
• set_stage2_increase_cycles() : protocols::hybridization::HybridizeProtocol
• set_stage2_repack_period() : protocols::relax::ClassicRelax
• set_stage2_scorefxn() : protocols::hybridization::HybridizeProtocol
• set_stage2min_scorefxn() : protocols::hybridization::HybridizeProtocol
• set_stage2pack_scorefxn() : protocols::hybridization::HybridizeProtocol
• set_stage3_cycles() : protocols::relax::ClassicRelax
• set_stage4_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• set_staged_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_standard_stub_atoms() : core::fragment::DownJumpSRFD
• set_start() : protocols::loophash::WorkUnit_LoopHash , protocols::loops::Loop , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::rbsegment_relax::RBResidueRange
• set_start_added_residue_in_aform() : protocols::stepwise::monte_carlo::mover::AddMover
• set_start_rep_weight() : protocols::relax::ClassicRelax
• set_start_res() : protocols::loophash::LoopHashSampler
• set_starter_for_sequential_distribution() : protocols::jd2::MPIWorkPoolJobDistributor
• set_starting_pdb() : protocols::forge::remodel::RemodelLoopMover
• set_starting_reference_energies() : protocols::optimize_weights::OptEMultifunc
• set_starting_rep() : protocols::docking::SlideIntoContact
• set_starting_sequence() : protocols::forge::remodel::RemodelLoopMover
• set_state() : protocols::forge::remodel::RemodelDesignMover
• set_state_for_node() : core::pack::interaction_graph::AnnealableGraphBase , 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::MultiplexedAnnealableGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• set_state_ind_for_this_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• set_statistics_filename() : protocols::backrub::BackrubSidechainMover
• set_stats_cutoff() : protocols::antibody::task_operations::AddCDRProfilesOperation
• set_status() : protocols::frag_picker::quota::ABEGO_SS_Map
• set_status_prefix() : protocols::jd2::Job , protocols::jd3::LarvalJob
• set_std_dev() : protocols::make_rot_lib::RotData
• set_stem_optimize() : protocols::antibody::GraftCDRLoopsProtocol
• set_stem_size() : protocols::antibody::GraftedStemOptimizer , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• set_step_size() : protocols::match::upstream::SampleStrategyData
• set_stepwise_modeler() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover
• set_stiffness() : core::scoring::dna::DNA_BasePotential
• set_stop() : protocols::loops::Loop
• set_stop_after_closure() : protocols::antibody::AntibodyCDRGrafter
• set_stop_res() : protocols::loophash::LoopHashSampler
• set_store_silents() : protocols::simple_moves::CombinePoseMover
• set_store_trj() : protocols::md::MDBase
• set_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_strand_pairs() : protocols::fldsgn::SheetConstraintGenerator
• set_strand_strand_weights() : core::scoring::methods::EnergyMethodOptions
• set_strategy() : protocols::hybridization::CartesianSampler , protocols::match::upstream::SampleStrategyData
• set_stretch_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_strict_looprelax_checks() : protocols::loops::Loops
• set_strict_loops() : protocols::loops::loop_mover::IndependentLoopMover
• set_strict_movemap() : protocols::abinitio::KinematicControl
• set_stride() : protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::features::TrajectoryReportToDB
• set_strip_existing_glycans() : protocols::carbohydrates::SimpleGlycosylateMover
• set_struct_id1() : protocols::rotamer_recovery::RRReporterSQLite
• set_struct_ids_from_sql() : protocols::features::DatabaseJobInputter
• set_struct_ids_from_strings() : protocols::features::DatabaseJobInputter
• set_structure() : core::io::rna::RDAT
• set_structure_input_tag() : protocols::features::ReportToDB
• set_structure_tag() : protocols::features::ReportToDB
• set_structures() : core::io::rna::RDAT
• set_stub_atoms() : core::fragment::DownJumpSRFD
• set_stub_transform() : core::conformation::Conformation , core::kinematics::AtomTree , protocols::environment::ProtectedConformation
• set_subbin_type_i() : core::scoring::bin_transitions::BinTransitionData
• set_subbin_type_iplus1() : core::scoring::bin_transitions::BinTransitionData
• set_submotif_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_submotif_library() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• set_subunits() : core::conformation::symmetry::SymmData
• set_sugar() : protocols::toolbox::AtomLevelDomainMap
• set_sugar_domain() : protocols::toolbox::AtomLevelDomainMap
• set_suite_cluster_radius() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_super_secret_fixed_interface_mode() : protocols::anchored_design::AnchorMoversData
• set_superenv() : core::environment::EnvCore
• set_superimpose_over_all() : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::setup::StepWiseJobDistributor
• set_superimpose_over_all_instantiated() : protocols::stepwise::modeler::align::StepWisePoseAligner
• set_superimpose_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• set_suppress_bp_constraint() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_suppress_zero_occ_pdb_output() : core::io::StructFileRepOptions
• set_surf() : core::scoring::packing::PoseBalls
• set_surface_contact_mover() : protocols::surface_docking::FullatomRelaxMover
• set_surface_esp_to_zero() : protocols::pockets::ElectrostaticpotentialGrid
• set_surface_orient_mover() : protocols::surface_docking::FullatomRelaxMover
• set_surface_parameters() : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover
• set_surface_score_weight() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_svn_version_and_url() : core::SVNVersion
• set_swap_file() : protocols::wum::WorkUnitQueue_Swapped
• set_sweep_nonpivot_torsions() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_sweep_nsteps() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_sweep_start_angle() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_sweep_step_size() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_switch_focus_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_sym_dof_names() : protocols::matdes::SymDofMoverSampler
• set_symm() : protocols::simple_filters::SymmetricMotifFilter
• set_symm_transforms() : core::conformation::symmetry::SymmData
• set_symmdef_file() : protocols::hybridization::MRMover
• set_symmetric_cenlist() : core::scoring::symmetry::SymmetricScoreFunction
• set_symmetric_pack() : protocols::scoring::Interface
• set_symmetric_residue_neighbors_hbonds() : core::scoring::symmetry::SymmetricScoreFunction
• set_symmetric_sequence() : protocols::simple_moves::symmetry::SetupNCSMover
• set_symmetry() : protocols::helical_bundle::MakeBundle , protocols::noesy_assign::PeakAssignment
• set_symmetry_copies() : protocols::helical_bundle::MakeBundle
• set_symmetry_name() : core::conformation::symmetry::SymmData
• set_symmetry_options_from_tag() : protocols::helical_bundle::MakeBundle
• set_symmetry_type() : core::conformation::symmetry::SymmData
• set_tag() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• set_tag_from_pose() : core::io::silent::SilentStruct
• set_tail_dihedrals() : protocols::helical_bundle::MakeBundleHelix
• set_tail_residue_name() : protocols::helical_bundle::MakeBundleHelix
• 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_targ_ang() : protocols::forge::remodel::ResidueVicinityInfo
• set_targ_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• set_targ_dih() : protocols::forge::remodel::ResidueVicinityInfo
• set_targ_res() : protocols::toolbox::match_enzdes_util::ResInteractions
• set_target() : protocols::simple_moves::MutateResidue
• set_target_and_tolerance() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• set_target_function() : core::scoring::cryst::PhenixInterface
• set_target_geomcst_id() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• set_target_proximity_to_starting_conformation() : protocols::enzdes::EnzdesFlexibleRegion
• set_target_range() : protocols::simple_moves::SuperimposeMover
• set_target_res() : protocols::pockets::PocketConstraint
• set_target_res_pdb() : protocols::pockets::PocketConstraint
• set_target_rotamer_coords() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• set_task() : core::pack::rotamer_set::RotamerSets , protocols::flexpack::FlexPacker , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::toolbox::task_operations::STMStoredTask
• set_task_factory() : protocols::anchored_design::AnchorMoversData , protocols::antibody::CDRsMinPackMin , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::backrub::BackrubSidechainMover , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::flexpack::FlexPacker , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::pack_daemon::DaemonSet , protocols::relax::RelaxProtocolBase , protocols::residue_selectors::TaskSelector , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• set_task_for_filters() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• set_task_for_filters_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• set_task_scaling() : protocols::simple_moves::GenericMonteCarloMover
• set_task_segments() : protocols::relax::AtomCoordinateCstMover
• set_taskfactory() : protocols::backrub::BackrubProtocol
• set_tau() : core::conformation::Residue
• set_temp() : core::io::ResidueInformation , protocols::canonical_sampling::CanonicalSamplingMover , protocols::cryst::DockLatticeMover , protocols::hybridization::CartesianSampler , protocols::multistate_design::PartitionAggregateFunction< T >
• set_temp_based_on_ens_diversity() : protocols::simple_moves::ShakeStructureMover
• set_temp_cycles() : protocols::loop_modeling::LoopProtocol
• set_temperature() : core::pack::annealer::SimAnnealerBase , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::BiasEnergy , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::docking::ConformerSwitchMover , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::hybridization::CartesianHybridize , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::magnesium::MgMonteCarlo , protocols::md::MDBase , protocols::moves::MonteCarlo , protocols::rbsegment_relax::RBSegmentRelax , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_temperature_observer() : protocols::canonical_sampling::MultiTemperatureTrialCounter
• set_temperature_ramping() : protocols::loop_modeling::LoopProtocol
• set_temperature_schedule() : protocols::loop_modeling::LoopProtocol
• set_temperatures() : protocols::canonical_sampling::TemperingBase
• set_tempering() : protocols::canonical_sampling::MetropolisHastingsMover
• set_template() : protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover
• set_templates_to_ignore() : protocols::hybridization::ChunkTrialMover
• set_terminal_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_test_all_moves() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_test_control_mode() : protocols::grafting::AnchoredGraftMover
• set_testing_phase() : protocols::simple_moves::ShakeStructureMover
• set_tether_jump() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_tether_to_closest_res() : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• set_theta() : core::conformation::Residue , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose
• set_three_prime_phosphate_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• set_threshold() : protocols::filters::CombinedFilter , protocols::simple_filters::ScoreTypeFilter , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• set_threshold_distance() : core::indexed_structure_store::ABEGOHashedFragmentStore
• set_thresholds() : protocols::simple_filters::SymmetricMotifFilter
• set_throw_on_double_registration() : core::select::residue_selector::ResidueSelectorFactory
• set_tilt() : protocols::docking::DockingInitialPerturbation
• set_tilt1_center() : protocols::docking::DockingInitialPerturbation
• set_tilt2_center() : protocols::docking::DockingInitialPerturbation
• set_titrate_stack_bonus() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_tm_helical_ : protocols::relax::membrane::MPRangeRelaxMover
• set_tmh_inserted() : core::scoring::MembraneTopology
• set_tmh_jump() : protocols::jumping::PairingLibrary
• set_to_default() : protocols::relax::FastRelax
• set_to_pose() : protocols::antibody::design::NativeAntibodySeq
• set_to_quench() : core::pack::annealer::SimAnnealerBase
• set_tolerance() : protocols::relax::ClassicRelax
• set_tolerated_overlap() : protocols::match::output::MatchCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• set_tool() : protocols::loop_modeling::LoopMover
• set_top_frag_num() : core::fragment::FragmentIO
• set_top_n_big_frag() : protocols::hybridization::FoldTreeHybridize
• set_top_n_small_frag() : protocols::hybridization::FoldTreeHybridize
• set_topology() : protocols::abinitio::abscript::FragmentJumpCM
• set_tor_U1D3_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• set_torsion() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::fragment::BBTorsionSRFD , core::pose::Pose , protocols::environment::ProtectedConformation , protocols::frags::TorsionFragment
• set_torsion_angle() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , protocols::environment::ProtectedConformation
• set_torsion_id() : protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• set_torsion_screen() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• set_torsion_to_pose() : protocols::simple_moves::bb_sampler::BBDihedralSampler , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::simple_moves::bb_sampler::SugarBBSampler
• set_torsion_type() : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• set_torsions() : protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• set_torsions_using() : protocols::normalmode::NormalMode
• set_total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_total_energy_current_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_total_jobs() : protocols::jd2::JobsContainer
• set_total_num_backbones() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_total_residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::solid_surface::SurfaceEnergies , protocols::optimize_weights::PNatStructureOptEData
• set_trace() : core::io::rna::RDAT
• set_traits() : protocols::genetic_algorithm::Entity
• set_traits_size() : protocols::genetic_algorithm::Entity
• set_trans_mag() : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::cryst::DockLatticeMover
• set_trans_magnitude() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes
• set_transition_threshold() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• set_translation() : core::kinematics::Jump , core::kinematics::RT
• set_translation_magnitude() : protocols::simple_moves::CoupledMover
• set_translation_matrix() : core::conformation::symmetry::SymmData
• set_transparent_facets() : protocols::match::Bool3DGridKinemageWriter
• set_trial_positions() : protocols::enzdes::SecondaryMatchProtocol
• set_trials() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::hConvergenceCheck , protocols::abinitio::MembraneAbinitio , protocols::denovo_design::connection::Connection , protocols::hybridization::hConvergenceCheck , protocols::seeded_abinitio::CloseFold
• set_trivial_decoy_compatibility_score() : protocols::noesy_assign::CrossPeakList
• set_turn_off_rna_chem_map_during_optimize() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_turnoff_minimization() : protocols::antibody::CDRsMinPackMin
• set_twist() : protocols::make_rot_lib::RotData
• 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_two_stage_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_type() : core::scoring::MultipoleElecResidueInfo , core::scoring::rna::data::RNA_Reactivity , protocols::checkpoint::CheckPointer , protocols::moves::Mover , protocols::moves::PyMolObserver , protocols::qsar::scoring_grid::SingleGrid
• set_unbound_mode() : protocols::anchored_design::AnchorMoversData
• set_undercount_sugar_rotamers() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• set_unfolded_energy_emap_vector() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• set_uniform_backrub() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• set_uniform_euler_angle_bin_width() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_uniform_modeler() : protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_StepWiseSampler
• set_uniform_trans() : protocols::docking::DockingInitialPerturbation
• set_uniform_xyz_bin_width() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_unselectable() : protocols::match::Bool3DGridKinemageWriter
• set_unset_defaults() : protocols::anchored_design::AnchorMoversData
• set_unset_packertask_factory() : protocols::anchored_design::AnchorMoversData
• set_unset_scorefunctions() : protocols::anchored_design::AnchorMoversData
• set_unweighted() : protocols::simple_filters::ScoreCutoffFilter
• set_up() : protocols::nonlocal::SimpleTreeBuilder , protocols::nonlocal::StarTreeBuilder , protocols::nonlocal::TreeBuilder
• set_up_atom_order() : protocols::frag_picker::CSTalosIO
• set_up_bin_cdfs() : core::scoring::bin_transitions::BinTransitionData
• set_up_bins() : core::scoring::bin_transitions::BinTransitionCalculator
• set_up_constraints() : protocols::relax::RelaxProtocolBase
• set_up_hbond_filter() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• set_up_metal_bonds() : core::import_pose::ImportPoseOptions
• set_up_metal_bonds_ : core::import_pose::ImportPoseOptions
• set_up_metal_constraints() : core::import_pose::ImportPoseOptions
• set_up_peptide_stub_mover() : protocols::helical_bundle::BackboneGridSampler
• set_up_q() : core::scoring::saxs::SAXSEnergy
• set_up_quota_nnmake_style() : protocols::frag_picker::FragmentPicker
• set_up_spline_from_data() : core::scoring::nv::NVlookup
• set_up_ss_abego_quota() : protocols::frag_picker::FragmentPicker
• set_up_subbins() : core::scoring::bin_transitions::BinTransitionData
• set_up_termini_mover() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• set_update_boinc() : protocols::moves::MonteCarlo
• set_update_pdb_numbering_mode() : protocols::cyclic_peptide::PeptideStubMover
• set_updates() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• set_upper_connect_atom() : core::chemical::ResidueType
• set_upper_overlap() : protocols::denovo_design::connection::Connection
• set_upper_residues() : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• set_upper_segment() : protocols::denovo_design::components::Segment
• set_upper_segment_id() : protocols::denovo_design::connection::Connection
• set_upper_threshold() : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• set_upper_value() : protocols::helical_bundle::PerturbBundleOptions
• set_upstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• set_use_big_polar_hydrogen() : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• set_use_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• set_use_cluster_csts() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_use_cluster_for_H3() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_use_conformer_population_stats() : protocols::carbohydrates::LinkageConformerMover
• set_use_constraints() : protocols::antibody::AntibodyModelerProtocol , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• set_use_coordinate_constraints() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• set_use_defaults() : protocols::helical_bundle::PerturbBundleOptions
• set_use_degrees() : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• set_use_dssp() : protocols::fldsgn::filters::SheetTopologyFilter
• set_use_ellipsoidal_randomization() : protocols::docking::DockingInitialPerturbation
• set_use_epitope_constraints() : protocols::antibody::design::AntibodyDesignMover
• set_use_fast_frame_heuristic() : protocols::magnesium::MgHydrater
• set_use_fast_heuristic() : protocols::magnesium::MgWaterHydrogenPacker
• set_use_first_jump_for_submotif() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_use_general_csts_on_cluster_failure() : protocols::antibody::constraints::CDRDihedralConstraintMover
• set_use_green_packer() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• set_use_increased_vdw_radii() : protocols::relax::CentroidRelax
• set_use_input_sidechain() : protocols::match::upstream::ProteinUpstreamBuilder
• set_use_jobname() : protocols::analysis::InterfaceAnalyzerMover
• set_use_legacy_protocol() : protocols::docking::DockingProtocol
• set_use_light_chain_type() : protocols::antibody::task_operations::AddCDRProfileSetsOperation
• set_use_loops_from_observer_cache() : protocols::loops::loop_mover::LoopMover
• set_use_nblist() : core::scoring::Energies
• set_use_outliers() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• set_use_packer_instead_of_rotamer_trials() : protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::options::StepWiseBasicOptions
• set_use_pdb_format_HETNAM_records() : core::io::StructFileRepOptions
• set_use_phenix_geo() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_use_pose_secstruct() : protocols::fldsgn::filters::SecondaryStructureFilter
• set_use_precomputed_library() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_use_rama2b() : protocols::relax::CentroidRelax
• set_use_relevant_residues_as_loop_length() : protocols::features::LoopAnchorFeatures
• set_use_resfile() : protocols::analysis::InterfaceAnalyzerMover
• set_use_sc_neighbors() : core::select::residue_selector::LayerSelector
• set_use_secondary_graft_mover_if_needed() : protocols::antibody::AntibodyCDRGrafter
• set_use_seqprof_constraints() : protocols::simple_moves::ConsensusDesignMover
• set_use_sidechain_neighbors() : protocols::flxbb::LayerDesignOperation
• set_use_single_residue_to_define_anchor_transfrom() : protocols::features::LoopAnchorFeatures
• set_use_statistical_potential() : protocols::denovo_design::filters::PreProlineFilter
• set_use_stored_energy() : protocols::vip::VIP_Mover
• set_use_sugar_bb_data_if_needed() : protocols::carbohydrates::LinkageConformerMover
• set_use_symmetry() : core::conformation::symmetry::SymmetryInfo , protocols::flxbb::LayerDesignOperation
• set_use_threeletter() : protocols::helical_bundle::BundleReporterFilter
• set_use_tracer() : protocols::analysis::InterfaceAnalyzerMover
• set_user_chain1() : protocols::denovo_design::connection::Connection
• set_user_chain2() : protocols::denovo_design::connection::Connection
• set_user_csts() : protocols::hybridization::FoldTreeHybridize
• set_user_defined_calc_rms_res() : protocols::stepwise::modeler::align::StepWisePoseAligner
• set_user_defined_cycles() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_user_defined_name() : protocols::filters::Filter , protocols::simple_filters::DomainInterfaceFilter
• set_user_input() : protocols::farna::libraries::ChunkSet
• set_user_input_chunk_library() : protocols::farna::RNA_FragmentMonteCarlo
• set_user_input_VDW_bin_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseConnectionSampler
• set_user_provided_movers() : protocols::forge::remodel::RemodelLoopMover
• set_userpos() : protocols::hybridization::CartesianSampler
• set_using() : core::scoring::methods::GoapRsdType
• set_valid() : core::fragment::FragData
• set_valid_energies() : core::io::silent::SilentStruct
• set_vall() : protocols::frag_picker::FragmentPicker
• set_vall_torsions_file() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• set_value() : core::scoring::rna::data::RNA_Reactivity , protocols::filters::ContingentFilter , protocols::qsar::qsarPoint
• set_value_for_bin() : protocols::match::Bool3DGrid
• set_value_from_pdb_line() : core::io::pdb::Field
• set_values() : protocols::stepwise::sampler::StepWiseSamplerOneValue
• set_variant_type() : core::chemical::ResidueProperties
• set_vary_bond_geometry() : protocols::farna::options::RNA_MinimizerOptions
• set_vary_bond_geometry_frequency() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• set_vary_bondangles() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_vary_ca_bond_angles() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• set_vary_cutpoints() : protocols::anchored_design::AnchoredDesignMover
• set_vary_loop_length_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• set_vary_polar_hydrogen_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• set_vary_rna_bond_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• set_vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• set_VDW_rep_alignment_RMSD_CUTOFF() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• set_VDW_rep_delete_matching_res() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• set_VDW_rep_screen_info() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::options::StepWiseBasicOptions
• set_VDW_rep_screen_physical_pose_clash_dist_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_VDW_weight() : protocols::anchored_design::AnchorMoversData
• set_vec() : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• set_vector_exclude_residues() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• set_vector_name_and_weight() : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• set_verbose() : core::io::silent::SilentFileData , core::scoring::rna::RNA_TorsionPotential , protocols::farna::movers::RNA_LoopCloser , protocols::farna::options::RNA_BasicOptions , protocols::flxbb::LayerDesignOperation , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::magnesium::MgHydrater , protocols::rbsegment_relax::SequenceShiftMover , protocols::simple_moves::ScoreMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::StepWiseSampleAndScreen
• set_verbose_sampler() : protocols::stepwise::options::StepWiseBasicOptions
• set_verbose_scores() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_version() : core::io::rna::RDAT
• set_vertex_member_of_group() : core::pack::interaction_graph::InteractionGraphBase
• set_vicinity_degree() : protocols::anchored_design::AnchoredRefineMover
• set_vicinity_sampling() : protocols::anchored_design::AnchoredRefineMover
• set_view() : protocols::symmetric_docking::SymDockProtocol
• set_virtual_anchor_attachment_points() : protocols::farna::setup::RNA_DeNovoParameters
• set_virtual_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• set_virtual_sugar_do_minimize() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_virtual_sugar_do_screens() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_virtual_sugar_is_from_prior_step() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• set_virtual_sugar_keep_base_fixed() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_virtual_sugar_legacy_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• set_virtualize_packable_moieties_in_screening_pose() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• set_visited() : protocols::pockets::SmallMol
• set_vlb() : protocols::forge::remodel::RemodelConstraintGenerator
• set_volume() : protocols::noesy_assign::CrossPeak
• set_voxel_spacing() : core::scoring::electron_density::ElectronDensity
• set_wallpaper_group() : protocols::cryst::WallpaperGroup
• set_water_base_atm() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• set_wdw_to_freeze() : protocols::hybridization::FragmentBiasAssigner
• 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 , protocols::abinitio::PairingStatEntry , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::fldsgn::SheetConstraintGenerator , protocols::forge::constraints::NtoCConstraintGenerator , protocols::jd2::archive::EvaluatedArchive , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::symmetry::SetupNCSMover
• set_weight_constraints_NtoC() : protocols::flxbb::FlxbbDesign
• set_weight_constraints_sheet() : protocols::flxbb::FlxbbDesign
• set_weight_if_zero() : core::scoring::ScoreFunction
• set_weights() : core::scoring::etable::EtableEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::moves::RampingMover , protocols::simple_filters::SymmetricMotifFilter , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::toolbox::DecoySetEvaluation
• set_weights_for_sfxn() : protocols::simple_moves::GreenPacker
• set_well_depth() : core::scoring::func::LinearPenaltyFunction
• set_which_side() : core::pose::rna::BaseStack
• set_width() : protocols::frag_picker::scores::FragmentScoreManager , protocols::qsar::scoring_grid::GridManager
• set_window() : protocols::noesy_assign::FoldResonance
• set_working_best_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_working_bridge_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_working_calc_rms_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_working_extra_minimize_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• set_working_fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_working_minimize_res() : protocols::stepwise::modeler::StepWiseModeler
• set_working_moving_partition_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_working_moving_res_list() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_working_native_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_working_native_pose() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• set_working_pack_res() : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::StepWiseMinimizer
• set_working_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::StepWiseModeler
• set_working_parameters_exist() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• set_working_prepack_res() : protocols::stepwise::modeler::StepWiseModeler
• set_working_set_size() : protocols::boinc::Boinc
• set_working_superimpose_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• set_worst() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• set_wrapping_optE_multifunc() : protocols::optimize_weights::WrappedOptEExpressionCreator
• set_write_all_connect_info() : core::io::StructFileRepOptions
• set_write_atom_names() : protocols::noesy_assign::PeakFileFormat
• set_write_dynamic_rsr() : protocols::md::MDBase
• set_write_empty_voxels() : protocols::match::Bool3DGridKinemageWriter
• set_write_facets() : protocols::match::Bool3DGridKinemageWriter
• set_write_no_structures() : protocols::jd2::SilentFileJobOutputter
• set_write_only_highest_VC() : protocols::noesy_assign::PeakFileFormat_Base
• set_write_pdb_link_records() : core::io::StructFileRepOptions
• set_write_pdb_parametric_info() : core::io::StructFileRepOptions
• set_write_separate_scorefile() : protocols::jd2::SilentFileJobOutputter
• set_wt_aa() : protocols::optimize_weights::DDGMutationOptEData
• set_wt_unfolded_energies_emap() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• set_wu_type() : protocols::wum::WorkUnitBase
• set_x() : protocols::membrane::SpinAroundPartnerMover
• set_x_middle() : core::scoring::func::LinearPenaltyFunction
• set_x_standard_deviations() : protocols::carbohydrates::LinkageConformerMover
• set_x_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• 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::io::ResidueInformation , core::kinematics::AtomTree , core::pose::Pose , protocols::environment::ProtectedConformation
• set_xyz_bin() : protocols::stepwise::modeler::rna::checker::VDW_Grid
• set_xyz_bin_widths() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_xyz_moved() : core::conformation::Conformation
• set_xyz_step() : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• set_xyz_target() : core::scoring::constraints::LocalCoordinateConstraint
• set_y() : protocols::membrane::SpinAroundPartnerMover
• set_y_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_z() : protocols::stepwise::sampler::rigid_body::EulerAngles
• set_z0_offset() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_z1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_z1_offset() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• set_z_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• set_zero_prob_weight_at() : protocols::antibody::design::AntibodySeqDesignTFCreator
• set_zeta() : core::pose::Pose
• SetAACompositionPotential() : protocols::fldsgn::potentials::SetAACompositionPotential
• setAlgorithm() : core::scoring::cryst::PhenixInterface
• setall() : protocols::hybridization::TemplateHistory
• SetAllAtomsRepulsive() : core::chemical::SetAllAtomsRepulsive
• SetAtomicCharge() : core::chemical::SetAtomicCharge
• SetAtomTree() : protocols::protein_interface_design::movers::SetAtomTree
• SetAtomType() : core::chemical::SetAtomType
• setB() : protocols::electron_density::DockIntoDensityMover
• SetBackboneHeavyatom() : core::chemical::SetBackboneHeavyatom
• setBase() : core::grid::CartGrid< T >
• setCartesianPositionsFromPose() : protocols::cartesian::MolecularDynamics
• SetCatalyticResPackBehavior() : protocols::enzdes::SetCatalyticResPackBehavior
• setCenterOnMiddleCA() : protocols::electron_density::DockIntoDensityMover
• SetChiMover() : protocols::simple_moves::sidechain_moves::SetChiMover
• setClusterOversamp() : protocols::electron_density::DockIntoDensityMover
• setClusterRadius() : protocols::electron_density::DockIntoDensityMover
• SetCrystWeightMover() : protocols::cryst::SetCrystWeightMover
• setData() : protocols::sparta::GDB
• setDefaultAnchors() : protocols::flexpep_docking::FlexPepDockingFlags
• setDelR() : protocols::electron_density::DockIntoDensityMover
• setDihedralDerivatives() : protocols::cartesian::MolecularDynamics
• setDimensions() : core::grid::CartGrid< T >
• setDoRefine() : protocols::electron_density::DockIntoDensityMover
• setEntry() : protocols::sparta::GDB
• SetFormalCharge() : core::chemical::SetFormalCharge
• setFragDens() : protocols::electron_density::DockIntoDensityMover
• setFullOccupied() : core::grid::CartGrid< T >
• setGridStep() : protocols::electron_density::DockIntoDensityMover
• SetICoor() : core::chemical::SetICoor
• SetIGTypeOperation() : protocols::toolbox::task_operations::SetIGTypeOperation
• setInitialSpeeds() : protocols::cartesian::MolecularDynamics
• SetInterchangeabilityGroup_String() : core::chemical::SetInterchangeabilityGroup_String
• SetIO_String() : core::chemical::SetIO_String
• setK() : core::scoring::constraints::KofNConstraint
• setmap_type_ : protocols::cryst::SetRefinementOptionsMover
• setMaxRotPerTrans() : protocols::electron_density::DockIntoDensityMover
• SetMembraneCenterMover() : protocols::membrane::SetMembraneCenterMover
• SetMembraneNormalMover() : protocols::membrane::SetMembraneNormalMover
• SetMembranePositionMover() : protocols::membrane::SetMembranePositionMover
• setMinBackbone() : protocols::electron_density::DockIntoDensityMover
• SetMMAtomType() : core::chemical::SetMMAtomType
• setNames() : core::io::sequence_comparation::DesignContrast
• setNative() : protocols::electron_density::DockIntoDensityMover
• SetNbrAtom() : core::chemical::SetNbrAtom
• SetNbrRadius() : core::chemical::SetNbrRadius
• setNCyc() : protocols::electron_density::DockIntoDensityMover
• setNeighbors() : core::io::sequence_comparation::DesignContrast
• setNormScores() : protocols::electron_density::DockIntoDensityMover
• setNRsteps() : protocols::electron_density::DockIntoDensityMover
• SetOrientAtom() : core::chemical::SetOrientAtom
• setOrigin() : core::scoring::electron_density::ElectronDensity
• setOutputSilent() : protocols::electron_density::DockIntoDensityMover
• setparent() : core::kinematics::Node
• setPassThrough() : protocols::electron_density::DockIntoDensityMover
• setPdbCodes() : core::io::sequence_comparation::DesignContrast
• SetPolymerConnectAtom() : core::chemical::SetPolymerConnectAtom
• setPose() : protocols::match::downstream::ScoringSecMatchRPE
• setPoseExtraScore() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::relax::ClassicRelax
• setPosePositionsFromCartesian() : protocols::cartesian::MolecularDynamics
• SetRefinementOptionsMover() : protocols::cryst::SetRefinementOptionsMover
• setResidueRange() : protocols::rbsegment_relax::RBSegmentMover
• setResLimits() : core::scoring::cryst::PhenixInterface
• SetReturningPackRotamersMover() : protocols::simple_moves::SetReturningPackRotamersMover
• 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
• SetSecStructEnergies() : protocols::fldsgn::potentials::SetSecStructEnergies
• setTag() : protocols::electron_density::DockIntoDensityMover
• SetTemperatureFactor() : protocols::protein_interface_design::movers::SetTemperatureFactor
• setting() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• setting_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• settings : core::scoring::sc::MolecularSurfaceCalculator
• setTop() : core::grid::CartGrid< T >
• setTopN() : protocols::electron_density::DockIntoDensityMover
• SetTorsion() : protocols::simple_moves::SetTorsion
• SetToType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• setTwinLaw() : core::scoring::cryst::PhenixInterface
• setup() : core::io::pose_from_sfr::PoseFromSFRBuilder , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::NeighborList , protocols::abinitio::AbrelaxApplication , protocols::antibody::AntibodyEnumManager , protocols::antibody::clusters::CDRClusterEnumManager , protocols::antibody::design::AntibodyDesignEnumManager , protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::PoolData , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::denovo_design::connection::Connection , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::loophash::LoopHashMap , protocols::pack_daemon::NPDPropCalculator , protocols::pack_daemon::PackDaemon , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters , protocols::stepwise::modeler::rna::checker::VDW_Grid
• setup_abinitio() : protocols::surface_docking::SurfaceDockingProtocol
• setup_additional_cutpoint_closed() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• setup_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• setup_all_bb_residues() : protocols::simple_moves::BBDihedralSamplerMover
• setup_all_moving_res() : protocols::stepwise::modeler::StepWiseMinimizer
• setup_and_load_iupac_sequences() : protocols::carbohydrates::SimpleGlycosylateMover
• setup_approximate_vdw_radii() : core::scoring::AtomVDW
• setup_atom_and_neighbor_list() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• setup_atom_id_mapper_to_vanilla_chunk_pose() : protocols::farna::libraries::ChunkSet
• setup_atom_id_mask() : protocols::farna::libraries::ChunkSet
• setup_atom_id_mask_and_mapper() : protocols::farna::libraries::ChunkSet
• 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::lkball::LKB_ResidueInfo
• setup_autoNOE() : protocols::abinitio::IterativeBase
• setup_base_pair_constraints() : protocols::farna::base_pairs::RNA_BasePairHandler
• setup_base_pair_step_chunks() : protocols::farna::libraries::RNA_ChunkLibrary
• setup_bbmin_foldtree() : protocols::ligand_docking::LigandBaseProtocol
• setup_bbmin_ft_and_csts() : protocols::enzdes::EnzdesBaseProtocol
• setup_ca_constraints() : protocols::simple_moves::ShakeStructureMover
• setup_cached_observers() : protocols::seeded_abinitio::GrowPeptides
• setup_cart_minimizer() : protocols::antibody::design::AntibodyDesignMover
• setup_catalytic_residue_minimization_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• setup_CDR_cluster() : protocols::antibody::AntibodyInfo
• setup_CDR_clusters() : protocols::antibody::AntibodyInfo
• setup_cdr_pose_sampling_strategies() : protocols::antibody::design::AntibodyDesignMover
• setup_CDRsInfo() : protocols::antibody::AntibodyInfo
• setup_centroid_screen() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• setup_chainbreak_variants() : protocols::farna::setup::RNA_DeNovoPoseSetup
• setup_charge_atoms() : protocols::qsar::scoring_grid::ChargeGrid
• setup_class_movemap_and_constraints() : protocols::relax::CentroidRelax
• setup_classes() : protocols::antibody::AntibodyCDRGrafter
• setup_CM_helical_constraint() : protocols::forge::remodel::RemodelGlobalFrame
• setup_colors() : protocols::qsar::RenderGridsToKinemage
• setup_complete_ : protocols::pack_daemon::PackDaemon
• setup_complex_fold_tree() : protocols::ub_e2c::ubi_e2c_modeler
• setup_connections() : protocols::simple_moves::CyclizationMover
• setup_connectivity() : core::scoring::methods::GoapRsdType
• setup_constraint() : protocols::md::Rattle
• setup_constraints() : core::scoring::dna::DNATorsionPotential , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::canonical_sampling::CanonicalSamplingMover , protocols::ddg::ddGMover , protocols::docking::DockingProtocol , protocols::ligand_docking::ResidueTorsionRestraints , protocols::simple_moves::CyclizationMover , protocols::simple_moves::DisulfideInsertionMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• setup_csts() : core::scoring::constraints::FabConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues
• setup_d2_bounds() : core::scoring::lkball::LK_BallEnergy
• setup_daemons() : protocols::pack_daemon::DaemonSet
• setup_data_map() : protocols::qsar::qsarOptFunc
• setup_default_evaluators() : protocols::abinitio::IterativeBase , protocols::jd2::archive::EvaluatedArchive
• setup_default_graft_settings() : protocols::antibody::design::AntibodyDesignMover
• setup_default_min_move() : protocols::abinitio::FoldConstraints
• setup_default_min_mover() : protocols::grafting::AnchoredGraftMover
• setup_default_options() : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::pockets::PocketGrid
• setup_default_small_mover() : protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover
• setup_defaults() : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol , protocols::sparta::Sparta::SpartaLib , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• setup_derived_free_and_fixed_data() : protocols::optimize_weights::IterativeOptEDriver
• setup_design_mover() : protocols::antibody::design::AntibodyDesignProtocol
• setup_disulf_kic_closure() : protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• setup_disulfides() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• setup_edge_counts() : core::kinematics::FoldTree
• setup_empty_config() : protocols::loop_modeling::LoopModeler
• setup_energycut_task() : protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• setup_entropy_correction() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• setup_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• setup_epitope_residues() : protocols::antibody::design::AntibodyDesignMover
• setup_exchange_schedule() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering
• setup_extra_patches() : core::io::silent::SilentFileData
• setup_extra_res() : core::io::silent::SilentFileData
• setup_fail_triangle_inequailty_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• setup_fastscoring_first_time() : core::scoring::electron_density::ElectronDensity
• setup_favor_native_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• setup_filter_cst() : protocols::abinitio::IterativeBase
• setup_floating_base_jump_to_anchor() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• setup_fold() : protocols::abinitio::AbrelaxApplication
• setup_fold_tree() : protocols::jumping::MembraneJump , protocols::loop_modeling::LoopMover , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• setup_fold_tree_and_jumps_and_variants() : protocols::farna::setup::RNA_DeNovoPoseSetup
• setup_foldtree() : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::hybridization::FoldTreeHybridize
• setup_foldtree_and_add_cutpoint_variants() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• setup_foldtree_around_anchor_invrot() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• setup_foldtype_names() : protocols::fldsgn::topology::SheetFoldTypeManager
• setup_foldtype_strand_pairings() : protocols::fldsgn::topology::SheetFoldTypeManager
• setup_for_apply() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• 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::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::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::RNA_MgPointEnergy , 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_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::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::VdWTinkerEnergy , 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_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 , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint
• setup_for_derivatives_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , 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_dock_chains() : protocols::analysis::InterfaceAnalyzerMover
• 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::P_AA_ss_Energy , 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::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , protocols::comparative_modeling::IgnoreSubsetConstraintSet
• 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::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::StackElecEnergy , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• 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::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::lkball::LK_BallEnergy , core::scoring::magnesium::RNA_MgPointEnergy , 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::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MultipoleElecPotential , core::scoring::nv::NVscore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::VdWTinkerPotential
• setup_for_residue_pair_energies() : core::scoring::hbonds::HBondSet
• setup_for_run() : protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• setup_for_sampling() : core::scoring::carbohydrates::CHIEnergyFunction
• 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::NamedAngleConstraint , 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_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::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , 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_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::MultipoleElecEnergy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::PairEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::MultipoleElecPotential , 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_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 , core::scoring::VdWTinkerPotential , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::sparta::Sparta::SpartaLib
• 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::lkball::LK_BallEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::orbitals::OrbitalsScore
• setup_for_scoring_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• setup_frag_scorefxn() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• setup_fragments() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::abscript::FragmentJumpCM
• setup_FrameWorkInfo() : protocols::antibody::AntibodyInfo
• setup_from_connection_info() : protocols::denovo_design::connection::Connection
• setup_from_ConnollySurface() : protocols::pockets::NonPlaidFingerprint
• setup_from_eggshell_pdb_file() : protocols::pockets::NonPlaidFingerprint
• setup_from_eggshell_triplet_file() : protocols::pockets::NonPlaidFingerprint
• setup_from_EggshellGrid() : protocols::pockets::NonPlaidFingerprint
• setup_from_espGrid() : protocols::pockets::NonPlaidFingerprint
• setup_from_kill_hairpins_file() : core::scoring::SS_Killhairpins_Info
• setup_from_PlaidFingerprint() : protocols::pockets::NonPlaidFingerprint
• setup_from_PocketGrid() : protocols::pockets::NonPlaidFingerprint
• setup_from_PocketGrid_and_known_ligand() : protocols::pockets::NonPlaidFingerprint
• setup_from_PocketGrid_using_bound_ligand() : protocols::pockets::NonPlaidFingerprint
• setup_from_psipred() : core::scoring::SS_Killhairpins_Info
• setup_from_random() : protocols::denovo_design::connection::Connection , protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• setup_from_rotamer_dots() : core::pack::interaction_graph::InvRotamerDots
• setup_full_model_info() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• setup_hash_maps() : protocols::loophash::LoopHashLibrary
• setup_helical_constraint() : protocols::forge::remodel::RemodelGlobalFrame
• setup_helper_cop() : core::scoring::aa_composition_energy::AACompositionEnergy
• setup_helper_count() : core::scoring::aa_composition_energy::AACompositionEnergy
• setup_helper_masks_for_packing_ : core::scoring::aa_composition_energy::AACompositionEnergy
• setup_helpers_ : core::scoring::aa_composition_energy::AACompositionEnergy
• setup_helpers_for_packing_ : core::scoring::aa_composition_energy::AACompositionEnergy
• setup_histograms() : protocols::backrub::BackrubSidechainMover
• setup_hitset_iterators_for_group() : protocols::match::output::CloudPDBWriter
• setup_hotspot_foldtree_() : protocols::hotspot_hashing::HotspotStubSet
• setup_idealize_constraints() : protocols::idealize::IdealizeMover
• setup_IG_res_res_weights() : core::pack::interaction_graph::InteractionGraphFactory
• setup_include_patches() : core::io::silent::SilentFileData
• setup_increased_vdw_radii() : protocols::relax::CentroidRelax
• setup_info_for_mg_calculation() : core::scoring::magnesium::MgKnowledgeBasedPotential , core::scoring::magnesium::RNA_MgPointEnergy
• setup_initial_jump() : protocols::stepwise::monte_carlo::mover::AddMover
• setup_initial_torsions() : protocols::stepwise::monte_carlo::mover::AddMover
• setup_interpolation() : core::scoring::OmegaTether , core::scoring::RamaPrePro
• setup_invrot_tree_in_vlb() : protocols::fldsgn::BluePrintBDR
• setup_iterations() : core::pack::annealer::SimAnnealerBase
• setup_jump_numbers_and_partner() : protocols::farna::MultipleDomainMover
• setup_jumps() : protocols::abinitio::AbrelaxApplication , protocols::farna::setup::RNA_DeNovoPoseSetup
• setup_key_residues() : protocols::ub_e2c::ubi_e2c_modeler
• setup_kic_closure() : protocols::denovo_design::connection::BridgeTomponents , protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• setup_kic_config() : protocols::loop_modeling::LoopModeler
• setup_kic_with_fragments_config() : protocols::loop_modeling::LoopModeler
• setup_killhairpins() : core::scoring::SS_Killhairpins_Info
• setup_kinematics() : protocols::star::StarAbinitio
• setup_known_types() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• setup_ligands_to_minimize() : protocols::ligand_docking::HighResDocker
• setup_list() : protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• setup_LJcorrection() : protocols::simple_moves::PeriodicBoxMover
• setup_loop_definition() : protocols::loop_build::LoopBuildMover
• setup_loop_refinement_movers() : protocols::antibody::SnugDockProtocol
• setup_loops_from_data() : protocols::loops::Loops
• setup_membrane_topology() : protocols::abinitio::AbrelaxApplication
• setup_mg_water_fold_tree() : protocols::magnesium::MgMonteCarlo
• setup_min_map() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• setup_minimization_graph() : protocols::ncbb::SecStructMinimizeMultiFunc
• setup_minimizer() : protocols::simple_moves::CyclizationMover
• setup_minimizers() : protocols::stepwise::modeler::StepWiseMinimizer
• setup_modeler() : protocols::antibody::design::AntibodyDesignMover
• setup_modeler_options() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• setup_monte_carlo_cycles() : protocols::farna::RNA_FragmentMonteCarlo
• setup_move_maps() : protocols::ub_e2c::ubi_e2c_modeler
• setup_movemap() : protocols::farna::movers::RNA_Minimizer , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::toolbox::AtomLevelDomainMap
• setup_movemap_and_regions() : protocols::grafting::AnchoredGraftMover
• setup_movemaps() : protocols::anchored_design::AnchorMoversData
• setup_mover() : protocols::simple_moves::MSDMover
• setup_movers() : protocols::simple_moves::ShakeStructureMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• setup_movers_ : protocols::forge::components::VarLengthBuild
• setup_multi_objective() : protocols::mpi_refinement::MPI_Refinement
• setup_native_clusters() : protocols::antibody::design::AntibodyDesignMover
• setup_native_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• setup_native_sequence() : protocols::antibody::design::AntibodyDesignMover
• setup_numbering_info_for_scheme() : protocols::antibody::AntibodyInfo
• setup_objects() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
• setup_ok_for_centroid_calculation() : protocols::farna::MultipleDomainMover
• setup_one_color_scheme() : protocols::qsar::RenderGridsToKinemage
• setup_options_classes() : protocols::antibody::design::AntibodyDesignMover
• setup_options_for_VDW_bin_checker() : protocols::stepwise::modeler::options::StepWiseModelerOptions
• setup_other_poses() : core::io::silent::BinarySilentStruct
• setup_pack_operation_movers() : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• setup_pack_task() : protocols::stepwise::modeler::packer::StepWisePacker
• setup_packer_and_movemap() : protocols::simple_moves::DesignRepackMover
• setup_packer_task() : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::ub_e2c::ubi_e2c_modeler
• setup_packer_task_for_mutations() : protocols::ddg::ddGMover
• setup_packertask() : protocols::ddg::ddGMover
• setup_packing() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• setup_parallel_antiparallel_weights() : core::scoring::SecondaryStructureWeights
• setup_paratope_epitope_constraints() : protocols::antibody::design::AntibodyDesignMover
• setup_paratope_residues_from_cdrs() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• setup_passports() : protocols::environment::EnvClaimBroker
• setup_pdbnames_next_round() : protocols::optimize_weights::IterativeOptEDriver
• setup_permutation() : protocols::denovo_design::components::NamedMover , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::Connection , protocols::denovo_design::connection::ExtendChain , protocols::denovo_design::connection::StapleChains
• setup_pose() : protocols::simple_moves::PeriodicBoxMover
• setup_pose_metric_calculators() : protocols::enzdes::EnzdesScorefileFilter
• setup_precise_zeta_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• setup_protocol() : protocols::antibody::GraftedStemOptimizer , protocols::docking::DockMCMCycle
• setup_pymol_observer() : protocols::jd2::JobDistributor
• setup_random_start_pose() : protocols::antibody::design::AntibodyDesignMover
• setup_reference_data() : protocols::simple_moves::GreenPacker
• setup_relax_foldtree() : protocols::relax::membrane::MPFastRelaxMover
• setup_relevant_chains() : protocols::moves::StructureRestrictor
• setup_remodel_constraints() : protocols::forge::components::VarLengthBuild
• setup_repack_constraints() : protocols::ddg::ddGMover
• setup_residue_list() : protocols::simple_moves::RingConformationMover
• setup_residue_type_map() : protocols::loops::JSONFormattedLoopsFileReader
• setup_residuearrayannealableenergy_for_packing() : core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::annealing::ResidueArrayAnnealableEnergy
• setup_rigid_body_mover() : protocols::farna::RNA_FragmentMonteCarlo
• setup_rotamer_constraints() : protocols::ddg::ddGMover
• setup_rotamer_couplings() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• setup_rotamer_links() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• setup_rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• setup_rots_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• setup_rsdtype() : core::scoring::methods::GoapRsdType
• setup_sampler_movemap_union() : protocols::simple_moves::BBDihedralSamplerMover
• setup_sampling_probs() : protocols::medal::MedalExchangeMover
• setup_sasa_method() : core::scoring::sasa::SasaCalc
• setup_score() : protocols::mpi_refinement::WorkUnit_PartialAbinitio
• setup_score_data() : protocols::analysis::InterfaceAnalyzerMover
• setup_score_type_names() : core::scoring::ScoreTypeManager
• setup_scorefunction() : protocols::grafting::AnchoredGraftMover , protocols::simple_moves::CyclizationMover
• setup_scorefunctions() : protocols::hybridization::FoldTreeHybridize
• setup_scorefxn() : protocols::analysis::InterfaceAnalyzerMover , protocols::antibody::design::AntibodyDesignMover
• setup_scorefxns() : protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::GeneralAntibodyModeler , protocols::stepwise::modeler::StepWiseMinimizer
• setup_secstruct() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• setup_seqpos_from_selectors() : protocols::match::MatcherMover
• setup_sequence_recovery_cache() : protocols::enzdes::EnzdesBaseProtocol
• setup_silent_file_stream() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• setup_silent_struct() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• setup_simple_fold_tree() : protocols::antibody::AntibodyInfo , protocols::antibody_legacy::AntibodyModeler , protocols::ub_e2c::ubi_e2c_modeler
• setup_slide_movers() : protocols::surface_docking::SurfaceDockingProtocol
• setup_spline() : protocols::denovo_design::filters::PreProlineFilter
• setup_stage() : protocols::abinitio::abscript::AbscriptStageMover
• setup_structuredata() : protocols::denovo_design::connection::BridgeTomponents , protocols::denovo_design::connection::Connection
• setup_sub_communicators() : protocols::jd2::MPIMultiCommJobDistributor
• setup_sugar_conformations() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• setup_sugar_modeling() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• setup_sugar_modeling_list() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• setup_sugar_ring_closure_constraints() : core::scoring::rna::RNA_SugarCloseEnergy
• setup_summary() : protocols::frag_picker::QuotaDebug
• setup_svm() : protocols::helix_capper::HelixNCapperMover
• setup_system_signal_handler() : protocols::jd2::JobDistributor
• setup_tag_to_source_map() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• setup_task() : protocols::analysis::InterfaceAnalyzerMover , protocols::simple_moves::ddG
• setup_task_operations() : protocols::antibody::design::GeneralAntibodyModeler
• setup_temperature() : core::pack::annealer::SimAnnealerBase
• setup_templates() : protocols::abinitio::AbrelaxApplication
• setup_tf() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• setup_three_color_scheme() : protocols::qsar::RenderGridsToKinemage
• setup_topology() : protocols::rbsegment_relax::AutoRBMover
• setup_torsion_list() : protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover
• setup_torsion_sets() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• setup_torsions() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• setup_two_color_scheme() : protocols::qsar::RenderGridsToKinemage
• setup_type_names() : core::scoring::hbonds::HBondTypeManager
• setup_unified_stepwise_modeler() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• setup_using_user_input_VDW_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• setup_using_working_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• setup_variants_and_free_pose_for_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• setup_variants_and_free_pose_for_terminal_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• setup_variants_and_free_pose_for_three_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• setup_variants_at_extra_cutpoints() : protocols::farna::movers::RNA_LoopCloser
• setup_vary_bond_geometry() : protocols::stepwise::modeler::StepWiseMinimizer
• setup_VDW_bin_checker() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• setup_vdw_cached_rep_screen_info() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• setup_virtual_phosphate_variants() : protocols::farna::setup::RNA_DeNovoPoseSetup
• setup_VL_VH_packing_angle() : protocols::antibody::AntibodyInfo
• setup_weight_triple() : core::scoring::elec::FA_ElecEnergy
• setup_working_native_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• setup_xtal_symminfo() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover
• setupBesselOrder() : core::scoring::fiber_diffraction::FiberDiffraction
• SetupForDensityScoringMover() : protocols::electron_density::SetupForDensityScoringMover
• SetupForFibrilMover() : protocols::fibril::SetupForFibrilMover
• SetupForSymmetryMover() : protocols::simple_moves::symmetry::SetupForSymmetryMover
• SetupHotspotConstraintsLoopsMover() : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• SetupHotspotConstraintsMover() : protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• SetupNCSMover() : protocols::simple_moves::symmetry::SetupNCSMover
• SetupPoissonBoltzmannPotential() : protocols::pb_potential::SetupPoissonBoltzmannPotential
• SetupPoissonBoltzmannPotentialCreator() : protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator
• SetupRamaTables() : protocols::frag_picker::scores::RamaScore
• setupZones() : core::grid::CartGrid< T >
• setValue() : core::grid::CartGrid< T >
• setVAR() : protocols::sparta::GDB
• setWindow() : core::scoring::electron_density::ElectronDensity
• SewGraph() : protocols::sewing::SewGraph
• SewResidue() : protocols::sewing::SewResidue
• SewSegment() : protocols::sewing::SewSegment
• sf_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::cryst::DockLatticeMover , protocols::simple_moves::PeriodicBoxMover
• SF_Replica() : protocols::toolbox::SF_Replica
• sf_vdw_ : protocols::cryst::DockLatticeMover
• sfd_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::SilentFileJobInputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::setup::StepWiseCSA_JobDistributor , protocols::viewer::SilentObserver
• sfd_req_1benmeths_ : core::scoring::MinimizationNode
• sfd_req_1benmeths_begin() : core::scoring::MinimizationNode
• sfd_req_1benmeths_end() : core::scoring::MinimizationNode
• sfd_req_2benmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfd_req_2benmeths_begin() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfd_req_2benmeths_end() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• sfr_ : core::import_pose::PDBSilentStruct , core::io::pose_from_sfr::PoseFromSFRBuilder , core::io::pose_to_sfr::PoseToStructFileRepConverter
• sfs_req_1benmeths_ : core::scoring::MinimizationNode
• sfs_req_1benmeths_begin() : core::scoring::MinimizationNode
• sfs_req_1benmeths_end() : core::scoring::MinimizationNode
• sfs_req_2benmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfs_req_2benmeths_begin() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfs_req_2benmeths_end() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• sfx_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• sfxn() : protocols::moves::RampingMover
• sfxn0_ : protocols::simple_moves::CombinePoseMover
• sfxn_ : core::pack::interaction_graph::SimpleInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::canonical_sampling::CanonicalSamplingMover , protocols::cluster::GatherPosesMover , protocols::denovo_design::DisulfidizeMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::forge::remodel::RemodelAccumulator , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::downstream::ScoringSecMatchRPE , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::mpi_refinement::StructAvrgMover , protocols::normalmode::NormalModeRelaxMover , protocols::pack_daemon::DynamicAggregateFunction , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• sfxn_cen_ : protocols::normalmode::NormalModeRelaxMover
• sfxn_cycles_ : protocols::loop_modeling::LoopProtocol
• sfxn_hires_ : protocols::docking::membrane::MPFindInterfaceMover
• sfxn_lowres_ : protocols::docking::membrane::MPFindInterfaceMover
• sfxn_nocst_ : protocols::relax::RangeRelaxMover
• sfxn_pack_ : protocols::docking::membrane::MPFindInterfaceMover
• sfxn_set() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• sfxn_set_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• sg() : protocols::cryst::MakeLatticeMover
• sg_ : protocols::cryst::MakeLatticeMover
• SG_Dist_Func() : core::scoring::disulfides::SG_Dist_Func
• sg_dist_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• sgn() : protocols::sparta::PDB
• SGSG_Dihedral_Func() : core::scoring::disulfides::SGSG_Dihedral_Func
• sgsg_dihedral_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• shadowed_ids_ : core::chemical::ResidueTypeSet
• ShakeStructureMover() : protocols::simple_moves::ShakeStructureMover
• shallow_copy() : core::scoring::constraints::ConstraintSet
• ShannonEntropy_n_derivs_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• ShapeComplementarityCalculator : core::scoring::sc::Atom , core::scoring::sc::ShapeComplementarityCalculator
• ShapeComplementarityCalculatorException() : core::scoring::sc::ShapeComplementarityCalculatorException
• ShapeComplementarityFilter() : protocols::simple_filters::ShapeComplementarityFilter
• ShapeGrid() : protocols::qsar::scoring_grid::ShapeGrid
• share_build_points_for_geomcsts_ : protocols::match::MatcherTask
• share_chains() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• share_packer_data_from() : protocols::multistate_design::PackingState
• shared_from_this() : core::io::silent::BinarySilentStruct , core::io::silent::ScoreJumpFileSilentStruct
• shared_mgs() : protocols::denovo_design::components::SolutionSorter
• shared_silent_data_ : core::io::silent::SilentFileData
• SharedSilentData() : core::io::silent::SharedSilentData
• sharpen_b_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• shave_frac_ : protocols::mpi_refinement::StructAvrgMover
• shave_library() : protocols::mpi_refinement::MPI_Refinement
• shave_poses() : protocols::mpi_refinement::StructAvrgMover
• shear() : protocols::dna::DNABasepair
• shear_ : protocols::dna::DNABasepair
• shear_min_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_min_protocol() : protocols::ligand_docking::LigandDockProtocol
• shear_min_type_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shear_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• shear_sequence_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• ShearMinCCDTrial() : protocols::loops::loop_mover::refine::ShearMinCCDTrial
• ShearMinCCDTrialCreator() : protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator
• ShearMover() : protocols::simple_moves::ShearMover
• Sheet() : protocols::fldsgn::topology::Sheet
• sheet() : protocols::fldsgn::topology::SheetSet
• sheet_ : protocols::nonlocal::SheetTranslate
• sheet_center_ : protocols::fldsgn::topology::Sheet
• sheet_dis_by_terminals() : protocols::features::strand_assembly::StrandBundleFeatures
• sheet_fraction() : core::fragment::SecondaryStructure
• sheet_id_ : protocols::features::strand_assembly::SandwichFragment
• sheet_name_ : protocols::fldsgn::SheetConstraintGenerator
• sheet_number_ : protocols::fldsgn::topology::SheetSet
• sheet_plane_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::Sheet
• sheet_pos_ : protocols::fldsgn::topology::BetaAlphaBetaMotif
• sheet_sizes_ : protocols::jumping::SheetBuilder
• sheet_torsion() : protocols::features::strand_assembly::StrandBundleFeatures
• SheetBuilder() : protocols::jumping::SheetBuilder
• SheetConstraintGenerator() : protocols::fldsgn::SheetConstraintGenerator
• SheetFilter() : protocols::simple_filters::SheetFilter
• SheetFoldTypeManager() : protocols::fldsgn::topology::SheetFoldTypeManager
• sheets() : protocols::fldsgn::topology::SheetSet
• sheets_ : protocols::fldsgn::topology::SheetSet , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::topology_broker::TemplateJumpClaimer
• sheets_from_dimers() : core::scoring::SecondaryStructurePotential
• SheetSet() : protocols::fldsgn::topology::SheetSet
• SheetSetCOP : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• SheetTopology : protocols::jumping::SheetBuilder
• SheetTopologyFilter() : protocols::fldsgn::filters::SheetTopologyFilter
• SheetTranslate() : protocols::nonlocal::SheetTranslate
• shift() : core::conformation::membrane::Span , core::scoring::SmoothScoreTermCoeffs , protocols::dna::DNABasestep , protocols::frags::FragLib , protocols::frags::TorsionFragmentLibrary
• shift_ : core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::SmoothScoreTermCoeffs , protocols::dna::DNABasestep
• shift_by() : core::fragment::FragSet , core::fragment::Frame , core::fragment::NonContinuousFrame
• SHIFT_DIR : protocols::sparta::Sparta::SpartaLib
• shift_span() : core::scoring::MembraneTopology
• shift_to() : core::fragment::Frame , core::fragment::NonContinuousFrame
• shifts() : protocols::frag_picker::CS2ndShift
• shmem_ : protocols::boinc::BoincCurrentPoseObserver
• sho_cutoff_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• sho_energies_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• sho_meth_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• SHOBuriedUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• short_affix : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• short_backrub_mover_ : protocols::simple_moves::CoupledMover
• short_frag_cycle_ratio() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• short_frag_cycle_ratio_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• short_insert_region_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• short_name() : core::chemical::carbohydrates::CarbohydrateInfo , update_ResidueType_enum_files.EnumInfo
• short_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• short_name_plural : update_ResidueType_enum_files.EnumInfo
• short_name_to_iupac_strings_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• short_name_to_iupac_strings_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• short_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• short_range_interactions_exist_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• ShortBackrubMover() : protocols::simple_moves::ShortBackrubMover
• shorten_long_terminal_loop() : protocols::LoopRebuild
• shorten_target_list() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• shortest_dis_sidechain() : protocols::features::strand_assembly::StrandBundleFeatures
• shortest_path() : protocols::constraints_additional::MaxSeqSepConstraintSet
• shortest_path_ : protocols::constraints_additional::MaxSeqSepConstraintSet
• shortest_paths_ : core::scoring::methods::LinearChainbreakEnergy
• ShortestPathInFoldTree() : core::kinematics::ShortestPathInFoldTree
• ShortLoopClosure() : protocols::loops::loop_closure::ccd::ShortLoopClosure
• shortRange_ : protocols::match::downstream::ScoringSecMatchRPE
• ShortRangeTwoBodyEnergy() : core::scoring::methods::ShortRangeTwoBodyEnergy
• shorts_ : protocols::moves::UDPSocketClient::UUID
• shove_residues_ : protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::TryRotamers
• ShoveResidueMover() : protocols::protein_interface_design::movers::ShoveResidueMover
• show() : core::chemical::Atom , core::chemical::AtomProperties , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::ResidueType , core::chemical::rings::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::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets , 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::HBEvalTuple , 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 , protocols::abinitio::AlternativePairings , protocols::abinitio::PairingStatEntry , protocols::abinitio::StrandConstraints , protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::AsyncMPITemperingBase::ExchangeRequest , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::denovo_design::components::EXCN_Apply , protocols::denovo_design::components::EXCN_Setup , protocols::denovo_design::connection::EXCN_ConnectionFailed , protocols::docking::ConformerSwitchMover , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::docking::SlideIntoContact , protocols::docking::TemperedDocking , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::evaluation::PCA , protocols::farna::movers::RNA_Minimizer , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::genetic_algorithm::Entity , protocols::jd2::archive::Batch , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob , protocols::jumping::SameStrand , protocols::loops::Loop , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::make_rot_lib::RotData , protocols::match::output::MatchScoreWriter , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::geometry::Embedding , protocols::membrane::geometry::EmbeddingDef , protocols::moves::EXCN_RemoveCstsFailed , protocols::moves::Mover , protocols::moves::PyMolMover , protocols::moves::TrialCounter , protocols::moves::UDPSocketClient , protocols::multistate_design::MultiStateEntity< T > , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::EXCN_NoesyAssign , protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::FoldResonance , protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::PeakAssignmentParameters , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::rotamer_recovery::RotamerRecovery , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterSQLite , protocols::scoring::Interface , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::GlobalRequirement , protocols::sewing::sampling::requirements::IntraSegmentRequirement , protocols::sewing::sampling::requirements::RequirementSet , protocols::sewing::sampling::requirements::ResidueRetentionRequirement , protocols::sewing::sampling::requirements::SegmentDsspRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement , protocols::sic_dock::JointScore , protocols::sic_dock::RigidScore , protocols::sic_dock::scores::MotifHashRigidScore , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::toolbox::AtomLevelDomainMap , protocols::toolbox::ClusterBase , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::DofClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::EXCN_FailedBroking , protocols::topology_broker::EXCN_FilterFailed , protocols::topology_broker::EXCN_Input , protocols::topology_broker::EXCN_TopologyBroker
• show_all_atom_names() : core::chemical::ResidueType
• show_all_fixes() : core::io::StructFileRepOptions
• show_all_fixes_ : core::io::StructFileRepOptions
• show_all_residue_tasks() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_availability() : protocols::frag_picker::quota::QuotaPool
• show_available_silent_struct_types() : core::io::silent::SilentStructFactory
• show_classic() : core::fragment::FragData , core::fragment::Frame
• show_cluster_assignments() : protocols::toolbox::KClusterData
• show_counters() : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• show_cst_definitions() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• show_current_dihedrals() : protocols::ncbb::SecStructFinder
• 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::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• show_def_nopose() : core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint
• 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::CircularSplineFunc , 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_definitions() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• show_extended_ : protocols::anchored_design::AnchoredDesignMover
• show_fragments() : core::fragment::Frame
• show_H_state : protocols::viewer::GraphicsState
• 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_on_tracer() : protocols::noesy_assign::PeakAssignmentParameters
• show_packer_task_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::RotamerTrialsMover
• show_params() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• show_pdb_ids() : protocols::frag_picker::PdbIdChunkFilter
• show_pos() : core::fragment::NonContinuousFrame
• show_pretty() : core::scoring::ScoreFunction
• show_protocol() : protocols::relax::membrane::MPFastRelaxMover
• show_rdc_values() : core::scoring::ResidualDipolarCoupling
• show_residue_connections() : core::conformation::Conformation
• show_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_scores() : protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• show_scoring_methods() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager
• show_state() : protocols::moves::MonteCarlo
• show_status() : protocols::jd2::MpiFileBuffer
• show_submotif_info_list() : core::pose::full_model_info::FullModelInfo
• 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_unmoved() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• show_valid() : protocols::frag_picker::quota::ABEGO_SS_Map
• show_values() : core::scoring::hbonds::Polynomial_1d
• show_viol_level_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• 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::CircularSplineFunc , 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 , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet
• show_weighted() : core::scoring::EMapVector
• showGDB() : protocols::sparta::GDB
• ShowViolation() : protocols::abinitio::ShowViolation
• shrink() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::frags::RMSVallData , protocols::frags::VallData
• shrink_cluster() : protocols::forge::remodel::RemodelAccumulator
• shrink_factor_ : protocols::match::Bool3DGridKinemageWriter
• shrink_frag_ends_ : protocols::simple_moves::BBGaussianMover
• shuffle() : protocols::cluster::Cluster , protocols::jd2::JobsContainer
• shuffle_order() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• shuffle_order_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• shuffle_sBR_rotamers() : core::pack::annealer::FASTERAnnealer
• shuffle_temperatures() : protocols::canonical_sampling::ParallelTempering
• ShuffleFileSystemJobDistributor() : protocols::jd2::ShuffleFileSystemJobDistributor
• shutdown() : protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• sibling() : core::scoring::trie::TrieNode< AT, CPDATA >
• sibling_ : core::scoring::trie::TrieNode< AT, CPDATA >
• sic_fast_ : protocols::hotspot_hashing::SICPatternAtTransform
• SICFast() : protocols::sic_dock::SICFast
• SICPatternAtTransform() : protocols::hotspot_hashing::SICPatternAtTransform
• side_chain_only_ : protocols::simple_moves::CopyDofMover
• side_chains_only_ : protocols::pockets::PocketGrid
• side_inv_ : protocols::scoring::ImplicitFastClashCheck
• side_ONE_NUM_pose_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_ONE_pose_list_id_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_one_tag : protocols::stepwise::modeler::rna::Combine_Tags_Info
• side_TWO_NUM_pose_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_TWO_pose_list_id_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_two_tag : protocols::stepwise::modeler::rna::Combine_Tags_Info
• sidechain() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• sidechain_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::AtomicContactFilter
• sidechain_atom_id_ : core::scoring::constraints::BackboneStubConstraint
• sidechain_contact_dist_cutoff_ : protocols::frag_picker::FragmentPicker
• sidechain_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• sidechain_mover_ : protocols::backrub::BackrubSidechainMover
• sidechain_sidechain_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::TwoBodyEnergy
• sidechain_target_ : core::scoring::constraints::BackboneStubConstraint
• sidechainAtoms_begin() : core::conformation::Residue
• SidechainContactDistCutoff() : protocols::frag_picker::SidechainContactDistCutoff
• SideChainCopier() : protocols::stepwise::modeler::packer::SideChainCopier
• SidechainMCMover() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• SidechainMetropolisHastingsMover() : protocols::canonical_sampling::SidechainMetropolisHastingsMover
• SidechainMinMover() : protocols::docking::SidechainMinMover
• SidechainMover() : protocols::simple_moves::sidechain_moves::SidechainMover
• sidechainmover_ : protocols::backrub::BackrubProtocol
• SidechainMoverBase() : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• SidechainRmsdFilter() : protocols::simple_filters::SidechainRmsdFilter
• SidechainStateAssignment() : core::pack::scmin::SidechainStateAssignment
• sig_ : protocols::simple_filters::MultipleSigmoids
• sig_centroid_ : core::scoring::fiber_diffraction::CentroidScatter
• sigAxisR_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigAxisT_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigma() : core::scoring::SecondaryStructurePotential , core::sequence::ChemicalShiftSequence , protocols::fldsgn::topology::DimerPairing
• sigma1() : core::scoring::CSA
• sigma1_ : core::scoring::CSA
• sigma2() : core::scoring::CSA
• sigma2_ : core::scoring::CSA
• sigma3() : core::scoring::CSA
• sigma3_ : core::scoring::CSA
• sigma_ : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering , protocols::fldsgn::topology::DimerPairing
• sigma_charge_to_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• sigma_charge_to_lone_pair_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• sigma_rot : protocols::rbsegment_relax::GaussianRBSegmentMover
• sigma_trans : protocols::rbsegment_relax::GaussianRBSegmentMover
• SigmaOrbitalElectronegativityMulliken : core::chemical::gasteiger::GasteigerAtomTypeData
• SigmaOrbitalElectronegativityPauling : core::chemical::gasteiger::GasteigerAtomTypeData
• SigmaValenceStateElectronAffinity : core::chemical::gasteiger::GasteigerAtomTypeData
• SigmaValenceStateIonizationPotential : core::chemical::gasteiger::GasteigerAtomTypeData
• sigmoid() : core::scoring::SmoothScoreTermCoeffs
• Sigmoid() : protocols::simple_filters::Sigmoid
• sigmoid_coeffs_ : core::scoring::SmoothScoreTermCoeffs
• sigmoid_deps_dr() : core::scoring::etable::coulomb::Coulomb
• sigmoid_eps() : core::scoring::etable::coulomb::Coulomb
• sigmoid_filter() : protocols::simple_filters::MultipleSigmoids
• SIGMOID_SLOPE : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• SIGMOID_WEIGHTED_CEN_LIST : core::pose::datacache::CacheableDataType
• SIGMOID_WEIGHTED_D_CEN_LIST : core::pose::datacache::CacheableDataType
• sigmoidal_D0_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_D_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_die_ : core::scoring::etable::coulomb::Coulomb
• sigmoidal_S_ : core::scoring::etable::coulomb::Coulomb
• 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 , protocols::fldsgn::topology::DimerPairing
• sign1_ : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• sign2() : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• sign2_ : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• signature_map_ : protocols::match::output::PDBWriter
• signature_string() : protocols::match::output::PDBWriter
• sigOffAxisR_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigOffAxisT_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• silent() : core::optimization::LineMinimizationAlgorithm , core::optimization::MinimizerOptions
• silent_ : core::optimization::MinimizerOptions , protocols::electron_density::DockIntoDensityMover , protocols::forge::remodel::RemodelMover::instruction_flags
• silent_comments_ : core::io::silent::SilentStruct
• silent_energies() : core::io::silent::SilentStruct
• silent_energies_ : core::io::silent::SilentStruct
• silent_Es() : protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• silent_Es_ : protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• silent_file() : protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::magnesium::MgScanner , protocols::stepwise::options::StepWiseBasicOptions
• silent_file_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::jd2::SilentFileJobOutputter , protocols::magnesium::MgScanner , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::setup::StepWiseJobDistributor
• silent_file_data() : core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::SilentFileJobInputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silent_file_data_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• silent_file_name_ : protocols::viewer::SilentObserver
• silent_file_out_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• silent_file_stream_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_stream_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_tags_ : protocols::jd2::SilentFileJobOutputter
• silent_files_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silent_files_in_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_in() : protocols::jd2::archive::Batch
• silent_job_outputter_ : protocols::enzdes::EnzdesJobOutputter
• silent_out() : protocols::jd2::archive::Batch
• silent_out_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• silent_output_ : protocols::enzdes::EnzdesJobOutputter
• silent_score_file_ : protocols::abinitio::AbrelaxApplication
• silent_struct_output_list() : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silent_struct_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silent_struct_type_ : core::io::silent::SilentFileData , core::io::silent::SilentFileOptions
• SilentEnergy() : core::io::silent::SilentEnergy
• SilentFileData() : core::io::silent::SilentFileData
• SilentFileJobInputter() : protocols::jd2::SilentFileJobInputter
• SilentFileJobOutputter() : protocols::jd2::SilentFileJobOutputter
• 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
• SilentInfoList : protocols::simple_filters::EvaluatedTrialMover
• silentname_ : protocols::md::MDBase
• SilentObserver() : protocols::viewer::SilentObserver
• silentout_file_name_ : protocols::abinitio::Protocol
• SilentStruct() : core::io::silent::SilentStruct
• SilentStructCreator() : core::io::silent::SilentStructCreator
• SilentStructCreatorMap : core::io::silent::SilentStructFactory
• SilentStructFactory() : core::io::silent::SilentStructFactory
• SilentStructRegistrator() : core::io::silent::SilentStructRegistrator< T >
• SilentStructs : protocols::abinitio::HedgeArchive , protocols::jd2::archive::ArchiveBase
• SilentStructStore() : protocols::wum::SilentStructStore
• SilentStructVector : protocols::abinitio::IterativeBase , protocols::jd2::archive::VarianceStatisticsArchive
• SilentTrajectoryRecorder() : protocols::canonical_sampling::SilentTrajectoryRecorder
• sim_anneal_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• sim_origin() : protocols::abinitio::abscript::RigidChunkCM
• sim_origin_ : protocols::abinitio::abscript::RigidChunkCM
• sim_replace_obj_ : protocols::mpi_refinement::Clusterer , protocols::mpi_refinement::MPI_Refinement
• sim_selector() : protocols::abinitio::abscript::RigidChunkCM
• sim_selector_ : protocols::abinitio::abscript::RigidChunkCM
• sim_type : core::scoring::APBSConfig::I_PARAM
• SimAnnealerBase() : core::pack::annealer::SimAnnealerBase
• similarity_measure_ : protocols::mpi_refinement::Clusterer
• similarity_method_ : protocols::mpi_refinement::Clusterer
• simple_append_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• simple_fold_tree_ : core::kinematics::ShortestPathInFoldTree
• simple_ft() : protocols::protein_interface_design::movers::SetAtomTree
• simple_ft_ : protocols::protein_interface_design::movers::SetAtomTree
• simple_inserter_ : protocols::loophash::FastGapMover
• simple_res_map() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• simple_rmsd_cutoff_relax() : protocols::farna::movers::RNA_Relaxer , protocols::farna::options::RNA_FragmentMonteCarloOptions
• simple_rmsd_cutoff_relax_ : protocols::farna::movers::RNA_Relaxer , protocols::farna::options::RNA_FragmentMonteCarloOptions
• simple_tree() : core::kinematics::FoldTree
• SimpleCycpepPredictApplication() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• SimpleDerivCheckResult() : core::optimization::SimpleDerivCheckResult
• SimpleEdge() : core::pack::interaction_graph::SimpleEdge
• SimpleGlycosylateMover() : protocols::carbohydrates::SimpleGlycosylateMover
• SimpleInteractionGraph() : core::pack::interaction_graph::SimpleInteractionGraph
• SimpleNode() : core::pack::interaction_graph::SimpleNode
• SimplePDB() : core::scoring::packstat::SimplePDB
• SimplePDB_Atom() : core::scoring::packstat::SimplePDB_Atom
• SimplePoseSelection() : protocols::stepwise::legacy::screener::SimplePoseSelection
• SimpleRMSD_Screener() : protocols::stepwise::legacy::screener::SimpleRMSD_Screener
• SimpleScoringScheme() : core::sequence::SimpleScoringScheme
• SimpleSequenceCreator() : core::sequence::SimpleSequenceCreator
• SimpleSequenceData() : core::io::silent::SimpleSequenceData
• SimpleThreadingMover() : protocols::simple_moves::SimpleThreadingMover
• simtol_ : protocols::mpi_refinement::Clusterer
• SimulatedTempering() : protocols::canonical_sampling::SimulatedTempering , protocols::moves::SimulatedTempering
• simultaneous_cycles() : protocols::forge::remodel::RemodelLoopMover
• simultaneous_cycles_ : protocols::forge::remodel::RemodelLoopMover
• simultaneous_stage() : protocols::forge::remodel::RemodelLoopMover
• sin_x_over_x_ : core::scoring::saxs::SinXOverX
• since_last_sonm_update_ : core::scoring::TenANeighborNode
• single_beta_sample() : protocols::docking::EllipsoidalRandomizationMover
• single_chain_ : protocols::frag_picker::nonlocal::NonlocalFrags
• SINGLE_RESID : core::pack::task::ResfileContents
• single_state_design() : protocols::multistate_design::MultiStatePacker
• single_state_entity_data() : protocols::multistate_design::MultiStateEntity< T >
• single_state_entity_data_ : protocols::multistate_design::MultiStateEntity< T >
• single_structure_data_for_pose() : protocols::optimize_weights::IterativeOptEDriver
• single_substitution() : protocols::protein_interface_design::filters::FilterScanFilter
• single_user_input_chunk() : protocols::farna::libraries::RNA_ChunkLibrary
• SingleBasicRotamerLibrary() : core::pack::rotamers::SingleBasicRotamerLibrary
• SingleChainStructureData() : protocols::denovo_design::components::SingleChainStructureData
• SingleConstraints : protocols::noesy_assign::DistanceScoreMover
• SingleDownstreamResidueWriter() : protocols::match::output::SingleDownstreamResidueWriter
• SingleFileBuffer() : protocols::jd2::SingleFileBuffer
• SingleFragmentMover() : protocols::nonlocal::SingleFragmentMover
• SingleGrid() : protocols::qsar::scoring_grid::SingleGrid
• SingleLigandRotamerLibrary() : core::pack::rotamers::SingleLigandRotamerLibrary
• SingleMotif() : protocols::motifs::SingleMotif
• SingleResidueCenrotLibrary() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• SingleResidueDunbrackLibrary : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• SingleResidueFragData() : core::fragment::SingleResidueFragData
• SingleResidueInvrotTarget() : protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget
• SingleResidueMultifunc() : core::optimization::SingleResidueMultifunc
• SingleResiduePeptoidLibrary : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleResiduePeptoidLibrary
• SingleResidueRotamerLibraryFactory() : core::pack::rotamers::SingleResidueRotamerLibraryFactory
• SingleResidueRotamerLibraryRegistrator() : core::pack::rotamers::SingleResidueRotamerLibraryRegistrator< T >
• SingleState() : protocols::multistate_design::SingleState
• SingleStateEntityData() : protocols::multistate_design::SingleStateEntityData
• SingleStateFitnessFunction() : protocols::multistate_design::SingleStateFitnessFunction
• SingleStructureData() : protocols::optimize_weights::SingleStructureData
• singleton_ : core::scoring::saxs::FormFactorManager
• SingleValuePoseEvaluator() : protocols::evaluation::SingleValuePoseEvaluator< T >
• SinXOverX() : core::scoring::saxs::SinXOverX
• SITE_CST : core::pose::datacache::CacheableDataType
• SiteConstraint() : core::scoring::constraints::SiteConstraint
• SiteConstraintCreator() : core::scoring::constraints::SiteConstraintCreator
• SiteConstraintResidues() : core::scoring::constraints::SiteConstraintResidues
• SiteConstraintResiduesCreator() : core::scoring::constraints::SiteConstraintResiduesCreator
• SixDCoordinateBinner : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• size() : core::chemical::rings::RingConformerSet , core::conformation::Conformation , core::conformation::PseudoBondCollection
• Size : core::conformation::ResidueKinWriter , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent
• size() : core::fragment::FragData , core::fragment::FragSet
• Size : core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::concepts::Book< Pages >
• size() : core::fragment::picking_old::concepts::Book< Pages >
• Size : core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• size() : core::fragment::picking_old::concepts::Library< Books >
• Size : core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallResidue
• size() : core::graph::Array0< T > , core::graph::ArrayPoolElement< T > , core::graph::EdgeList
• Size : core::id::AtomID_Map< T >
• size() : core::id::AtomID_Map< T >
• Size : core::id::DOF_ID_Map< T >
• size() : core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• Size : core::id::NamedAtomID_Map< T >
• size() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::AtomTree , core::kinematics::FoldTree , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• Size : core::pack::task::operation::OptH
• size() : core::pack::task::TaskFactory
• Size : core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver
• size() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , core::pose::MiniPose
• Size : core::pose::PDBInfo , core::pose::PDBPoseMap
• size() : core::pose::PDBPoseMap , core::scoring::CenListInfo
• Size : core::scoring::ChemicalShiftAnisotropy
• size() : core::scoring::constraints::Constraints , core::scoring::constraints::MultiConstraint , core::scoring::constraints::ResidueConstraints , core::scoring::DenseEnergyContainer
• Size : core::scoring::DipolarCoupling
• size() : 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::lkball::LKB_ResiduesInfo , core::scoring::loop_graph::LoopCycle , core::scoring::MembraneEmbed , core::scoring::motif::Xfrag , core::scoring::MultipoleElecPoseInfo , core::scoring::MultipoleElecRotamerSetInfo , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• Size : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl
• size() : 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::scoring::VdWTinkerPoseInfo , core::scoring::VdWTinkerRotamerSetInfo
• Size : core::select::util::SelectResiduesByLayer , core::sequence::ABEGOManager
• size() : core::sequence::SequenceAlignment , core::sequence::SequenceProfile , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::PairingStatEntry , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::backrub::BackrubSegment , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::checkpoint::FileBuffer , protocols::cluster::Cluster , protocols::coarse_rna::SourcePositions , protocols::comparative_modeling::AlignmentCluster , protocols::comparative_modeling::AlignmentSet , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::dna::DnaChains , protocols::docking::DockingEnsemble , protocols::electron_density::ResultDB< T, Tcomp >
• Size : protocols::enzdes::ModifyStoredRBConfs
• size() : protocols::evaluation::MetaPoseEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::farna::secstruct::RNA_SecStructInfo , protocols::features::helixAssembly::HelicalFragment , protocols::filters::FilterCollection
• Size : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::MyAtom , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintGenerator
• size() : protocols::fldsgn::topology::BB_Pos
• Size : protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• size() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• Size : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet
• size() : protocols::fldsgn::topology::HelixPairingSet
• Size : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet
• size() : protocols::fldsgn::topology::HSSTripletSet
• Size : protocols::fldsgn::topology::Sheet
• size() : protocols::fldsgn::topology::SheetSet
• Size : protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing
• size() : protocols::fldsgn::topology::StrandPairingSet
• Size : protocols::fldsgn::topology::StrandPairingSet , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction
• size() : protocols::forge::build::BuildManager
• Size : protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::Interval , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveConstraints , protocols::forge::remodel::RemodelAccumulator
• size() : protocols::forge::remodel::RemodelAccumulator
• Size : protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• size() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Config , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::FragmentScoreMap , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider
• Size : protocols::frag_picker::VallResidue , protocols::frags::FragLib
• size() : protocols::frags::RMSVallData , protocols::frags::SingleResidueTorsionFragmentLibrary
• Size : protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragment
• size() : protocols::frags::TorsionFragment
• Size : protocols::frags::TorsionFragmentLibrary
• size() : protocols::frags::TorsionFragmentLibrary
• Size : protocols::frags::TorsionFragmentMover
• size() : protocols::frags::VallData
• Size : protocols::genetic_algorithm::EntityElement
• size() : protocols::hotspot_hashing::HotspotStubSet , protocols::hybridization::TemplateHistory
• Size : protocols::indexed_structure_store::filters::FragmentLookupFilter
• size() : protocols::jd2::JobsContainer
• Size : protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader
• size() : protocols::jumping::DisulfPairingLibrary , protocols::jumping::JumpSample , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::PairingLibrary , protocols::jumping::ResiduePairJumpSetup , protocols::loophash::BackboneDB
• Size : protocols::loophash::FastGapMover
• size() : protocols::loops::Loop , protocols::loops::Loops , protocols::loops::LoopsFileData
• Size : protocols::match::Bool3DGridKinemageWriter , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::match::downstream::TargetRotamerCoords , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::match_lite_hasher , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherMover , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::output::BestMatchesCollection , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchConsolidator , protocols::match::output::PoseInserter , protocols::match::output::ProcessorFactory , protocols::match::output::ResidueKinemageWriter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::SampleStrategyData , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover
• size() : protocols::moves::MoverContainer
• Size : protocols::moves::ReplicaExchangeMC
• size() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::ResonanceList
• Size : protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::nonlocal::SingleFragmentMover
• size() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData
• Size : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData
• size() : protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData
• Size : protocols::optimize_weights::PNatAAOptERotamerData
• size() : protocols::optimize_weights::PNatRotOptEPositionData
• Size : protocols::optimize_weights::PNatRotOptERotamerData
• size() : protocols::optimize_weights::PNatStructureOptEData
• Size : protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::EntityFunc
• size() : protocols::pack_daemon::IterativeVectorExpression
• Size : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon
• size() : protocols::pack_daemon::TopEntitySet , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression , protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet
• Size : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter
• size() : protocols::protein_interface_design::movers::PlacementAuctionMover
• Size : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences
• size() : protocols::qsar::qsarMap , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::ParsedProtocol , protocols::scoring::ImplicitFastClashCheck
• Size : protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose
• size() : protocols::simple_filters::BatchEvaluator
• Size : protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::UserDefinedGroupDiscriminator
• size() : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::rna::checker::VDW_Grid , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::JumpStepWiseSampler , protocols::stepwise::sampler::NoOpStepWiseSampler , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::toolbox::ClusterBase
• Size : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::LinkResidues , protocols::topology_broker::claims::DofClaim
• size() : protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::viewer::triangleIterator , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• size1() : core::id::SequenceMapping , protocols::fldsgn::topology::StrandPairing
• size2() : core::id::SequenceMapping
• Size2 : core::scoring::methods::ResidueCartBondedParameters
• size2() : protocols::fldsgn::topology::StrandPairing
• Size2 : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• size2_ : core::id::SequenceMapping
• Size2Tuple : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size3 : core::scoring::methods::ResidueCartBondedParameters , protocols::match::OccupiedSpaceHash
• Size4 : core::scoring::methods::ResidueCartBondedParameters
• Size6 : protocols::match::VoxelSetIterator
• size_ : core::graph::Array0< T > , core::io::serialization::BUFFER , core::optimization::ParticleSwarmMinimizer , core::scoring::DenseEnergyContainer , core::scoring::Energies , core::scoring::motif::Xfrag , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer , protocols::backrub::BackrubSegment , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::farna::fragments::TorsionSet , protocols::moves::ReplicaExchangeMC , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• size_left() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• size_list_ : protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• size_of_query() : protocols::frag_picker::FragmentPicker
• size_per_coords_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• size_type : boost::unordered_object_pool< T, UserAllocator > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• size_x_ : protocols::pockets::PocketGrid
• size_y_ : protocols::pockets::PocketGrid
• size_z_ : protocols::pockets::PocketGrid
• SizeFilter_map : protocols::protein_interface_design::movers::MapHotspot
• SizeList : core::scoring::dssp::StrandPairing
• SizePair : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::output::PDBWriter
• SizeRealPair : protocols::enzdes::EnzdesFlexibleRegion , protocols::pack_daemon::DaemonSet
• SizeRealPairs : protocols::pack_daemon::DaemonSet
• Sizes : core::scoring::lkball::LK_BallEnergy , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::sic_dock::RigidScore
• SizeSet : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• SizeToStringMap : protocols::environment::EnvClaimBroker
• skip_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• skip_ala_scan_ : protocols::simple_filters::RotamerBoltzmannWeight
• skip_antigen_reports_ : protocols::antibody::AntibodyFeatures
• skip_best_check() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• skip_best_check_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• skip_bulge_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• skip_bulge_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• skip_ccd_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• skip_chainbreak_torsions_ : core::scoring::rna::RNA_TorsionPotential
• skip_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• skip_completely_buried_positions_ : protocols::match::Bool3DGridKinemageWriter
• skip_complicated_stuff_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• skip_connect_info() : core::io::StructFileRepOptions
• skip_connect_info_ : core::io::StructFileRepOptions
• skip_coord_constraints() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_coord_constraints_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_deletions() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_deletions_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_long_min_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• skip_low_temp_phase : protocols::simple_moves::ShakeStructureMover
• skip_minimize() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• skip_minimize_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• skip_o2prime_trials() : protocols::farna::options::RNA_MinimizerOptions
• skip_o2prime_trials_ : protocols::farna::options::RNA_MinimizerOptions
• skip_preminimize() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_preminimize_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_rate() : protocols::loops::Loop , protocols::loops::LoopFromFileData , protocols::loops::SerializedLoop
• skip_rate_ : protocols::loops::Loop , protocols::loops::LoopFromFileData
• skip_redundant() : protocols::abinitio::abscript::ConstraintPreparer
• skip_redundant_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• skip_redundant_width() : protocols::abinitio::abscript::ConstraintPreparer
• skip_redundant_width_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• skip_relax() : protocols::vip::VIP_Mover
• skip_report_ : protocols::simple_filters::RotamerBoltzmannWeight
• skip_reporting_ : protocols::analysis::InterfaceAnalyzerMover
• skip_ring_closure() : core::scoring::methods::ProClosureEnergy
• skip_ring_closure_ : core::scoring::methods::ProClosureEnergy
• skip_same_pucker_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• skip_sampling() : protocols::grafting::AnchoredGraftMover
• skip_sampling_ : protocols::grafting::AnchoredGraftMover
• skip_set_reasonable_fold_tree() : core::import_pose::ImportPoseOptions
• skip_set_reasonable_fold_tree_ : core::import_pose::ImportPoseOptions
• skip_stages_ : protocols::abinitio::FragmentSampler
• skip_torsion() : core::scoring::dna::DNA_DihedralPotential
• skip_unknown_mutant_ : protocols::simple_moves::SimpleThreadingMover
• SkipViolFunc() : core::scoring::func::SkipViolFunc
• slash_char : protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib
• slave_add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• slave_current_batch_id_ : protocols::jd2::MPIFileBufJobDistributor
• slave_current_job_id_ : protocols::jd2::MPIFileBufJobDistributor
• slave_current_runtime_ : protocols::jd2::MPIFileBufJobDistributor
• slave_gather_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• slave_get_new_job_id() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• slave_go() : protocols::jd2::MPIWorkPoolJobDistributor
• slave_job_succeeded() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• slave_mark_current_job_id_for_repetition() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• slave_remove_bad_inputs_from_job_list() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• slave_report_no_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• slave_set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• slave_to_master() : protocols::jd2::MPIFileBufJobDistributor
• slaves_finished_ : protocols::mpi_refinement::MPI_Refine_Master
• slice() : core::pose::full_model_info::FullModelParameters
• Slice() : core::scoring::packstat::Slice
• slice_coords_ : core::scoring::packstat::LeeRichards
• slice_res() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• slice_res_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• slice_res_list() : core::pose::full_model_info::FullModelParameters
• slice_res_list_ : core::pose::full_model_info::FullModelParameters
• sliced_pose_best_alignment : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_calc_rms_res : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_full_to_sub : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_is_prepend_map : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_job_params_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• sliced_to_working_res_map_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• SlicedPoseWorkingParameters() : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• slices_ : core::scoring::packstat::LeeRichards
• slide() : core::conformation::UltraLightResidue , protocols::dna::DNABasestep , protocols::simple_moves::symmetry::SymmetrySlider
• slide_ : protocols::dna::DNABasestep , protocols::docking::DockingInitialPerturbation , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SymDockingInitialPerturbation
• slide_away() : protocols::simple_moves::symmetry::SymmetrySlider
• slide_away_from_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• slide_axis() : protocols::docking::SlideIntoContact , protocols::surface_docking::SurfaceParameters
• slide_axis_ : protocols::docking::DockingInitialPerturbation , protocols::docking::DockingSlideIntoContact , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::docking::SlideIntoContact , protocols::surface_docking::SurfaceParameters
• slide_back_to_origin() : protocols::farna::MultipleDomainMover
• slide_cutpoint() : core::kinematics::FoldTree
• slide_docking_jumps_ : protocols::stepwise::monte_carlo::mover::ResampleMover
• slide_info_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• slide_into_contact() : protocols::sic_dock::SICFast , protocols::simple_moves::symmetry::SetupForSymmetryMover
• slide_into_contact_DEPRICATED() : protocols::sic_dock::SICFast
• slide_into_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• slide_jump() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData
• slide_jump_randomly() : protocols::stepwise::monte_carlo::mover::ResampleMover
• slide_lattice() : protocols::cryst::DockLatticeMover
• slide_order_ : core::conformation::symmetry::SymSlideInfo , protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider , protocols::simple_moves::symmetry::SequentialSymmetrySlider
• slide_order_string_ : core::conformation::symmetry::SymmData
• slide_pattern_ : protocols::hotspot_hashing::SICPatternAtTransform
• slide_score() : protocols::simple_moves::symmetry::SymmetrySlider
• slide_type_ : core::conformation::symmetry::SymSlideInfo
• SlideCriteriaType_ : protocols::simple_moves::symmetry::SymmetrySlider
• SlideCriteriaVal_ : core::conformation::symmetry::SymSlideInfo
• SlideIntoContact() : protocols::docking::SlideIntoContact
• slideintocontact : protocols::flexpep_docking::FlexPepDockingFlags
• SlideIntoContact() : protocols::flexpep_docking::FlexPepDockingProtocol
• SlideThreshold_ : protocols::simple_moves::symmetry::SymmetrySlider
• SlideTogether() : protocols::ligand_docking::SlideTogether
• SlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• slim_ : core::scoring::etable::Etable
• slim_etable_ : core::scoring::lkball::LK_BallEnergy
• slope : core::scoring::etable::ExtraQuadraticRepulsion , core::scoring::func::SigmoidFunc , core::sequence::Line
• slope_ : core::scoring::func::LinearPenaltyFunction , core::scoring::func::SigmoidFunc
• sm_prob_ : protocols::backrub::BackrubProtocol
• small_ : protocols::seeded_abinitio::SegmentHybridizer
• small_angle_ : protocols::simple_moves::BackboneMover
• small_big() : protocols::hybridization::DDomainParse
• SMALL_BULGE_LIMIT : core::scoring::dssp::StrandPairing
• small_cutoff_square_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• small_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• small_min_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_min_type_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• small_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• small_move_stage() : protocols::forge::remodel::RemodelLoopMover
• small_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• small_scores_ : protocols::frag_picker::scores::FragmentScoreMap
• small_sequence_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• SmallAtNb() : core::scoring::SmallAtNb
• SmallBBSampler() : protocols::simple_moves::bb_sampler::SmallBBSampler
• SMALLER : protocols::enzdes::ValueEvaluator
• smallest_native_violation() : protocols::noesy_assign::CrossPeak
• smallest_ring_size() : core::chemical::ResidueType
• SmallFragWeight() : protocols::topology_broker::weights::SmallFragWeight
• SmallMinCCDTrial() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• SmallMinCCDTrialCreator() : protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator
• SmallMol() : protocols::pockets::SmallMol
• SmallMover() : protocols::simple_moves::SmallMover
• smallmover_ : protocols::backrub::BackrubProtocol
• smax_ : protocols::noesy_assign::PeakAssignmentParameters
• smooth() : protocols::hybridization::TMalign
• smooth_ : core::scoring::func::SOGFunc_Impl , core::scoring::hbonds::FadeInterval
• smooth_env_pair_potential_ : core::scoring::ScoringManager
• smooth_etables() : core::scoring::etable::MembEtable
• smooth_etables_one_pair() : core::scoring::etable::Etable
• smooth_fa_elec : core::init::pre_talaris_2013_behavior_settings , core::scoring::etable::coulomb::Coulomb , core::scoring::methods::EnergyMethodOptions
• smooth_fa_elec_ : core::scoring::etable::coulomb::Coulomb , core::scoring::methods::EnergyMethodOptions
• smooth_hb_env_dep() : core::scoring::hbonds::HBondOptions
• smooth_hb_env_dep_ : core::scoring::hbonds::HBondOptions
• smooth_intensities() : core::scoring::electron_density::ElectronDensity
• smooth_move_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• smooth_move_frac_ : core::scoring::MembranePotential
• smooth_move_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• smooth_move_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• smooth_nb() : core::scoring::packing::PoseBalls
• smooth_nb_ : core::scoring::packing::PoseBalls
• smooth_to_zero() : core::scoring::func::SOGFunc_Impl
• smooth_trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• smooth_trial_small_pack_ : protocols::abinitio::ClassicAbinitio
• SmoothCenPairEnergy() : core::scoring::methods::SmoothCenPairEnergy
• SmoothEnvEnergy() : core::scoring::methods::SmoothEnvEnergy
• SmoothEnvPairPotential() : core::scoring::SmoothEnvPairPotential
• SmoothFragmentMover() : protocols::simple_moves::SmoothFragmentMover
• SmoothFragWeight() : protocols::topology_broker::weights::SmoothFragWeight
• smoothing_factor_ : protocols::ligand_docking::ComputeLigandRDF
• SmoothPolicy() : protocols::nonlocal::SmoothPolicy
• SmoothScoreTermCoeffs() : core::scoring::SmoothScoreTermCoeffs
• SmoothSymmetricFragmentMover() : protocols::simple_moves::SmoothSymmetricFragmentMover
• SmotifFeatures() : protocols::features::SmotifFeatures
• SmotifFeaturesCreator() : protocols::features::SmotifFeaturesCreator
• smove_angle_range : protocols::flexpep_docking::FlexPepDockingFlags
• smpbe_size : core::scoring::APBSConfig::R_PARAM
• smpbe_vol : core::scoring::APBSConfig::R_PARAM
• smUR_pose_build_resids_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• snapshot_counter_ : protocols::hybridization::BackboneTorsionPerturbation
• snapshot_interval_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• snapshot_prefix_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• snn : core::scoring::fiber_diffraction::Hankel
• snug_fit_ : protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody_legacy::CDRH3Modeler
• SnugDock() : protocols::antibody::SnugDock
• SnugDockProtocol() : protocols::antibody::SnugDockProtocol
• snugfit_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody_legacy::AntibodyModeler
• snugfit_MC_min() : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody_legacy::AntibodyModeler
• snugfit_mcm_protocol() : protocols::antibody::LHSnugFitLegacy , protocols::antibody_legacy::AntibodyModeler
• socket_addr_ : protocols::moves::UDPSocketClient
• socket_h_ : protocols::moves::UDPSocketClient
• SoedingFunc() : core::scoring::func::SoedingFunc
• soft_scorefxn_ : protocols::ligand_docking::LigandBaseProtocol
• sog_cst_param() : core::scoring::func::SOGFunc_Impl
• sog_cst_param_ : core::scoring::func::SOGFunc_Impl
• SOGFunc() : core::scoring::func::SOGFunc
• SOGFunc_Impl() : core::scoring::func::SOGFunc_Impl
• sol_dist_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• sol_prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• sol_sec_struct_ : protocols::surface_docking::FullatomRelaxMover
• sol_stack_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• sol_weight() : core::scoring::etable::EtableEvaluator
• sol_weight_ : core::scoring::etable::EtableEvaluator
• SOLID_STATE_NMR : core::io::HeaderInformation
• solo_res_ : protocols::protein_interface_design::movers::TryRotamers
• SOLUTION_NMR : core::io::HeaderInformation
• solution_picker_ : protocols::kinematic_closure::KicMover
• SOLUTION_SCATTERING : core::io::HeaderInformation
• SOLUTION_SCATTERING_THEORETICAL_MODEL : core::io::HeaderInformation
• solutions_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• SolutionSorter() : protocols::denovo_design::components::SolutionSorter
• solv1() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solv1_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::etable::TableLookupEvaluator , core::scoring::lkball::LK_BallEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
• solv2() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solv2_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::etable::TableLookupEvaluator , core::scoring::lkball::LK_BallEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
• solvation : core::scoring::etable::AtomPairEnergy
• solvation_ : protocols::make_rot_lib::RotData
• SolvationGrid() : protocols::qsar::scoring_grid::SolvationGrid
• SolvationMetaGrid() : protocols::qsar::scoring_grid::SolvationMetaGrid
• solve() : protocols::kinematic_closure::ClosureProblem , protocols::normalmode::NormalMode
• solve_pb() : core::scoring::PoissonBoltzmannPotential
• SOLVENT : protocols::pockets::ElectrostaticpotentialGrid
• SolventAccessibility() : protocols::frag_picker::scores::SolventAccessibility
• solventExposed_ : protocols::pockets::CCluster , protocols::pockets::PCluster
• solvF2BR() : core::scoring::FACTSResidueInfo
• solvF2BR_ : core::scoring::FACTSResidueInfo
• solvF2d() : core::scoring::FACTSResidueInfo
• solvF2d_ : core::scoring::FACTSResidueInfo
• some_claim_ : protocols::topology_broker::SuggestValueMessage
• some_node_in_state_0_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• some_private_int_ : protocols::toolbox::SF_Replica
• sor_ : protocols::md::Rattle
• sort() : protocols::jd2::archive::EvaluatedArchive , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap
• sort_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• sort_by() : core::import_pose::atom_tree_diffs::AtomTreeDiff , protocols::wum::SilentStructStore
• sort_by_rms_and_energy() : core::scoring::motif::MotifHits
• sort_by_weighted_energy() : core::scoring::hbonds::HBondSet
• sort_Combine_Tags_Info() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• sort_each_group_by_energy() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• sort_ensemble_by_designability() : protocols::enzdes::EnzdesFlexibleRegion
• sort_fill_energies() : protocols::vip::VIP_Mover
• sort_groups_by_energy() : protocols::cluster::ClusterBase
• sort_into_segments() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• sort_pool() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• sort_pose_list() : protocols::stepwise::modeler::align::StepWiseClusterer
• sort_R_function() : core::optimization::EItem
• sort_relaxed_poses() : protocols::vip::VIP_Mover
• sort_silent_scores() : core::io::silent::SilentStruct
• sort_SilentStructOPs() : protocols::wum::sort_SilentStructOPs
• sort_solutions() : protocols::denovo_design::components::FoldGraph
• sorted_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• sorted_capacity_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• sorted_res_list() : core::pose::full_model_info::SubMotifInfo
• SortPredicate() : protocols::jd2::archive::SortPredicate
• source_ : protocols::comparative_modeling::StealLigandMover , protocols::comparative_modeling::StealSideChainsMover
• source_chain() : protocols::simple_moves::AlignChainMover
• source_chain_ : protocols::simple_moves::AlignChainMover
• SOURCE_FILE : protocols::jd2::archive::ArchiveBase
• source_file : update_ResidueType_enum_files.EnumInfo
• source_file_name() : protocols::frag_picker::quota::ABEGO_SS_Config
• source_file_name_ : protocols::frag_picker::quota::ABEGO_SS_Config
• source_filename() : protocols::toolbox::KClusterData
• source_pattern_ : protocols::hotspot_hashing::PartitionedSearchPattern , protocols::hotspot_hashing::SearchPatternExpansion , protocols::hotspot_hashing::SearchPatternTransform , protocols::hotspot_hashing::SICPatternAtTransform
• source_pattern_a : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pattern_b : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pose() : protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• source_pose_ : protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• source_pose_residues_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• source_positions_ : protocols::coarse_rna::SourcePositions
• source_positions_map_ : protocols::coarse_rna::CoarseRNA_Fragments
• sourceName : protocols::sparta::Sparta::SpartaLib
• SourcePositions() : protocols::coarse_rna::SourcePositions
• sources_same() : protocols::jd3::InnerLarvalJob
• south_pucker_dof_key_values_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• south_pucker_dofs_have_not_been_initialized_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• SP : core::chemical::gasteiger::GasteigerAtomTypeData
• SP2 : core::chemical::gasteiger::GasteigerAtomTypeData
• sp2_BAH180_rise() : core::scoring::hbonds::HBondOptions
• sp2_BAH180_rise_ : core::scoring::hbonds::HBondOptions
• sp2_outer_width() : core::scoring::hbonds::HBondOptions
• sp2_outer_width_ : core::scoring::hbonds::HBondOptions
• SP3 : core::chemical::gasteiger::GasteigerAtomTypeData
• space : core::scoring::APBSConfig
• space_ : protocols::match::downstream::DownstreamBuilder
• spacegroup() : core::io::CrystInfo , protocols::cryst::MakeLatticeMover
• Spacegroup() : protocols::cryst::Spacegroup
• spacegroup_ : core::io::CrystInfo
• spacing() : protocols::pockets::PocketGrid
• spacing_ : protocols::membrane::visualize::VisualizeMembraneMover , protocols::pockets::PocketGrid
• spairs2foldtype_ : protocols::fldsgn::topology::SheetFoldTypeManager
• spairs_ : protocols::fldsgn::SheetConstraintGenerator
• spairs_from_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• spairset() : protocols::fldsgn::topology::SheetSet
• spairset_ : protocols::fldsgn::topology::SheetSet
• spairset_name_ : protocols::fldsgn::topology::StrandPairingSet
• Span() : core::conformation::membrane::Span
• span() : core::conformation::membrane::SpanningTopology
• span_ : core::scoring::MembraneTopology , protocols::grafting::simple_movers::ReplaceRegionMover
• span_begin() : core::scoring::MembraneTopology
• span_end() : core::scoring::MembraneTopology
• span_file() : protocols::simple_moves::MembraneTopology
• span_file_ : protocols::simple_moves::MembraneTopology
• span_vector_ : protocols::seeded_abinitio::CoordinateCst
• spanfile() : protocols::membrane::AddMembraneMover
• spanfile_ : core::scoring::MembraneTopology , protocols::membrane::AddMembraneMover
• spanfiles_ : protocols::docking::membrane::MPDockingSetupMover
• spanning() : core::conformation::membrane::SpanningTopology , core::scoring::MembraneEmbed
• spanning_ : core::scoring::MembraneEmbed
• spanning_topology() : core::conformation::membrane::MembraneInfo
• spanning_topology_ : core::conformation::membrane::MembraneInfo
• SpanningTopology() : core::conformation::membrane::SpanningTopology
• sparse_aa_neighbors_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• sparse_mat_info_for_state_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• sparse_matrix_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• SparseMatrixIndex() : core::pack::interaction_graph::SparseMatrixIndex
• Sparta() : protocols::sparta::Sparta
• sparta_ : protocols::sparta::ChemicalShiftEvaluator
• SPARTA_ANN : protocols::sparta::Sparta::SpartaLib
• SPARTA_DIR : protocols::sparta::Sparta::SpartaLib
• SPARTA_ERR_SURF : protocols::sparta::Sparta::SpartaLib
• SpartaLib() : protocols::sparta::Sparta::SpartaLib
• spec_segments_ : protocols::enzdes::EnzdesScorefileFilter
• special_edge_data_ : protocols::sewing::SewGraph
• special_region1_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region1_intra_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region1_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region1_to_other_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region2_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region2_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• special_region_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• special_region_bur_unsat_polars_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• special_region_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• special_region_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• special_region_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• special_rotweight_ : protocols::motifs::MotifDnaPacker
• SPECIAL_SEGMENTS_OBSERVER : core::pose::datacache::CacheableObserverType
• specialized_commands_exist_for_residue() : core::pack::task::ResfileContents
• SpecialRotamerEnergy() : protocols::scoring::methods::SpecialRotamerEnergy
• SpecialRotamerRSO() : protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• SpecialSegmentsObserver() : core::pose::datacache::SpecialSegmentsObserver
• specific_name : core::chemical::rings::RingConformer
• specificity_repacks_ : protocols::dna::DnaInterfacePacker
• SpecificResiduesNearInterfaceFilter() : protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter
• specify_both_spans_ : protocols::protein_interface_design::filters::RmsdFilter
• sphere() : core::scoring::packstat::CavityBall
• Sphere() : core::scoring::packstat::Sphere , protocols::match::BumpGrid
• sphere_ : core::scoring::packstat::CavityBall
• sphere_sasa : core::scoring::packstat::SasaResult
• SpherePointNo : protocols::sparta::PDB
• SpherePoints : protocols::sparta::PDB
• spheres : core::scoring::packstat::PosePackData
• spherical() : core::kinematics::Stub , core::scoring::SecondaryStructurePotential
• spherical_wave_ : protocols::relax::RangeRelaxMover
• SphericalRotationSearchPattern() : protocols::hotspot_hashing::SphericalRotationSearchPattern
• spin() : protocols::noesy_assign::CrossPeak
• Spin() : protocols::noesy_assign::CrossPeak::Spin
• spin_ : protocols::docking::DockingInitialPerturbation
• spin_assign_index1_ : protocols::noesy_assign::PeakAssignment
• spin_assign_index2_ : protocols::noesy_assign::PeakAssignment
• spin_axis() : protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTiltMover
• spin_axis_ : protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTiltMover
• spin_center_ : protocols::docking::DockingInitialPerturbation
• spin_id() : protocols::noesy_assign::PeakAssignment
• SpinAroundPartnerMover() : protocols::membrane::SpinAroundPartnerMover
• SpinAssignments : protocols::noesy_assign::CrossPeak::Spin
• SpinMover() : protocols::protein_interface_design::movers::SpinMover
• spline_ : core::scoring::func::CircularSplineFunc , protocols::denovo_design::filters::PreProlineFilter
• spline_coeffs() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• spline_interpolation() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• spline_interpolator_ : core::scoring::saxs::FormFactor
• SplineFunc() : core::scoring::func::SplineFunc
• SplineParameters() : core::scoring::etable::SplineParameters
• split() : core::grid::CartGrid< T > , protocols::hybridization::DDomainParse
• split_ : protocols::fldsgn::CircularPermutation
• split_by_chain() : core::pose::Pose
• split_chains() : protocols::fldsgn::CircularPermutation
• split_existing_edge_at_residue() : core::kinematics::FoldTree
• split_pose_into_groups() : protocols::simple_moves::GreenPacker
• split_protein_surface_poses() : protocols::surface_docking::SurfaceDockingProtocol
• split_unfolded_label_type() : core::scoring::methods::EnergyMethodOptions
• split_unfolded_label_type_ : core::scoring::methods::EnergyMethodOptions
• split_unfolded_value_type() : core::scoring::methods::EnergyMethodOptions
• split_unfolded_value_type_ : core::scoring::methods::EnergyMethodOptions
• splitkv() : core::chemical::sdf::CtabV3000Parser
• splitString() : protocols::forge::remodel::RemodelData
• SplitUnfoldedTwoBodyEnergy() : core::scoring::methods::SplitUnfoldedTwoBodyEnergy
• SplitUnfoldedTwoBodyPotential() : core::scoring::SplitUnfoldedTwoBodyPotential
• spread_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::kinematic_closure::perturbers::VicinityPerturber
• spring_constant_ : protocols::optimize_weights::WeightRangeConstraint
• sqr_num_aa_types_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• sqrt_HH_cutoff_ : core::scoring::NeighborList
• sqrt_XH_cutoff_ : core::scoring::NeighborList
• sqrt_XX_cutoff_ : core::scoring::NeighborList
• square_distance() : core::scoring::EnergyEdge
• square_obs_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• SquareWell2Func() : core::scoring::func::SquareWell2Func
• SquareWellFunc() : core::scoring::func::SquareWellFunc
• sr_aa_neighbors_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• sr_As_ : core::scoring::CenHBPotential
• sr_mus_ : core::scoring::CenHBPotential
• sr_sigmas_ : core::scoring::CenHBPotential
• SR_total_charge_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• SR_total_neg_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• SR_total_pos_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• srad : core::scoring::APBSConfig::R_PARAM
• srbl_ : core::select::residue_selector::LayerSelector , protocols::flxbb::LayerDesignOperation
• src_ : protocols::simple_moves::symmetry::SetupNCSMover
• src_begin : protocols::forge::remodel::RemodelWorkingSet
• src_end : protocols::forge::remodel::RemodelWorkingSet
• src_pose() : protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::ReplaceRegionMover
• src_pose_ : protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::ReplaceRegionMover
• src_pose_start() : protocols::grafting::simple_movers::ReplaceRegionMover
• src_pose_start_ : protocols::grafting::simple_movers::ReplaceRegionMover
• srcD_ : protocols::simple_moves::symmetry::SetupNCSMover
• srcE_ : protocols::simple_moves::symmetry::SetupNCSMover
• SRelaxPose() : protocols::relax::SRelaxPose
• SRFD_List : core::fragment::FragData
• SRFD_Types : core::fragment::FragFactory
• srfm : core::scoring::APBSConfig::I_PARAM
• ss() : core::fragment::picking_old::vall::VallResidue , core::scoring::motif::Xfres , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::Connection::Motif , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet , protocols::frag_picker::VallResidue
• ss1() : core::scoring::motif::ResPairMotif
• ss1_ : core::scoring::methods::ProQ_Energy , core::scoring::motif::ResPairMotif , protocols::sewing::NodeConstraint , protocols::sic_dock::scores::MotifHashRigidScore
• ss2() : core::scoring::motif::ResPairMotif
• ss2_ : core::scoring::motif::ResPairMotif , protocols::sewing::NodeConstraint , protocols::sic_dock::scores::MotifHashRigidScore
• ss_ : core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::VallResidue , core::scoring::motif::Xfres , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::frag_movers::FragSetFromH5Mover , protocols::frag_picker::VallResidue , protocols::jd2::parser::FragmentReader
• ss_abego_types_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• ss_around : protocols::denovo_design::task_operations::LoopInfo
• SS_Base() : protocols::fldsgn::topology::SS_Base
• ss_chunks_pose_ : protocols::hybridization::FoldTreeHybridize
• ss_cutoff_ : core::scoring::SecondaryStructureWeights
• ss_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::LoopJumpFoldCst , protocols::topology_broker::TemplateJumpClaimer
• SS_dimer : core::scoring::Strands
• ss_dist() : protocols::fldsgn::topology::HSSTriplet
• ss_dist_ : protocols::fldsgn::topology::HSSTriplet
• ss_element_id() : protocols::fldsgn::topology::SS_Info2
• ss_element_id_ : protocols::fldsgn::topology::SS_Info2
• ss_entrpy_ : protocols::fldsgn::NcontactsCalculator
• ss_feature() : core::scoring::methods::ProQ_Energy
• ss_from_blueprint() : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies
• ss_from_blueprint_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies
• ss_helix_nres : protocols::analysis::InterfaceData
• SS_INFO : core::pose::datacache::CacheableDataType
• SS_Info2 : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairingSet
• SS_Info2_COP : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet
• SS_Info2_OP : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::StrandPairing
• ss_info_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• ss_insert() : protocols::denovo_design::connection::BridgeChains
• ss_key() : protocols::denovo_design::components::Picker
• SS_KILLHAIRPINS_INFO : core::pose::datacache::CacheableDataType
• SS_Killhairpins_Info() : core::scoring::SS_Killhairpins_Info
• ss_loop_nres : protocols::analysis::InterfaceData
• ss_lowstrand_ : core::scoring::SecondaryStructureWeights
• ss_motifs_ : protocols::match::SecondaryStructureMPM
• ss_only_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• ss_orient() : protocols::fldsgn::topology::HSSTriplet
• ss_orient_ : protocols::fldsgn::topology::HSSTriplet
• ss_pair_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• ss_penalty() : core::fragment::picking_old::vall::eval::IdentityEval
• ss_penalty_ : core::fragment::picking_old::vall::eval::IdentityEval
• ss_penalty_initializer() : core::scoring::SecondaryStructurePotential
• ss_pred_ : core::scoring::methods::ProQ_Energy
• SS_predictor() : protocols::ss_prediction::SS_predictor
• ss_predictor_ : protocols::denovo_design::filters::SSPredictionFilter , protocols::frag_picker::frag_movers::FragSetFromH5Mover
• SS_resnum : core::scoring::Strands
• ss_sc_feature() : core::scoring::methods::ProQ_Energy
• ss_select_task_factory_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• ss_sheet_nres : protocols::analysis::InterfaceData
• ss_str() : core::fragment::picking_old::vall::eval::IdentityEval , protocols::frag_picker::VallResidue
• ss_str_ : protocols::frag_picker::VallResidue
• SS_strand : core::scoring::Strands
• SS_strand_end : core::scoring::Strands
• ss_strings() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• ss_strings_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• ss_strings_specified() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• ss_stub_to_abego_ : core::indexed_structure_store::ABEGOHashedFragmentStore
• ss_type() : protocols::comparative_modeling::features::SSFeature , protocols::jumping::DisulfPairing , protocols::ss_prediction::SS_predictor
• ss_type_ : protocols::comparative_modeling::features::SSFeature , protocols::frag_picker::quota::SecondaryStructurePool
• ss_type_convert() : protocols::simple_moves::StructProfileMover
• ss_type_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• SS_TYPES : protocols::flxbb::LayerDesignOperation
• ss_types_ : core::io::silent::SilentStructFactory
• ss_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• ss_weights_ : core::scoring::methods::EnergyMethodOptions
• SSamountFilter() : protocols::protein_interface_design::filters::SSamountFilter
• ssbond_map() : core::io::StructFileRep
• ssbond_map_ : core::io::StructFileRep
• sscomp() : core::scoring::motif::Xfrag
• sscomp_ : core::scoring::motif::Xfrag
• ssdep_ : core::scoring::hbonds::SSWeightParameters
• ssdist_ : core::scoring::SecondaryStructurePotential
• ssdist_initializer() : core::scoring::SecondaryStructurePotential
• sse_residues_ : protocols::toolbox::task_operations::DsspDesignOperation
• SSElementMotifContactEnergy() : core::scoring::methods::SSElementMotifContactEnergy
• SSElementMotifContactFilter() : protocols::simple_filters::SSElementMotifContactFilter
• SSFeature() : protocols::comparative_modeling::features::SSFeature
• ssids_by_name_ : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• ssinfo1_ : protocols::sic_dock::scores::MotifHashRigidScore
• ssinfo2_ : protocols::sic_dock::scores::MotifHashRigidScore
• ssinfo_ : protocols::fldsgn::filters::SheetTopologyFilter
• SSMotifFinder() : protocols::simple_filters::SSMotifFinder
• sspair() : core::scoring::SecondaryStructurePotential
• SSPairPotential() : protocols::fldsgn::potentials::sspot::SSPairPotential
• sspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• ssPred_cutoff_ : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• SSPredictionFilter() : protocols::denovo_design::filters::SSPredictionFilter
• sstype : protocols::forge::remodel::LineObject
• sstype_ : protocols::jd2::parser::BluePrint , protocols::simple_filters::AbinitioBaseFilter
• SSWeightParameters() : core::scoring::hbonds::SSWeightParameters
• st_atr() : core::scoring::etable::EtableEvaluator
• st_atr_ : core::scoring::etable::EtableEvaluator , protocols::relax::ClassicRelax
• st_rep() : core::scoring::etable::EtableEvaluator
• st_rep_ : core::scoring::etable::EtableEvaluator , protocols::relax::ClassicRelax
• st_sol() : core::scoring::etable::EtableEvaluator
• st_sol_ : core::scoring::etable::EtableEvaluator , protocols::relax::ClassicRelax
• ST_SURFACE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• stability_metric_ : core::chemical::gasteiger::GasteigerAtomTypeData
• stack_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• stacked_on_terminal_res_in_original_pose_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• StackElecEnergy() : core::scoring::rna::StackElecEnergy
• stage() : protocols::abinitio::IterativeBase
• stage1_1_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_2_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_3_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_4_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage1_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage1_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage1_mover() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio
• stage1_probability_ : protocols::hybridization::HybridizeProtocol
• stage1_sampler_ : protocols::abinitio::DoubleLayerKinematicAbinitio
• stage1_scorefxn_ : protocols::hybridization::HybridizeProtocol
• Stage1Sampler() : protocols::abinitio::Stage1Sampler
• stage25_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage2_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::relax::ClassicRelax
• stage2_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage2_decoys_ : protocols::abinitio::IterativeCentroid
• stage2_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage2_mover() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• stage2_repack_period : protocols::relax::ClassicRelax
• STAGE2_RESAMPLING : protocols::abinitio::IterativeBase
• stage2_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage2_temperature_ : protocols::hybridization::HybridizeProtocol
• stage2min_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage2pack_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage3_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::relax::ClassicRelax
• stage3_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage3_mover() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• stage4_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage4_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage4_cycles_pack_rate_ : protocols::abinitio::ClassicAbinitio
• stage4_mover() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• stage4rot_mover() : protocols::abinitio::ClassicAbinitio
• stage5_cycles() : protocols::abinitio::ClassicAbinitio
• stage5_cycles_ : protocols::abinitio::ClassicAbinitio
• stage5_mover() : protocols::abinitio::ClassicAbinitio
• stage_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::IterativeBase
• STAGE_1 : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_2 : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_3a : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_3b : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_4 : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_4rot : protocols::abinitio::ClassicAbinitio
• STAGE_5 : protocols::abinitio::ClassicAbinitio
• stage_movers_ : protocols::abinitio::abscript::AbscriptMover
• staged_constraints() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• staged_constraints_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• staged_manual_design_ : protocols::forge::remodel::RemodelMover::instruction_flags
• StageID : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::topology_broker::TopologyBroker
• stagename_ : protocols::abinitio::abscript::AbscriptMover::StageTracker
• StageTracker() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• stagger() : protocols::dna::DNABasepair
• stagger_ : protocols::dna::DNABasepair
• stagger_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• stagger_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• stagger_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• standard_atomtype_to_carbon_donor_index_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• standard_packing() : protocols::dna::DnaInterfacePacker
• StandardDisulfPairingLibrary() : protocols::jumping::StandardDisulfPairingLibrary
• StandardJobQueen() : protocols::jd3::StandardJobQueen
• StandardPairingLibrary() : protocols::jumping::StandardPairingLibrary
• StandardPivots() : protocols::kinematic_closure::pivot_pickers::StandardPivots
• staple_gap_ : protocols::simple_moves::PeptideStapleMover
• StapleChains() : protocols::denovo_design::connection::StapleChains
• stapler_ : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• StarAbinitio() : protocols::star::StarAbinitio
• start() : core::conformation::membrane::Span , core::fragment::Frame , core::io::pdb::Field , core::kinematics::Edge , core::select::residue_selector::ResidueRange , core::sequence::Sequence , protocols::anchored_design::Anchor , protocols::antibody::clusters::CDRCluster , protocols::antibody::FrameWork , protocols::denovo_design::components::Segment , protocols::environment::Environment , protocols::features::helixAssembly::HelicalFragment , protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::jumping::Interval , protocols::loops::Loop , protocols::loops::SerializedLoop , protocols::noesy_assign::FoldResonance , protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::rbsegment_relax::RBResidueRange , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• start_ : core::chemical::RigidDistanceVisitor , core::conformation::membrane::Span , core::fragment::Frame , core::io::serialization::BUFFER , core::kinematics::Edge , core::scoring::packstat::trace , core::scoring::ResRangePredicate , core::sequence::Sequence , protocols::anchored_design::Anchor , protocols::antibody::clusters::CDRCluster , protocols::denovo_design::components::Segment , protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::floppy_tail::FloppyTailMover , protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::jumping::Interval , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::noesy_assign::FoldResonance , protocols::nonlocal::Region , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::simple_filters::GeometryFilter , protocols::simple_filters::RmsdEvaluator
• start_added_residue_in_aform_ : protocols::stepwise::monte_carlo::mover::AddMover
• start_atom() : core::kinematics::Edge
• start_atom_ : core::kinematics::Edge , protocols::topology_broker::BasicJumpClaimer
• start_atomid() : protocols::backrub::BackrubSegment
• start_atomid1() : protocols::backrub::BackrubSegment
• start_atomid1_ : protocols::backrub::BackrubSegment
• start_atomid2() : protocols::backrub::BackrubSegment
• start_atomid2_ : protocols::backrub::BackrubSegment
• start_atomid_ : protocols::backrub::BackrubSegment
• start_atoms1() : protocols::backrub::BackrubSegment
• start_atoms2() : protocols::backrub::BackrubSegment
• start_bond_angle_key() : protocols::backrub::BackrubSegment
• start_centroid_ : protocols::abinitio::ResolutionSwitcher
• start_coords_ : protocols::sic_dock::ConstraintSetScore , protocols::sic_dock::NoPoseXYX_Func
• start_database_session() : protocols::antibody::AntibodyDatabaseManager
• start_eval_time_ : protocols::jd2::archive::EvaluatedArchive
• start_evaluation_timer() : protocols::jd2::archive::EvaluatedArchive
• start_from_centroid() : protocols::abinitio::Protocol
• start_from_pts_ : protocols::ligand_docking::LigandDockProtocol
• start_from_random_rb_conf_ : protocols::enzdes::EnzdesFixBBProtocol
• start_index_ : core::chemical::RigidDistanceVisitor , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixMultiFunc
• start_key() : protocols::noesy_assign::ResonanceList
• start_label() : protocols::topology_broker::BasicJumpClaimer
• start_label_ : protocols::topology_broker::BasicJumpClaimer
• start_listening() : protocols::canonical_sampling::AsyncMPITemperingBase
• start_new_batch() : protocols::jd2::archive::BaseArchiveManager
• start_new_match() : protocols::match::output::WriteUpstreamHitKinemage
• start_pdb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• start_pdb_chain() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• start_pos_ : core::chemical::RigidDistanceVisitor
• start_pose() : protocols::abinitio::ResolutionSwitcher
• start_pose_ : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::helix_capper::HelixNCapperMover , protocols::stepwise::setup::StepWiseJobDistributor , protocols::topology_broker::StartStructClaimer
• start_pose_cuts_ : protocols::topology_broker::TopologyBroker
• start_position() : protocols::topology_broker::BasicJumpClaimer
• start_position_ : protocols::simple_moves::SimpleThreadingMover , protocols::topology_broker::BasicJumpClaimer
• start_protocol() : protocols::loop_modeling::LoopProtocol
• start_ramp_cstweight_ : protocols::abinitio::FoldConstraints
• start_rep_weight : protocols::relax::ClassicRelax
• start_res() : protocols::docking::DockingEnsemble , protocols::indel::IndelOptimizationMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• start_res_ : protocols::docking::DockingEnsemble , protocols::indel::IndelOptimizationMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::rigid::RollMover , protocols::sewing::AddStartnodeFragments , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ReturnSidechainMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• start_seq2() : core::sequence::DerivedSequenceMapping
• start_seq2_ : core::sequence::DerivedSequenceMapping
• start_struct : protocols::relax::SRelaxPose
• start_time() : protocols::jd2::Job , protocols::simple_filters::ExpiryFilter
• start_time_ : protocols::canonical_sampling::ParallelTempering , protocols::evaluation::TimeEvaluator , protocols::jd2::Job , protocols::jobdist::BaseJobDistributor , protocols::simple_filters::ExpiryFilter , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• start_time_wall_clock_ : protocols::wum::MPI_WorkUnitManager
• start_timer() : protocols::wum::MPI_WorkUnitManager
• start_timing() : protocols::jd2::Job
• start_tree_at_chain() : protocols::protein_interface_design::movers::SetAtomTree
• start_tree_at_chain_ : protocols::protein_interface_design::movers::SetAtomTree
• start_vertex() : core::chemical::RerootRestypeVisitor
• start_weight() : protocols::moves::RampingMover
• start_weight_ : protocols::moves::TrialMover
• start_weights_ : protocols::moves::RampingMover
• start_with_current() : core::pack::annealer::SimAnnealerBase
• start_with_current_ : core::pack::annealer::SimAnnealerBase
• startAtRepeat_ : protocols::simple_filters::RepeatParameterFilter
• starter_for_sequential_distribution() : protocols::jd2::MPIWorkPoolJobDistributor
• starter_for_sequential_distribution_ : protocols::jd2::MPIWorkPoolJobDistributor
• StartFrom() : protocols::ligand_docking::StartFrom
• starting_displacement_ : protocols::hotspot_hashing::SICPatternAtTransform
• starting_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• starting_node() : protocols::sewing::Assembly
• starting_pose() : protocols::dna::PDBOutput , protocols::jd2::JobOutputter
• starting_pose_ : protocols::motifs::MotifDnaPacker
• starting_positions_ : protocols::ligand_docking::StartFrom
• starting_rama_scores_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase
• starting_reference_energies_ : protocols::optimize_weights::OptEMultifunc
• starting_rep_ : protocols::docking::SlideIntoContact
• starting_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• starting_z_ : protocols::membrane::OptimizeMembranePositionMover
• startpos_ : core::fragment::AnnotatedFragData
• StarTreeBuilder() : protocols::nonlocal::StarTreeBuilder
• startres : protocols::denovo_design::task_operations::LoopInfo
• StartStructClaimer() : protocols::topology_broker::StartStructClaimer
• starttime_ : protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::mpi_refinement::MPI_Refinement , protocols::rpc::JSON_RPC
• startup() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• stat_motifs() : core::scoring::motif::MotifHits
• state() : protocols::forge::build::BuildInstruction
• state_ : protocols::forge::build::BuildInstruction , protocols::forge::remodel::RemodelDesignMover , protocols::toolbox::task_operations::SelectBySASAOperation
• state_assignments_ : core::pack::scmin::SidechainStateAssignment
• state_check() : protocols::environment::ClientMover
• state_energies() : protocols::pack_daemon::MultistateFitnessFunction
• state_energies_ : protocols::pack_daemon::MultistateFitnessFunction
• state_energies_in_current_context_ : core::pack::interaction_graph::FASTERNode
• state_energies_in_current_state_assignment_ : core::pack::interaction_graph::FASTERNode
• state_has_same_backbone_as_current() : protocols::flexpack::interaction_graph::FlexbbNode
• state_in_rh : core::pack::interaction_graph::history_queue_struct
• state_ind_for_this_aa_type_ : core::pack::interaction_graph::SparseMatrixIndex
• state_indices_for_state_vector_ : protocols::pack_daemon::DynamicAggregateFunction
• state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• state_is_glycine() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• state_is_proline() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• state_momento() : core::pack::scmin::SidechainStateAssignment
• state_name() : protocols::pack_daemon::DynamicAggregateFunction
• state_offset_for_aatype_ : core::pack::interaction_graph::OnTheFlyNode
• state_offset_for_restype_group_ : core::pack::interaction_graph::SymmOnTheFlyNode
• state_offsets_for_aa_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• state_offsets_for_aa_for_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• state_offsets_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• state_offsets_for_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• state_poses_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• state_positive_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• state_task_factory_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• 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 , protocols::flexpack::interaction_graph::FlexbbNode
• state_unbound_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• state_unfolded_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• state_variable_name_2_state_index_ : protocols::pack_daemon::DynamicAggregateFunction
• state_variable_names_ : protocols::pack_daemon::DynamicAggregateFunction
• state_vector_data_file_names_ : protocols::pack_daemon::DynamicAggregateFunction
• state_vector_variable_names_ : protocols::pack_daemon::DynamicAggregateFunction
• state_vector_variables_ : protocols::pack_daemon::DynamicAggregateFunction
• StateAccumulatingMatchFilter() : protocols::match::output::StateAccumulatingMatchFilter
• StateEnergies : protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• StateEnergiesAndNPDs : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• StateEsAndNPDs : protocols::pack_daemon::DaemonSet
• StateIndices : protocols::pack_daemon::MultistateAggregateFunction
• states() : protocols::multistate_design::MultiStateFitnessFunction
• states_ : protocols::multistate_design::MultiStateFitnessFunction
• static_grid_ : protocols::pockets::PocketGrid
• stationary_label_ : protocols::environment::CoMTrackerCM , protocols::rigid::UniformRigidBodyCM
• statistics_ : protocols::frag_picker::scores::PValuedFragmentScoreManager
• statistics_filename() : protocols::backrub::BackrubSidechainMover
• statistics_filename_ : protocols::backrub::BackrubSidechainMover
• statistics_output_ : core::scoring::orbitals::OrbitalsStatistics
• statistics_valid() : protocols::jd2::archive::ArchiveBase
• Stats : protocols::sic_dock::scores::MotifHashRigidScore
• stats_ : protocols::moves::TrialMover
• stats_cutoff_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::task_operations::AddCDRProfilesOperation
• stats_file() : protocols::canonical_sampling::TemperingBase
• stats_file_ : protocols::canonical_sampling::TemperingBase
• stats_line_output() : protocols::canonical_sampling::TemperingBase
• stats_line_output_ : protocols::canonical_sampling::TemperingBase
• stats_silent_output() : protocols::canonical_sampling::TemperingBase
• stats_silent_output_ : protocols::canonical_sampling::TemperingBase
• stats_type_ : protocols::moves::TrialMover
• status() : protocols::jd3::JobResult , protocols::jd3::PoseJobResult
• status_prefix() : protocols::jd2::Job , protocols::jd3::LarvalJob
• status_prefix_ : protocols::jd2::Job , protocols::jd3::LarvalJob
• stb_ : protocols::kinmatch::FunGroupTK
• std_dev_ : protocols::make_rot_lib::RotData
• std_dev_sq_ : core::scoring::methods::RingClosureEnergy
• std_devs_ : core::scoring::func::USOGFunc
• stddev() : core::scoring::dna::DNA_BasePotential
• stddev_ : core::scoring::dna::DNA_BasePotential , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst
• stddev_degrees_ : protocols::ligand_docking::ResidueTorsionRestraints
• stdev_ : protocols::stepwise::sampler::MC_OneTorsion
• stdRes : core::io::ModifiedResidueInformation
• stdv_ : protocols::constraints_additional::COMCoordinateConstraint
• 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_frags() : protocols::abinitio::Template
• steal_inversion() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• steal_jumps() : protocols::jumping::JumpSample
• steal_orientation_and_pleating() : protocols::jumping::JumpSample
• steal_rotamer() : core::pack::rotamer_set::RotamerSubset
• steal_times_ : protocols::jd2::parser::FragmentReader
• stealBfactorsFromFile() : core::scoring::cryst::PhenixInterface
• StealLigandMover() : protocols::comparative_modeling::StealLigandMover
• StealSideChainsMover() : protocols::comparative_modeling::StealSideChainsMover
• steepness() : core::scoring::Membrane_FAEmbed , protocols::simple_filters::Sigmoid
• steepness_ : core::conformation::membrane::MembraneInfo , core::scoring::hbonds::HBondEnergy , core::scoring::Membrane_FAEmbed , protocols::membrane::AddMembraneMover , protocols::simple_filters::Sigmoid
• stem_copy_size_ : protocols::antibody::GraftOneCDRLoop
• stem_not_graft_ : protocols::antibody::GraftOneCDRLoop
• stem_optimize_ : protocols::antibody::GraftCDRLoopsProtocol
• stem_pairing_sets_ : protocols::farna::setup::RNA_DeNovoParameters
• stem_size_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::GraftedStemOptimizer , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• StemFinder() : protocols::simple_filters::StemFinder
• stems_are_neighbors() : protocols::simple_filters::StemFinder
• stems_are_neighbors_ : protocols::simple_filters::StemFinder
• stems_on_sse() : protocols::simple_filters::StemFinder
• stems_on_sse_ : protocols::simple_filters::StemFinder
• step() : core::optimization::GA_Minimizer , protocols::make_rot_lib::TorsionRange , protocols::matdes::SymDofMoverSampler , protocols::pockets::CCluster , protocols::pockets::PCluster
• step_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_count() : protocols::canonical_sampling::TrajectoryRecorder
• step_count_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• step_counter_ : protocols::canonical_sampling::BiasEnergy
• step_data() : core::optimization::SimpleDerivCheckResult
• step_data_ : core::optimization::SimpleDerivCheckResult
• step_penalty_ : protocols::rbsegment_relax::OptimizeThreadingMover
• step_size : core::scoring::carbohydrates::CHIDihedralSamplingData
• STEP_SIZE : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• step_size() : protocols::match::upstream::SampleStrategyData , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyTransMover , protocols::simple_moves::symmetry::SymmetrySlider , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• step_size_ : protocols::match::upstream::SampleStrategyData , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• step_x_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_y_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_z_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• stepsize() : protocols::docking::SlideIntoContact
• stepsize_ : core::scoring::func::EtableFunc , protocols::docking::SlideIntoContact
• stepSize_ : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• stepsize_angle_ : protocols::membrane::OptimizeMembranePositionMover
• stepsize_z_ : protocols::membrane::OptimizeMembranePositionMover
• stepwise_clusterer_ : protocols::stepwise::screener::PoseSelectionScreener
• stepwise_modeler_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• stepwise_monte_carlo_ : protocols::stepwise::setup::StepWiseJobDistributor
• stepwise_move_selector() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• stepwise_move_selector_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• stepwise_packer_ : protocols::stepwise::screener::PackScreener
• stepwise_pose_setup_ : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• StepWiseBasicModelerOptions() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• StepWiseBasicOptions() : protocols::stepwise::options::StepWiseBasicOptions
• StepWiseBasicWorkingParameters() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• StepWiseClusterer() : protocols::stepwise::modeler::align::StepWiseClusterer
• StepWiseConnectionSampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• StepWiseCSA_JobDistributor() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• StepWiseJobDistributor() : protocols::stepwise::setup::StepWiseJobDistributor
• StepWiseLegacyClusterer() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• StepWiseLegacyClustererSilentBased() : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• StepWiseMasterMover() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• StepWiseMasterPacker() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• StepWiseMinimizer() : protocols::stepwise::modeler::StepWiseMinimizer
• StepWiseModeler() : protocols::stepwise::modeler::StepWiseModeler
• StepWiseModelerOptions() : protocols::stepwise::modeler::options::StepWiseModelerOptions
• StepWiseMonteCarlo() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• StepWiseMonteCarloJobDistributor() : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• StepWiseMonteCarloOptions() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• StepWiseMove() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• StepWiseMoveSelector() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• StepWiseMoveSelectorOptions() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• StepWisePacker() : protocols::stepwise::modeler::packer::StepWisePacker
• StepWisePoseAligner() : protocols::stepwise::modeler::align::StepWisePoseAligner
• StepWiseProteinBackboneSampler() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• StepWiseProteinCCD_Closer() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• StepWiseProteinCCD_MultiPoseCloser() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• StepWiseProteinKIC_LoopBridger() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• StepWiseProteinMinimizer() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• StepWiseProteinModelerOptions() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• StepWiseProteinPoseSetup() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• StepWiseResiduePairScreener() : protocols::stepwise::screener::StepWiseResiduePairScreener
• StepWiseRNA_Clusterer() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• StepWiseRNA_CombineLongLoopFilterer() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• StepWiseRNA_CountStruct() : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• StepWiseRNA_Minimizer() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• StepWiseRNA_ModelerOptions() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• StepWiseRNA_PoseSelection() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• StepWiseRNA_PoseSetup() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• StepWiseSampleAndScreen() : protocols::stepwise::StepWiseSampleAndScreen
• StepWiseSamplerAny() : protocols::stepwise::sampler::StepWiseSamplerAny
• StepWiseSamplerBase() : protocols::stepwise::sampler::StepWiseSamplerBase
• StepWiseSamplerComb() : protocols::stepwise::sampler::StepWiseSamplerComb
• StepWiseSamplerOneTorsion() : protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• StepWiseSamplerOneValue() : protocols::stepwise::sampler::StepWiseSamplerOneValue
• StepWiseSamplerOneValueComb() : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• StepWiseSamplerSized() : protocols::stepwise::sampler::StepWiseSamplerSized
• StepWiseSamplerSizedAny() : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• StepWiseSamplerSizedComb() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• StepWiseScreener() : protocols::stepwise::screener::StepWiseScreener
• StepWiseWorkingParameters() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• StepWiseWorkingParametersSetup() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• stereochem() : core::chemical::carbohydrates::CarbohydrateInfo
• stereochem_ : core::chemical::carbohydrates::CarbohydrateInfo
• steric_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• stf() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• stf_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• stich_motif_in_scaffold_by_indexes_rotation_and_translation() : protocols::motif_grafting::movers::MotifGraftMover
• stiffness() : core::scoring::dna::DNA_BasePotential
• stiffness_ : core::scoring::dna::DNA_BasePotential
• still_interested() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase
• STM_STORED_TASKS : core::pose::datacache::CacheableDataType
• STMStoredTask() : protocols::toolbox::task_operations::STMStoredTask
• StochasticFilter() : protocols::filters::StochasticFilter
• stop() : core::fragment::Frame , core::kinematics::Edge , core::select::residue_selector::ResidueRange , protocols::antibody::FrameWork , protocols::denovo_design::components::Segment , protocols::jd2::MpiFileBuffer , protocols::jumping::Interval , protocols::loops::Loop , protocols::loops::SerializedLoop , protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• stop_ : core::kinematics::Edge , protocols::denovo_design::components::Segment , protocols::floppy_tail::FloppyTailMover , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::nonlocal::Region , protocols::rbsegment_relax::CCDMoveWrapper
• stop_after_closure_ : protocols::antibody::AntibodyCDRGrafter
• stop_at_closure() : protocols::grafting::AnchoredGraftMover
• stop_at_closure_ : protocols::grafting::AnchoredGraftMover
• stop_atom() : core::kinematics::Edge
• stop_atom_ : core::kinematics::Edge
• stop_before_condition() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• stop_before_condition_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• stop_pdb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• stop_pdb_chain() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• stop_res() : protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• stop_res_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::rigid::RollMover , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• stop_running_worker() : protocols::boinc::Boinc
• stopping_condition() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_moves::GenericMonteCarloMover
• stopping_condition_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_moves::GenericMonteCarloMover
• Storage : protocols::simple_moves::LoggedFragmentMover
• storage_ : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool
• store() : boost::unordered_object_pool< T, UserAllocator > , core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T > , core::indexed_structure_store::FragmentLookup , protocols::wum::SilentStructStore
• store_ : core::indexed_structure_store::FragmentLookup , protocols::wum::SilentStructStore
• store_active_energies() : core::scoring::EnergyEdge
• store_argv_in_file() : core::io::silent::SilentFileData
• store_argv_in_file_ : core::io::silent::SilentFileData
• store_classification() : core::io::HeaderInformation
• store_compound() : core::io::HeaderInformation
• store_const_data() : core::pose::Pose
• store_constraints() : protocols::moves::ConstraintGenerator
• 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::HeaderInformation
• store_disulfides() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• store_energies() : protocols::ddg::ddGMover
• store_energies_ : protocols::toolbox::DecoySetEvaluation
• store_experimental_technique() : core::io::HeaderInformation
• store_experimental_techniques() : core::io::HeaderInformation
• store_H3_cter_fragment() : protocols::antibody_legacy::CDRH3Modeler
• store_idCode() : core::io::HeaderInformation
• store_induced_dipoles() : core::scoring::MultipoleElecPotential
• store_interaction_energy_first_node() : core::pack::interaction_graph::LazyEdge
• store_interaction_energy_second_node() : core::pack::interaction_graph::LazyEdge
• store_jobs_for_current_round() : protocols::jd3::JobDistributor
• store_keywords() : core::io::HeaderInformation
• store_line() : protocols::jd2::SingleFileBuffer
• store_path() : protocols::motifs::Motif
• store_properties() : core::scoring::bin_transitions::BinTransitionCalculator
• store_random_seed_info() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• store_record() : core::io::HeaderInformation
• store_reference_pose_geometry() : protocols::simple_moves::GreenPacker
• store_remark() : protocols::motifs::Motif
• store_residue_identities() : core::scoring::bin_transitions::BinTransitionCalculator
• store_rotamer_coords() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• store_rpes_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• store_silents_ : protocols::simple_moves::CombinePoseMover
• store_string_pair() : protocols::jd3::PoseInputSource
• store_title() : core::io::HeaderInformation
• store_to_channel() : protocols::jd2::MpiFileBuffer
• store_to_decoys() : protocols::mpi_refinement::WorkUnit_Sampler
• 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_trj() : protocols::md::MDBase
• store_trj_ : protocols::md::MDBase
• store_xyz() : core::scoring::FACTSResidueInfo
• StoreCombinedStoredTasksMover() : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• StoreCompoundTaskMover() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• stored_angle() : protocols::stepwise::sampler::MC_OneTorsion
• stored_angle_ : protocols::stepwise::sampler::MC_OneTorsion
• stored_induced_dipole() : core::scoring::MultipoleElecResidueInfo
• stored_induced_dipole_ : core::scoring::MultipoleElecResidueInfo
• stored_induced_rf_dipole() : core::scoring::MultipoleElecResidueInfo
• stored_induced_rf_dipole_ : core::scoring::MultipoleElecResidueInfo
• stored_pucker_state_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• stored_rpes_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• stored_task_names() : protocols::matdes::MatDesPointMutationCalculator
• stored_task_names_ : protocols::matdes::MatDesPointMutationCalculator
• StoredRotamerLibrarySpecification() : core::chemical::rotamers::StoredRotamerLibrarySpecification
• storeJobStatistics() : protocols::flexpep_docking::FlexPepDockingProtocol
• StorePoseSnapshot() : protocols::simple_moves::StorePoseSnapshot
• stores_residue_map() : core::pose::reference_pose::ReferencePose
• stores_residue_map_ : core::pose::reference_pose::ReferencePose
• StoreTaskMover() : protocols::toolbox::task_operations::StoreTaskMover
• str() : core::kinematics::Node , core::scoring::packstat::CavityBall
• str2cell() : core::io::rna::RDAT
• str_access_ : protocols::environment::Comparator
• str_type() : protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::DofClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim
• strand() : protocols::fldsgn::topology::SS_Info2
• Strand() : protocols::fldsgn::topology::Strand
• strand1() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand1_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand2() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand2_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• strand_fraction() : core::fragment::SecondaryStructure
• strand_fraction_ : core::fragment::SecondaryStructure
• strand_id() : protocols::fldsgn::topology::SS_Info2
• strand_id_ : protocols::features::strand_assembly::SandwichFragment , protocols::fldsgn::topology::SS_Info2
• strand_order() : protocols::fldsgn::topology::Sheet
• strand_order_ : protocols::fldsgn::topology::Sheet
• strand_pair_library_positions_ : protocols::hybridization::HybridizeFoldtreeDynamic
• strand_pairing() : core::scoring::dssp::StrandPairingSet , protocols::fldsgn::topology::StrandPairingSet
• strand_pairing_ : protocols::abinitio::PairingStatEntry
• strand_pairing_set() : core::scoring::dssp::Dssp
• strand_pairing_stats() : protocols::abinitio::Templates
• strand_pairings() : protocols::abinitio::Template , protocols::fldsgn::topology::StrandPairingSet , protocols::jd2::parser::BluePrint
• strand_pairings_ : protocols::abinitio::Template , protocols::fldsgn::topology::StrandPairingSet , protocols::jd2::parser::BluePrint
• strand_pairings_template_indices_ : protocols::hybridization::FoldTreeHybridize
• strand_pairs_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::hybridization::HybridizeProtocol
• strand_sigOffAxisR : protocols::rbsegment_relax::RBSegmentRelax
• strand_sigOffAxisT : protocols::rbsegment_relax::RBSegmentRelax
• strand_sigR : protocols::rbsegment_relax::RBSegmentRelax
• strand_sigT : protocols::rbsegment_relax::RBSegmentRelax
• strand_stats_ : protocols::abinitio::TemplateJumpSetup , protocols::abinitio::Templates
• strand_sum_ : protocols::jumping::SameStrand
• strand_weight() : protocols::abinitio::PairingStatistics
• StrandBundleFeatures() : protocols::features::strand_assembly::StrandBundleFeatures
• StrandBundleFeaturesCreator() : protocols::features::strand_assembly::StrandBundleFeaturesCreator
• StrandConstraints() : protocols::abinitio::StrandConstraints
• StrandFragment() : protocols::features::strand_assembly::StrandFragment
• StrandMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• StrandPairing() : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• StrandPairings : core::scoring::dssp::StrandPairingSet
• StrandPairingSet() : core::scoring::dssp::StrandPairingSet , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet
• StrandPairingSetCOP : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::topology::SheetSet
• StrandPairingSetOP : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• strands() : core::scoring::SS_Info
• Strands() : core::scoring::Strands
• strands() : protocols::fldsgn::topology::SS_Info2
• strands_ : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2
• StrandTwistingMover() : protocols::rbsegment_relax::StrandTwistingMover
• strategy() : protocols::match::upstream::SampleStrategyData
• strategy_ : protocols::match::upstream::SampleStrategyData
• strength() : protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim
• stretch() : protocols::dna::DNABasepair
• stretch_ : protocols::dna::DNABasepair
• stretch_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• strict_base_pairing_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• strict_column_mode() : core::io::silent::SilentFileData
• strict_column_mode_ : core::io::silent::SilentFileData , core::io::silent::SilentStruct
• strict_looprelax_checks() : protocols::loops::Loops
• strict_looprelax_checks_on_file_reads_ : protocols::loops::Loops
• strict_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• strict_movemap_ : protocols::abinitio::KinematicControl
• stride() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• stride_ : protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::TrajectoryRecorder , protocols::features::TrajectoryReportToDB , protocols::qsar::RenderGridsToKinemage
• stride_feature() : core::scoring::methods::ProQ_Energy
• String : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::VallResidue
• string : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentStruct
• String : core::pose::PDBInfo
• string : core::scoring::dna::DirectReadoutPotential
• String : core::select::util::SelectResiduesByLayer , core::sequence::ABEGO , core::sequence::ABEGOManager
• string : core::sequence::ChemicalShiftSequence , core::sequence::CompositeSequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• String : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::DesignTask , protocols::flxbb::FilterStructs , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frag_picker::VallResidue , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SSElementMotifContactFilter
• string : protocols::simple_moves::ExtendedPoseMover
• String : protocols::simple_moves::GenericMonteCarloMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• string_around_resnums_ : protocols::simple_filters::EnergyPerResidueFilter
• string_blosum() : protocols::sewing::Assembly
• string_exclude_resnums_ : protocols::simple_moves::FavorSequenceProfile
• string_from_property() : core::chemical::AtomPropertiesManager
• string_groups : core::indexed_structure_store::FragmentStore
• string_key_ : protocols::simple_moves::AddJobPairData
• string_list() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• STRING_MAP : core::pose::datacache::CacheableDataType
• string_path() : protocols::sewing::Assembly
• string_properties() : core::chemical::ResidueProperties
• string_properties_ : core::chemical::ResidueProperties
• string_real_pairs_ : protocols::jd2::Job
• string_refine() : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• string_refine_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• string_rep() : protocols::contact_map::Contact , protocols::contact_map::ContactPartner
• string_resnums_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::toolbox::task_operations::DesignAroundOperation
• string_string_map() : protocols::jd3::PoseInputSource
• string_string_map_ : protocols::jd3::PoseInputSource
• string_string_pairs_ : protocols::jd2::Job
• string_target_seqpos_ : protocols::toolbox::task_operations::InteractingRotamerExplosion
• string_to_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• string_to_compound_token() : core::io::HeaderInformation
• string_to_enum_ : protocols::antibody::clusters::CDRClusterEnumManager
• string_to_experimental_technique() : core::io::HeaderInformation
• string_to_farray() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• string_to_property_map() : core::chemical::AtomPropertiesManager
• string_to_property_map_ : core::chemical::AtomPropertiesManager
• string_to_record_type_map_ : core::io::pdb::RecordCollection
• string_value() : core::io::silent::SilentEnergy , protocols::simple_moves::AddJobPairData
• string_value_ : core::io::silent::SilentEnergy , protocols::simple_moves::AddJobPairData
• StringList : protocols::sparta::GDB
• StringRealPairs : protocols::jd2::Job
• Strings : core::io::StructFileRep , protocols::dna::PDBOutput , protocols::jd2::Job , protocols::moves::Mover
• StringsMap : protocols::dna::PDBOutput
• StringStringMap : protocols::jd3::PoseInputSource
• StringStringPairs : protocols::jd2::Job
• StringToSizePairMap : protocols::environment::EnvClaimBroker
• StringToStringPairMap : protocols::environment::EnvClaimBroker
• strip_existing_glycans_ : protocols::carbohydrates::SimpleGlycosylateMover
• StrongWolfe() : core::optimization::StrongWolfeLineMinimization
• StrongWolfeLineMinimization() : core::optimization::StrongWolfeLineMinimization
• struct_file_rep() : core::import_pose::PDBSilentStruct
• struct_from_job() : protocols::jd2::LazySilentFileJobInputter , protocols::jd2::SilentFileJobInputter
• struct_id : protocols::sewing::segment
• struct_id1_ : protocols::rotamer_recovery::RRReporterSQLite
• struct_id_selection_ : protocols::qsar::qsarOptFunc
• StructAvrgMover() : protocols::mpi_refinement::StructAvrgMover
• StructFileReaderOptions() : core::io::StructFileReaderOptions
• StructFileRep() : core::io::StructFileRep
• StructFileRepOptions() : core::io::StructFileRepOptions
• StructPerturberCM() : protocols::abinitio::abscript::StructPerturberCM
• StructProfileMover() : protocols::simple_moves::StructProfileMover
• STRUCTURAL_CONSERVATION : core::pose::datacache::CacheableDataType
• StructuralSimilarityEvaluator() : protocols::simple_filters::StructuralSimilarityEvaluator
• structure() : core::io::rna::RDAT
• structure_ : core::io::rna::RDAT
• structure_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• structure_has_moved() : core::scoring::Energies
• structure_id_ : protocols::sewing::Model
• structure_input_tag_ : protocols::features::ReportToDB
• structure_is_outdated_ : core::pose::metrics::PoseMetricContainer , core::pose::metrics::StructureDependentCalculator
• structure_list() : core::io::silent::SilentFileData
• structure_list_ : core::io::silent::SilentFileData
• structure_map_ : core::io::raw_data::RawFileData , core::io::silent::SilentFileData , protocols::features::ProteinSilentReport
• structure_moved() : core::conformation::Conformation
• structure_moved_ : core::conformation::Conformation
• structure_score : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy
• structure_scores_features_ : protocols::features::ProteinSilentReport
• structure_tag_ : protocols::features::ReportToDB
• StructureData() : protocols::denovo_design::components::StructureData
• StructureDependentCalculator() : core::pose::metrics::StructureDependentCalculator
• StructureDependentPeakCalibrator() : protocols::noesy_assign::StructureDependentPeakCalibrator
• StructureFeatures() : protocols::features::StructureFeatures
• StructureFeaturesCreator() : protocols::features::StructureFeaturesCreator
• StructureIndependentPeakCalibrator() : protocols::noesy_assign::StructureIndependentPeakCalibrator
• StructureMap : protocols::abinitio::StructureStore , protocols::features::ProteinSilentReport
• StructureOutputMode : protocols::hotspot_hashing::movers::PlaceProbeMover
• StructureRestrictor() : protocols::moves::StructureRestrictor
• structures() : core::io::rna::RDAT
• structures_ : core::io::rna::RDAT , protocols::noesy_assign::StructureDependentPeakCalibrator
• structures_per_cluster_ : protocols::pose_selectors::ClusterPoseSelector
• StructureScoresFeatures() : protocols::features::StructureScoresFeatures
• StructureScoresFeaturesCreator() : protocols::features::StructureScoresFeaturesCreator
• StructureSimilarityEvaluatorCreator() : protocols::simple_filters::StructureSimilarityEvaluatorCreator
• StructureStoreManager() : core::indexed_structure_store::StructureStoreManager
• Stub() : core::kinematics::Stub
• stub1_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub2_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub3_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub_ : protocols::stepwise::screener::StubApplier
• stub_abego_ : protocols::pose_length_moves::PossibleLoop
• stub_anchor_rsd_ : protocols::cyclic_peptide::PeptideStubMover
• stub_anchor_rsd_connecting_atom_ : protocols::cyclic_peptide::PeptideStubMover
• 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_ : core::chemical::Adduct , core::chemical::AtomICoor
• 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_ : core::chemical::Adduct , core::chemical::AtomICoor
• 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_ : core::chemical::Adduct , core::chemical::AtomICoor
• stub_atom3_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_based_atom_tree() : protocols::protein_interface_design::movers::PlaceStubMover
• stub_defined() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_energy_fxn_ : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• stub_energy_threshold_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• stub_from_id() : core::conformation::Conformation , core::kinematics::AtomTree , core::pose::Pose
• stub_index_ : protocols::pose_length_moves::PossibleLoop
• stub_insert_pos_ : protocols::cyclic_peptide::PeptideStubMover
• stub_minimize_movers() : protocols::protein_interface_design::movers::PlaceStubMover
• stub_minimize_movers_ : protocols::protein_interface_design::movers::PlaceStubMover
• stub_mode_ : protocols::cyclic_peptide::PeptideStubMover
• stub_offset() : protocols::hotspot_hashing::HotspotStubSet
• stub_rmsd_ : protocols::pose_length_moves::PossibleLoop
• stub_rsd_connecting_atom_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_jumping_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_names_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_repeat_ : protocols::cyclic_peptide::PeptideStubMover
• stub_score_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_set_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceStubMover
• stub_set_filters_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_set_vec_ : protocols::hotspot_hashing::HotspotStubSet
• stub_sets() : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_sets_ : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• StubApplier() : protocols::stepwise::screener::StubApplier
• StubDistanceScreener() : protocols::stepwise::screener::StubDistanceScreener
• StubGenerator() : protocols::hotspot_hashing::StubGenerator
• StubID() : core::id::StubID , core::kinematics::AtomTree
• StubMinimize() : protocols::protein_interface_design::movers::PlaceStubMover
• stubs_intra_residue() : protocols::environment::claims::JumpClaim
• stubs_intra_residue_ : protocols::environment::claims::JumpClaim
• StubScoreFilter() : protocols::protein_interface_design::filters::StubScoreFilter
• StubScoreLoopsFilter() : protocols::protein_interface_design::filters::StubScoreLoopsFilter
• StubsetStubPair : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• StubSetStubPos : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stuck_in_network_state_loop() : core::pack::annealer::FASTERAnnealer
• stwist_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• style_ : protocols::loops::loop_mover::LoopCM
• sub_filters_ : core::pack::task::operation::ResFilterComposition
• sub_matrix_ : protocols::frag_picker::scores::ProfileScoreSubMatrix
• sub_ndx_deque_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• sub_rank() : protocols::jd2::MPIMultiCommJobDistributor
• sub_rank_ : protocols::jd2::MPIMultiCommJobDistributor
• sub_to_full() : core::pose::full_model_info::FullModelInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• sub_to_full_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• SubArc() : core::scoring::sc::MolecularSurfaceCalculator
• subbin_cdf_i() : core::scoring::bin_transitions::BinTransitionData
• subbin_cdf_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_cdf_iplus1() : 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_ranges_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_ranges_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_i_ : core::scoring::bin_transitions::BinTransitionData
• subbin_type_iplus1() : core::scoring::bin_transitions::BinTransitionData
• subbin_type_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• SubCir() : core::scoring::sc::MolecularSurfaceCalculator
• subclusters_ : protocols::toolbox::KClusterElement
• subdir() : protocols::farna::libraries::BasePairStepSequence
• SubDiv() : core::scoring::sc::MolecularSurfaceCalculator
• subexpression_name_dec_line_ : protocols::pack_daemon::EntityFunc
• subexpression_name_map_ : protocols::pack_daemon::EntityFunc
• subfilter() : protocols::filters::ReplicateFilter
• subfilter_ : protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter
• SubgraphContainer : core::pack::interaction_graph::MultiplexedAnnealableGraph
• subgraphs : core::pack::interaction_graph::MultiplexedAnnealableGraph
• SUBjump_ : protocols::cryst::DockLatticeMover
• submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• submatrix_size() : core::pack::interaction_graph::DoubleLazyEdge
• subMatrixFile_ : protocols::frag_picker::scores::ProfileScoreSubMatrix
• submotif_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• submotif_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• submotif_info() : core::pose::full_model_info::FullModelInfo
• submotif_info_containing_residues() : core::pose::full_model_info::FullModelInfo
• submotif_info_list() : core::pose::full_model_info::FullModelInfo
• submotif_info_list_ : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• submotif_library() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• submotif_library_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• submotif_mappings_by_sequence_set_ : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• submotif_poses_by_tag_ : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• submotif_sequence_sets_ : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• submotif_tag() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• submotif_tag_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• SubMotifInfo() : core::pose::full_model_info::SubMotifInfo
• SubMotifLibrary() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• submover() : protocols::moves::IteratedConvergenceMover
• submover_ : protocols::filters::MoveBeforeFilter , protocols::moves::IteratedConvergenceMover
• subpools_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• subprio() : protocols::environment::claims::ClaimStrength
• subprio_ : protocols::environment::claims::ClaimStrength
• SubroutineMover() : protocols::protein_interface_design::movers::SubroutineMover
• subsample_hits() : protocols::match::Matcher
• subset() : protocols::hotspot_hashing::HotspotStubSet
• Subsitution : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• substituent_full_name : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• substitute_variables() : protocols::denovo_design::components::StructureData
• substitute_variables_in_stream() : protocols::rosetta_scripts::RosettaScriptsParser
• SUBTARGET : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• subtarget_ : protocols::pockets::CCluster , protocols::pockets::PCluster
• subtract() : protocols::match::Bool3DGrid
• subtract_neighbors_mass() : core::scoring::TenANeighborNode
• subtree_interaction_sphere_square_radius() : core::scoring::trie::TrieNode< AT, CPDATA >
• subtree_intxn_sphere_radius_sqr_ : core::scoring::trie::TrieNode< AT, CPDATA >
• subtype() : protocols::environment::claims::ClaimStrength
• subtype_ : protocols::environment::claims::ClaimStrength
• subunit_index() : core::conformation::symmetry::SymmetryInfo
• subunit_num_to_virt_id_ : core::conformation::symmetry::SymmData
• subunit_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• subunits() : core::conformation::symmetry::SymmetryInfo
• subunits_ : core::conformation::symmetry::SymmData
• subunits_moved_by_jump() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• success() : protocols::hybridization::InsertChunkMover , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• success_ : protocols::hybridization::InsertChunkMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• successful_loop_closure() : protocols::motifs::IRCollection
• successfully_initialized_ : protocols::canonical_sampling::HamiltonianExchange
• SuckerEnergy() : core::scoring::methods::SuckerEnergy
• suffix_ : protocols::jd2::JobOutputter , protocols::matdes::ExtractSubposeMover
• sugar_edge_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• sugar_edge_paired_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• sugar_modeling_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• sugar_modeling_sets_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• sugar_rotamer_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• sugar_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sugar_screening_pose_ : protocols::stepwise::screener::AnchorSugarScreener
• sugar_set() : core::io::NomenclatureManager
• sugar_set_ : core::io::NomenclatureManager
• sugar_setup_success_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• SugarBackboneEnergy() : core::scoring::methods::carbohydrates::SugarBackboneEnergy
• SugarBBSampler() : protocols::simple_moves::bb_sampler::SugarBBSampler
• SugarInstantiateMover() : protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover
• SugarInstantiator() : protocols::stepwise::screener::SugarInstantiator
• SugarModeling() : protocols::stepwise::modeler::rna::sugar::SugarModeling
• SugarVirtualizeMover() : protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover
• suggest_residue_number() : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• suggest_topology() : protocols::abinitio::PairingStatistics
• SuggestValueMessage() : protocols::topology_broker::SuggestValueMessage
• suite_cluster_radius_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• suite_num_ : protocols::stepwise::monte_carlo::mover::AddMover
• suite_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite
• suite_undefined : core::pose::rna::RNA_SuiteName
• suitename_ : core::scoring::rna::RNA_JR_SuiteEnergy , protocols::stepwise::sampler::screener::RNA_TorsionScreener
• suiteness : core::pose::rna::RNA_SuiteAssignment
• suiteness_bonus() : core::scoring::rna::RNA_EnergyMethodOptions
• suiteness_bonus_ : core::scoring::rna::RNA_EnergyMethodOptions
• sulfur_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• sum() : core::grid::CartGrid< T > , core::scoring::EMapVector , protocols::cluster::DataPoint , protocols::ddg::ddGMover , protocols::frag_picker::scores::AdaptiveScoreHistogram
• sum_all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• sum_ddG() : protocols::simple_moves::ddG
• sum_deriv_contributions_for_heavyatom_pair() : core::scoring::lkball::LK_BallEnergy
• sum_deriv_contributions_for_heavyatom_pair_one_way() : core::scoring::lkball::LK_BallEnergy
• sum_energies() : core::scoring::etable::EtableEvaluator
• sum_Hbond_terms() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• sum_obs_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• sum_of_neighbors_masses() : core::scoring::TenANeighborNode
• sum_of_neighbors_masses_ : core::scoring::TenANeighborNode
• sum_probabilities() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• 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
• summary_lines() : protocols::residue_optimization::MetapatchEnumeration
• summary_lines_ : protocols::residue_optimization::MetapatchEnumeration
• sumName : protocols::sparta::Sparta::SpartaLib
• Super : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::conformation::signals::XYZEvent , core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pose::datacache::CacheableObserver , core::pose::datacache::ObserverCache , core::pose::PDBInfo , core::pose::PDBPoseMap , core::pose::signals::ConformationEvent , core::pose::signals::EnergyEvent , protocols::enzdes::EnzdesFlexibleRegion , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• Super2 : core::fragment::IndependentBBTorsionSRFD
• super_quick_relax_of_centroids() : protocols::abinitio::IterativeBase
• super_quick_relax_of_centroids_ : protocols::abinitio::IterativeBase
• super_secret_fixed_interface_mode_ : protocols::anchored_design::AnchorMoversData
• superenv() : core::environment::EnvCore , protocols::environment::Environment
• superenv_ : core::environment::EnvCore
• superimpose() : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_moves::SuperimposeMover , protocols::toolbox::DecoySetEvaluation , protocols::topology_broker::CoordConstraintClaimer
• superimpose_ : protocols::fldsgn::MatchResiduesMover , protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::LoopRmsdEvaluator
• superimpose_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_comb() : protocols::fldsgn::MatchResidues
• superimpose_on_all() : protocols::protein_interface_design::filters::RmsdFilter
• superimpose_on_all_ : protocols::protein_interface_design::filters::RmsdFilter
• superimpose_over_all() : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::setup::StepWiseJobDistributor
• superimpose_over_all_ : protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::setup::StepWiseJobDistributor
• superimpose_over_all_instantiated() : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_over_all_instantiated_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_pose_on_template() : protocols::simple_filters::SSMotifFinder
• superimpose_recursively() : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_regions_ : protocols::topology_broker::CoordConstraintClaimer
• superimpose_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• superimpose_res_in_pose() : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_res_in_pose_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_rmsd() : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_rmsd_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_strand_pairings_to_templates() : protocols::hybridization::FoldTreeHybridize
• superimpose_to_ref() : protocols::mpi_refinement::WorkUnit_Sampler
• superimpose_to_single_user_input_chunk() : protocols::farna::libraries::RNA_ChunkLibrary
• superimpose_upstream_partner() : protocols::docking::membrane::MPFindInterfaceMover
• superimposebb() : protocols::simple_moves::SuperimposeMover
• SuperimposeMover() : protocols::simple_moves::SuperimposeMover
• superposition_bonus_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• superposition_transform() : protocols::motif_grafting::movers::MotifGraftMover , protocols::protein_interface_design::filters::RmsdSimpleFilter
• supervoxel_dimprods_ : protocols::match::Bool3DGrid
• supervoxel_dimsizes_ : protocols::match::Bool3DGrid
• suppress_bp_constraint() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• suppress_bp_constraint_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• suppress_zero_occ_pdb_output() : core::io::StructFileRepOptions
• suppress_zero_occ_pdb_output_ : core::io::StructFileRepOptions
• surf() : core::scoring::packing::PoseBalls , core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• surf_ : core::scoring::packing::PoseBalls
• surf_dist_ : protocols::pockets::PocketGrid
• surf_feature() : core::scoring::methods::ProQ_Energy
• surf_score_ : protocols::pockets::PocketGrid
• SURFA0_ : protocols::surface_docking::SurfaceParameters
• SURFA1_ : protocols::surface_docking::SurfaceParameters
• SURFA2_ : protocols::surface_docking::SurfaceParameters
• surface : core::scoring::sc::_RESULTS
• SURFACE : protocols::pockets::ElectrostaticpotentialGrid
• surface_ : core::select::util::SelectResiduesByLayer , protocols::toolbox::task_operations::SelectBySASAOperation
• surface_accessibility : core::scoring::packstat::CavityBallCluster
• surface_accessibility_ : protocols::analysis::PackStatMover
• surface_area : core::scoring::packstat::CavityBallCluster
• surface_area_ : core::scoring::packstat::LeeRichards
• surface_asa_ : protocols::toolbox::task_operations::SelectBySASAOperation
• surface_contact_mover_ : protocols::surface_docking::FullatomRelaxMover
• surface_density_ : protocols::hotspot_hashing::SurfaceSearchPattern
• surface_energy_weight_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_exposed() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_exposed_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• SURFACE_EXPOSED_CUTOFF : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• surface_exposed_nb_cutoff() : protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
• surface_exposed_nb_cutoff_ : protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
• SURFACE_EXPOSURE : protocols::sparta::Sparta::SpartaLib
• surface_exposure_ : protocols::toolbox::pose_metric_calculators::SequenceComparison
• surface_orient_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• surface_parameters_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover
• SURFACE_PARAMS : core::pose::datacache::CacheableDataType
• SURFACE_SCORE_BIN_SIZE : core::pack::interaction_graph::SurfacePotential
• surface_score_min_last_100_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_score_min_recent_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• surface_score_weight() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• surface_score_weight_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• surface_selection_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• surface_vectors() : protocols::hotspot_hashing::SurfaceSearchPattern
• surface_vectors_ : protocols::hotspot_hashing::SurfaceSearchPattern
• SurfaceBackgroundEdge() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• SurfaceBackgroundNode() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• SurfaceCalculator() : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• SurfaceDockingProtocol() : protocols::surface_docking::SurfaceDockingProtocol
• SurfaceEdge() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• SurfaceEnergies() : core::scoring::solid_surface::SurfaceEnergies
• SurfaceEnergy() : core::pack::interaction_graph::SurfaceEnergy
• SurfaceExposureMap : protocols::sparta::Sparta::SpartaLib
• SurfaceInteractionGraph() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• SurfaceNode() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• SurfaceOrientMover() : protocols::surface_docking::SurfaceOrientMover
• SurfaceParameters() : protocols::surface_docking::SurfaceParameters
• SurfacePotential() : core::pack::interaction_graph::SurfacePotential
• SurfaceSearchPattern() : protocols::hotspot_hashing::SurfaceSearchPattern
• SurfaceVectorFallbackConfiguration() : protocols::surface_docking::SurfaceVectorFallbackConfiguration
• SurfaceVectorLoader() : protocols::surface_docking::SurfaceVectorLoader
• SurfaceVectorOptions() : protocols::surface_docking::SurfaceVectorOptions
• SurfEnergy() : core::scoring::packing::SurfEnergy
• SurfPrec : protocols::sparta::PDB
• SurfVolEnergy() : core::scoring::packing::SurfVolEnergy
• surrogate_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• SurrogateVariableExpression() : protocols::pack_daemon::SurrogateVariableExpression
• surrounding_sasa_smoothing_window : core::scoring::packstat::SasaOptions
• SurroundingSS() : protocols::denovo_design::task_operations::SurroundingSS
• sutbp_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::ScoringManager
• svbksb() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• svd_s_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• svdcmp() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• svm_energies : protocols::simple_filters::nmer_svm_res_data
• svm_model_ : core::scoring::ProQPotential
• SVNVersion() : core::SVNVersion
• sw_can_by_sh_id_ : protocols::features::strand_assembly::SandwichFragment
• swa_move_ : protocols::stepwise::monte_carlo::mover::AddMover
• swa_move_selector_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::ResampleMover
• swa_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• swa_moves_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• swap : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• swap_atoms() : protocols::noesy_assign::FragsToAtomDist
• swap_buffer_ : protocols::wum::WorkUnitQueue_Swapped
• swap_chain() : protocols::seeded_abinitio::SwapSegment , protocols::simple_moves::AddChainMover
• swap_chain_ : protocols::seeded_abinitio::SwapSegment
• swap_chain_number() : protocols::simple_moves::AddChainMover
• swap_chain_number_ : protocols::simple_moves::AddChainMover
• swap_coordinates_in_pose() : protocols::enzdes::ModifyStoredRBConfs
• swap_edge_energies() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph
• swap_file() : protocols::wum::WorkUnitQueue_Swapped
• swap_file_ : protocols::wum::WorkUnitQueue_Swapped
• swap_in() : protocols::forge::build::SegmentSwap
• swap_in_ : protocols::forge::build::SegmentSwap
• swap_in_movemap() : protocols::forge::build::SegmentSwap
• swap_in_movemap_ : protocols::forge::build::SegmentSwap
• swap_invite_recv_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• swap_invite_send_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• swap_replicas() : protocols::canonical_sampling::BiasEnergy
• swap_residue_types() : protocols::simple_moves::ResTypeFragmentMover
• swap_segment() : protocols::seeded_abinitio::SwapSegment
• swap_segment_ : protocols::seeded_abinitio::SwapSegment
• SwapSegment() : protocols::seeded_abinitio::SwapSegment
• sweep_incomplete() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sweep_iterator_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_nonpivot_torsion_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sweep_nonpivot_torsion_starts_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_step_sizes_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_torsion_ids_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• swell_bounding_box() : protocols::match::downstream::ActiveSiteGrid
• swin : core::scoring::APBSConfig::R_PARAM
• switch_conformer() : protocols::docking::ConformerSwitchMover
• switch_edge() : protocols::sewing::MonteCarloAssemblyMover
• switch_focus_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• switch_focus_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• switch_movemap() : protocols::loops::Loop , protocols::loops::Loops
• switch_probability_ : protocols::sewing::MonteCarloAssemblyMover
• switch_residue_type_set() : protocols::denovo_design::components::StructureData , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• switch_to_fullatom() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• SwitchChainOrderMover() : protocols::simple_moves::SwitchChainOrderMover
• SwitchResidueTypeSetMover() : protocols::simple_moves::SwitchResidueTypeSetMover
• sym1 : core::io::SSBondInformation
• sym2 : core::io::SSBondInformation
• sym_docking_mover_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• sym_dof_name() : protocols::matdes::GetRBDOFValues , protocols::simple_filters::ShapeComplementarityFilter
• sym_dof_name_ : protocols::matdes::GetRBDOFValues , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::simple_filters::ShapeComplementarityFilter
• sym_dof_names() : protocols::matdes::ClashCheckFilter , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• sym_dof_names_ : protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::matdes::SymUnsatHbondFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectBySASAOperation
• sym_rotamer_sets_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• SymAtomTreeMinimizer() : core::optimization::symmetry::SymAtomTreeMinimizer
• SymAtomTreeMultifunc() : core::optimization::symmetry::SymAtomTreeMultifunc
• symbol2index() : core::sequence::ABEGOManager
• symbolString2base5index() : core::sequence::ABEGOManager
• SymDockBaseProtocol() : protocols::symmetric_docking::SymDockBaseProtocol
• SymDockingHiRes() : protocols::symmetric_docking::SymDockingHiRes
• SymDockingInitialPerturbation() : protocols::simple_moves::symmetry::SymDockingInitialPerturbation
• SymDockingLowRes() : protocols::symmetric_docking::SymDockingLowRes
• SymDockingSlideIntoContact() : protocols::simple_moves::symmetry::SymDockingSlideIntoContact
• SymDockProtocol() : protocols::symmetric_docking::SymDockProtocol
• SymDof() : core::conformation::symmetry::SymDof
• SymDofMover() : protocols::matdes::SymDofMover
• SymDofMoverSampler() : protocols::matdes::SymDofMoverSampler
• symdofs_ : protocols::cryst::DockLatticeMover
• symEnergy() : core::scoring::sym_e::symEnergy
• SymEnergyCutRotamerTrialsMover() : protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• SymFoldandDockMoveRbJumpMover() : protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover
• SymFoldandDockRbTrialMover() : protocols::symmetric_docking::SymFoldandDockRbTrialMover
• SymFoldandDockSlideTrialMover() : protocols::symmetric_docking::SymFoldandDockSlideTrialMover
• SymInterfaceSidechainMinMover() : protocols::symmetric_docking::SymInterfaceSidechainMinMover
• symm_axes : protocols::simple_filters::SymmetricMotifFilter
• symm_data_ : protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::SymmetryClaimer
• symm_def_file_ : protocols::hybridization::MRMover
• symm_definition_file_ : protocols::symmetric_docking::SymDockBaseProtocol
• symm_file_ : protocols::matdes::SymDofMover
• symm_info() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symm_info_ : core::conformation::symmetry::SymmetricConformation , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symm_min_map_ : core::optimization::symmetry::SymAtomTreeMultifunc
• symm_orders : protocols::simple_filters::SymmetricMotifFilter
• symm_transforms_ : core::conformation::symmetry::SymmData
• symm_type_ : protocols::simple_filters::SymmetricMotifFilter
• symmap : core::scoring::electron_density::ElectronDensity
• SymmData() : core::conformation::symmetry::SymmData
• symmdata_ : protocols::simple_filters::RelativePoseFilter
• SymmDataOptions() : core::conformation::symmetry::SymmDataOptions
• SymmDataOptionsCreator() : core::conformation::symmetry::SymmDataOptionsCreator
• symmdef_ : protocols::simple_moves::symmetry::SetupForSymmetryMover
• symmdef_files_ : protocols::hybridization::HybridizeProtocol
• symmetric_gly_tables() : core::scoring::methods::EnergyMethodOptions
• symmetric_gly_tables_ : core::scoring::methods::EnergyMethodOptions
• symmetric_ig_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symmetric_protein_calculate() : protocols::scoring::Interface
• symmetric_rmsd_ : protocols::relax::FastRelax
• symmetric_secstruct() : protocols::fldsgn::potentials::SetSecStructEnergies
• symmetric_sequence() : protocols::simple_moves::symmetry::SetupNCSMover
• symmetric_sequence_ : protocols::simple_moves::symmetry::SetupNCSMover
• symmetric_task() : protocols::toolbox::task_operations::RestrictToInterface
• symmetric_task_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symmetric_transform() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetric_transforms_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetric_units_ : protocols::simple_moves::FavorSymmetricSequence
• SymmetricAddMembraneMover() : protocols::membrane::symmetry::SymmetricAddMembraneMover
• symmetrical_allow_hbonds() : core::scoring::symmetry::SymmetricScoreFunction
• SymmetricConformation() : core::conformation::symmetry::SymmetricConformation , core::optimization::symmetry::SymAtomTreeMinimizer , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::scoring::SecondaryStructurePotential , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymmetricRMSMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover
• SymmetricEnergies() : core::scoring::symmetry::SymmetricEnergies
• SymmetricFragmentMover() : protocols::simple_moves::SymmetricFragmentMover
• SymmetricLigandEnergy() : core::scoring::methods::SymmetricLigandEnergy
• SymmetricMotifFilter() : protocols::simple_filters::SymmetricMotifFilter
• SymmetricRmsdEvaluator() : protocols::simple_filters::SymmetricRmsdEvaluator
• SymmetricRMSMover() : protocols::simple_moves::symmetry::SymmetricRMSMover
• SymmetricRotamerSet_() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• SymmetricRotamerSets() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• SymmetricScoreFunction : core::scoring::ScoreFunctionFactory , 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_
• symmetrize_gly_table() : core::scoring::P_AA , core::scoring::Ramachandran , core::scoring::RamaPrePro
• symmetry() : protocols::helical_bundle::MakeBundle
• symmetry_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::simple_filters::AlaScan , protocols::simple_moves::DesignRepackMover
• symmetry_compliance() : protocols::noesy_assign::PeakAssignment
• symmetry_compliance_ : protocols::noesy_assign::PeakAssignment
• symmetry_compliance_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• symmetry_copies() : protocols::helical_bundle::MakeBundle
• symmetry_definition() : protocols::simple_filters::RelativePoseFilter
• symmetry_definition_ : protocols::simple_filters::RelativePoseFilter
• symmetry_duplicate() : protocols::topology_broker::SymmetryClaimer
• Symmetry_Info() : core::conformation::symmetry::SymmetricConformation
• symmetry_info() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• symmetry_name_ : core::conformation::symmetry::SymmData
• symmetry_status_ : core::pack::task::PackerTask_
• symmetry_type_ : core::conformation::symmetry::SymmData
• SymmetryClaim() : protocols::topology_broker::claims::SymmetryClaim
• SymmetryClaimer() : protocols::topology_broker::SymmetryClaimer
• SymmetryInfo() : core::conformation::symmetry::SymmetryInfo , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover
• SymmetryInfoCOP : core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::scoring::SecondaryStructurePotential , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction
• SymmetryInfoOP : core::optimization::symmetry::SymAtomTreeMinimizer , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::simple_moves::symmetry::SymmetricRMSMover
• SymmetrySlider() : protocols::simple_moves::symmetry::SymmetrySlider
• SymmetryTransform() : core::conformation::symmetry::SymmetryTransform
• symminfo_ : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , protocols::hybridization::FragmentBiasAssigner , protocols::topology_broker::FibrilModelingClaimer
• SymMinimizerMap() : core::optimization::symmetry::SymMinimizerMap
• SymMinMover() : protocols::simple_moves::symmetry::SymMinMover
• 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
• symmop() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• symmOps : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• symmops() : protocols::cryst::MakeLatticeMover , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• symmops_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• symmRotOps : core::scoring::electron_density::ElectronDensity
• SymPackRotamersMover() : protocols::simple_moves::symmetry::SymPackRotamersMover
• SymRestrictTaskForDocking() : protocols::symmetric_docking::SymRestrictTaskForDocking
• SymRotamerTrialsMover() : protocols::simple_moves::symmetry::SymRotamerTrialsMover
• SymShakeStructureMover() : protocols::simple_moves::symmetry::SymShakeStructureMover
• SymSidechainMinMover() : protocols::symmetric_docking::SymSidechainMinMover
• SymSlideInfo() : core::conformation::symmetry::SymSlideInfo
• SymUnsatHbondFilter() : protocols::matdes::SymUnsatHbondFilter
• syn_G_potential_bonus() : core::scoring::rna::RNA_EnergyMethodOptions
• syn_G_potential_bonus_ : core::scoring::rna::RNA_EnergyMethodOptions , core::scoring::rna::RNA_TorsionPotential
• sync_batches() : protocols::jd2::archive::MPIArchiveJobDistributor
• sync_objects_with_flags() : protocols::antibody::AntibodyModelerProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• synch_mirror_jumps_with_atomtree() : core::conformation::symmetry::MirrorSymmetricConformation
• SYNONYM : core::io::HeaderInformation