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

- s -

• s : core::optimization::lbfgs_iteration_data
• 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_ik : protocols::cluster::Exemplar
• s_kk : protocols::cluster::DataPoint
• s_mean : core::scoring::sc::_RESULTS
• s_median : core::scoring::sc::_RESULTS
• S_p_sp3 : core::scoring::orbitals::OrbitalsStatistics
• s_stub1_ : core::chemical::orbitals::ICoorOrbitalData
• s_stub2_ : core::chemical::orbitals::ICoorOrbitalData
• s_stub3_ : core::chemical::orbitals::ICoorOrbitalData
• 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_max_dis2 : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::etable::BaseEtableEnergy< Derived >
• safe_max_dis2_ : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack , core::scoring::rna::RNA_LJ_BaseEnergy
• safe_root_ : protocols::forge::remodel::WorkingRemodelSet
• safe_secstruct() : protocols::jumping::JumpSample
• safely_append_polymer_residue_after_seqpos() : core::conformation::Conformation
• safely_prepend_polymer_residue_before_seqpos() : core::conformation::Conformation
• salt_bridge_total_ : protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• SaltBridgeCalculator() : protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• SaltBridgeFeatures() : protocols::features::SaltBridgeFeatures
• SaltBridgeFeaturesCreator() : protocols::features::SaltBridgeFeaturesCreator
• same() : protocols::simple_moves::MinimalRotamer
• same_build_resids_for_all_csts_ : protocols::match::Matcher
• same_chain() : protocols::frag_picker::FragmentCandidate
• 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::SymmetricConformation , core::scoring::Energies , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies
• SameChiBinComboGrouper() : protocols::match::output::SameChiBinComboGrouper
• SameRotamerComboGrouper() : protocols::match::output::SameRotamerComboGrouper
• SameSequenceAndDSPositionGrouper() : protocols::match::output::SameSequenceAndDSPositionGrouper
• SameSequenceGrouper() : protocols::match::output::SameSequenceGrouper
• SameStrand() : protocols::jumping::SameStrand
• sample_all_o2star_ : protocols::swa::monte_carlo::RNA_O2StarMover
• sample_alternative_chain_connection() : protocols::rna::RNA_StructureParameters
• sample_both_sugar_base_rotamer_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• sample_chi_torsion_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• sample_cis_omega() : protocols::swa::protein::StepWiseProteinScreener
• sample_extra_rotamers_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• sample_generator_ : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinPacker
• sample_junction_ : protocols::swa::protein::StepWiseProteinPoseSetup
• 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_sugar_and_base_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• sample_native_torsion_ : protocols::swa::rna::RNA_LoopCloseSampler
• sample_near_nucleoside_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• sample_near_o2star_torsion() : protocols::swa::monte_carlo::RNA_O2StarMover
• sample_near_suite_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• sample_nonpivot_torsions_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sample_o2star_hydrogen() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• sample_omega_for_pre_prolines_ : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• sample_omega_recursively() : protocols::swa::protein::StepWiseProteinLoopBridger
• sample_only_ : protocols::swa::rna::RNA_LoopCloseSampler
• sample_ONLY_multiple_virtual_sugar_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• sample_proton_chi() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• sample_proton_chi_ : core::pack::task::ResidueLevelTask_
• sample_range_large_ : protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_O2StarMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• sample_range_small_ : protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_O2StarMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• sample_residues() : protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::StepWiseResidueSampler , protocols::swa::protein::StepWiseProteinPacker
• sample_residues_recursively() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• sample_rna_chi() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• sample_rna_chi_ : core::pack::task::ResidueLevelTask_
• sample_rotwells_unif_ : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• sample_source_ : protocols::features::ReportToDB
• sample_strategy_for_chi() : protocols::match::upstream::BuildSet
• sample_strategy_for_chi_ : protocols::match::upstream::BuildSet
• sample_sugar : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• sample_sugar_and_base1_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• sample_sugar_and_base2_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• sample_type_ : protocols::enzdes::DiffAtomSasaFilter , protocols::simple_moves::GenericMonteCarloMover
• sample_types() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator
• sample_types_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::simple_moves::GenericMonteCarloMover
• sample_upper_sugar_and_base_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• sample_weight_const_ : protocols::loophash::LoopHashMoverWrapper
• sample_weight_str_ : protocols::loophash::MPI_LoopHashRefine_Master
• sampler_ : protocols::docking::TemperedDocking , protocols::match::upstream::ProteinUpstreamBuilder , protocols::nonlocal::Chunk
• samples() : protocols::match::upstream::ProteinSCSampler , protocols::match::upstream::DunbrackSCSampler
• samples_ : core::chemical::AddProtonChi , core::pack::rotamer_set::ContinuousRotamerSet
• SampleStrategyData() : protocols::match::upstream::SampleStrategyData
• sampling_fold_tree() : protocols::abinitio::KinematicControl
• sampling_fold_tree_ : protocols::abinitio::KinematicControl
• sampling_id_for_current_rotamer() : core::pack::rotamer_set::ContinuousRotamerSet
• sampling_protocol() : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicTaskControl
• sampling_protocol_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicTaskControl
• sampling_scorefxn_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• sampling_temperature() : protocols::simple_moves::sidechain_moves::SidechainMover
• sampling_temperature_ : protocols::simple_moves::sidechain_moves::SidechainMover
• samplingrot_offsets_ : core::pack::rotamer_set::ContinuousRotamerSet
• SaneMinMover() : protocols::simple_moves::SaneMinMover
• sanity_check() : core::conformation::symmetry::SymmData
• sasa : core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere , core::scoring::FACTSResidueInfo , protocols::features::helixAssembly::HelicalFragment
• sasa_ : core::pack::interaction_graph::RotamerDots , core::scoring::FACTSResidueInfo , protocols::features::helixAssembly::HelicalFragment
• Sasa_ : protocols::analysis::InterfaceAnalyzerMover
• sasa_arrays_initialized_ : core::pack::interaction_graph::RotamerDots
• sasa_core() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• sasa_cutoff_ : 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() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• sasa_threshold_ : protocols::simple_filters::ChiWellRmsdEvaluator
• SasaCalculator() : core::pose::metrics::simple_calculators::SasaCalculator
• SasaOptions() : core::scoring::packstat::SasaOptions
• SasaResult() : core::scoring::packstat::SasaResult
• satisfaction_cutoff() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• save_all_in_one() : protocols::toolbox::KClusterData
• save_all_solutions_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• save_archive() : protocols::jd2::archive::ArchiveManager
• 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_db() : protocols::loophash::LoopHashLibrary
• save_decoys() : protocols::abinitio::HedgeArchive
• save_energy() : core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::ResidueNeighborIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator
• save_fragments() : protocols::frag_picker::FragmentPicker
• save_in_jump_library() : protocols::rna::RNA_JumpLibrary
• save_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• save_momento() : core::pack::scmin::ResidueAtomTreeCollection
• save_phi_psi_offsets() : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::StepWisePoseSetup
• save_phi_psi_omega_over_loop_residues() : protocols::swa::protein::StepWiseProteinCCD_Closer
• save_rigid_body_settings() : protocols::swa::RigidBodySampler
• save_silent_struct() : protocols::swa::RigidBodySampler
• save_state() : protocols::loophash::MPI_LoopHashRefine , protocols::moves::Mover
• save_state_auto() : protocols::loophash::MPI_LoopHashRefine
• save_state_interval_ : protocols::loophash::MPI_LoopHashRefine
• save_status() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::DebugArchive
• save_to_checkpoint() : protocols::protein_interface_design::movers::Splice
• save_to_file() : protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::abinitio::IterativeAbrelax
• save_trial_number_to_checkpoint() : protocols::simple_moves::GenericMonteCarloMover
• save_values() : protocols::protein_interface_design::movers::Splice
• 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_fold_tree_ : protocols::protein_interface_design::movers::Splice
• saved_from_res_ : protocols::protein_interface_design::movers::Splice
• 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_to_res_ : protocols::protein_interface_design::movers::Splice
• 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
• SavePoseMover() : protocols::rosetta_scripts::SavePoseMover
• 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
• sc_min_ : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• sc_min_only : protocols::simple_moves::ShakeStructureMover
• sc_only() : protocols::hotspot_hashing::HotspotStubSet
• SC_ONLY : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• sc_only_ : protocols::hotspot_hashing::HotspotStubSet
• sc_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• sc_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• SC_SC_EnergyInvoker() : core::scoring::etable::SC_SC_EnergyInvoker< Evaluator >
• sc_value_ : protocols::analysis::InterfaceAnalyzerMover
• 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_match() : protocols::hotspot_hashing::HotspotStub
• scaffold_movemap_ : protocols::grafting::GraftMoverBase
• scaffold_status_ : protocols::hotspot_hashing::HotspotStub
• ScaffoldBuildPoint() : protocols::match::upstream::ScaffoldBuildPoint
• 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::constraints::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_factor() : core::scoring::GenBornResidueInfo , protocols::frag_picker::SidechainContactDistCutoff , protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scale_factor_ : 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
• ScaleAnnealerTemperatureOperation() : protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scaling() : protocols::protein_interface_design::movers::SetTemperatureFactor
• scaling_ : protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_moves::FavorSequenceProfile
• scan_output_and_setup_to_receive() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• 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
• schema() : protocols::features::FeaturesReporter
• scheme_types_ : core::sequence::ScoringSchemeFactory
• scmin_ : protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scmin_mover_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• scminmap_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• SCMinMinimizerMap() : core::pack::scmin::SCMinMinimizerMap
• SCMinMultifunc() : core::pack::scmin::SCMinMultifunc
• scNV_ : core::scoring::methods::ProClosureEnergy
• scOrb_scHpol_weight_ : core::scoring::orbitals::OrbitalsLookup
• scOrb_scOrb_weight_ : core::scoring::orbitals::OrbitalsLookup
• score() : 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::jd2::archive::DebugArchive , protocols::jd2::archive::EvaluatedArchive , protocols::loophash::MPI_LoopHashRefine , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::MatchEvaluator , protocols::nonlocal::SmoothPolicy::Candidate , protocols::pmut_scan::AlterSpecDisruptionDriver , protocols::pmut_scan::PointMutScanDriver , protocols::pockets::PocketConstraint , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::sic_dock::XfoxmScore , protocols::sic_dock::RigidScore , protocols::sic_dock::CBScore , protocols::sic_dock::LinkerScore , protocols::sic_dock::JointScore , protocols::simple_moves::GunnCost , protocols::simple_moves::FragmentCost , core::fragment::picking_old::vall::scores::VallFragmentScore , core::scoring::dna::DirectReadoutPotential , core::scoring::packing::HolesResult , protocols::hybridization::TMalign , protocols::sic_dock::CBScoreVisitor , protocols::simple_filters::SAXSScoreFilter , protocols::swa::rna::pose_data_struct2 , protocols::swa::rna::Cluster_Member , protocols::swa::rna::FB_Pose_Data , core::fragment::FragData , core::optimization::Particle , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::mm::MMBondAngleScore , core::scoring::mm::MMBondLengthScore , core::scoring::mm::MMLJEnergyTable , core::scoring::mm::MMLJScore , core::scoring::mm::MMTorsionScore , core::scoring::packstat::PackingScore , core::scoring::ScoreFunction , core::scoring::DimerPairing , core::scoring::SecondaryStructurePotential , core::sequence::ChemicalShiftScoringScheme , core::sequence::CompassScoringScheme , core::sequence::CompositeScoringScheme , core::sequence::Cell , 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::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::NatbiasSheetPotential , 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::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoringMethod
• score_ : core::fragment::FragData , core::scoring::DimerPairing , core::sequence::Cell , core::util::ChainbreakUtil , protocols::abinitio::Template , protocols::fldsgn::topology::DimerPairing , protocols::moves::MoverStatistics , protocols::nonlocal::SmoothPolicy::Candidate , 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::hackelec::HackElecEnergy
• score_bias_ : core::scoring::saxs::SAXSEnergy
• score_criteria_ : core::conformation::symmetry::SymSlideInfo
• score_cut_count : protocols::swa::rna::Filterer_Count
• score_cut_per_batch_ : protocols::abinitio::HedgeArchive
• score_cutoff_ : protocols::docking::DockingProtocol , protocols::swa::RigidBodySampler
• score_d2() : protocols::simple_filters::SymmetricMotifFilter
• score_d8 : protocols::hybridization::TMalign
• score_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• score_diff_cut_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• score_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential , core::scoring::disulfides::DisulfideMatchingPotential
• score_expression_ : protocols::pack_daemon::EntityFunc
• score_file() : protocols::jd2::archive::Batch
• score_file_tags_ : protocols::jd2::ScoreOnlyJobOutputter
• score_filt_ : protocols::loophash::LoopHashSampler
• score_filter : protocols::flexpep_docking::FlexPepDockingFlags , core::io::silent::SilentFileData
• 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_fun8() : protocols::hybridization::TMalign
• 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::ddg::ddGMover , protocols::dna::PDBOutput , protocols::medal::MedalMover , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::rna::RNA_Minimizer , protocols::rotamer_recovery::RotamerRecoveryMover , 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 , protocols::swa::RigidBodySampler
• 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::dna::PDBOutput , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::RotamerDump::RotamerDumpMover , protocols::simple_moves::ScoreMover
• score_function_info_ : core::scoring::ScoreFunction
• score_function_info_current_ : core::scoring::ScoreFunction
• score_fxn() : protocols::ligand_docking::InterfaceScoreCalculator
• score_fxn_ : protocols::forge::remodel::RemodelDesignMover , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator
• 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 : protocols::qsar::qsarOptData , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor
• SCORE_MAP : core::pose::datacache::CacheableDataType
• score_map_ : protocols::antibody::AntibodyModeler , protocols::ub_e2c::ubi_e2c_modeler , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::qsar::scoring_grid::GridManager , protocols::simple_moves::ScoreMover , protocols::symmetric_docking::SymDockProtocol
• 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_min_ : protocols::swa::StepWiseClusterer
• score_min_defined_ : protocols::swa::StepWiseClusterer
• 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_offset_ : protocols::canonical_sampling::SimulatedTempering
• score_only : protocols::flexpep_docking::FlexPepDockingFlags , protocols::outputter::SilentFileOutputter , protocols::symmetric_docking::SymDockProtocol
• score_only_ : protocols::enzdes::DetectProteinLigandInterface , protocols::outputter::SilentFileOutputter
• score_pairmatrix() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• score_pairmatrix_ : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• 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_stage5_ : protocols::abinitio::ClassicAbinitio
• score_stride_ : protocols::canonical_sampling::SilentTrajectoryRecorder
• score_subunit_ : core::conformation::symmetry::SymmData
• score_term_ : protocols::features::TopCountOfEachInput , protocols::features::TopCountOfAllInputs
• score_this_disulfide() : core::scoring::disulfides::FullatomDisulfidePotential
• score_threshold() : protocols::hotspot_hashing::HotspotStubSet
• score_threshold_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::PlaceStubMover
• 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::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter
• score_type2name_ : core::scoring::ScoreTypeManager
• score_type_ : core::scoring::constraints::Constraint , core::scoring::constraints::DOF_Constraint , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseEnergyContainer , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllEnergyContainer , protocols::canonical_sampling::PatchOperation , protocols::enzdes::EnzScoreFilter , protocols::moves::RampingMover , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ScoreTypeFilter
• 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_threshold_ : protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ScoreTypeFilter
• score_type_weights_ : core::scoring::methods::UnfoldedStateEnergy
• score_types() : core::scoring::methods::EnergyMethod
• score_types_ : core::scoring::methods::EnergyMethod , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedEnergyContainer , 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::DunbrackEnergyCreator , core::pack::interaction_graph::HPatchEnergyCreator , core::pack::interaction_graph::SurfaceEnergyCreator , core::scoring::carbon_hbonds::CarbonHBondEnergyCreator , core::scoring::constraints::ConstraintsEnergyCreator , 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::electron_density::ElecDensAllAtomCenEnergyCreator , core::scoring::electron_density::ElecDensCenEnergyCreator , core::scoring::electron_density::ElecDensEnergyCreator , core::scoring::electron_density::FastDensEnergyCreator , core::scoring::electron_density::PattersonCorrEnergyCreator , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator , core::scoring::etable::CoarseEtableEnergyCreator , core::scoring::etable::EtableEnergyCreator , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator , core::scoring::geometric_solvation::GeometricSolEnergyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator , core::scoring::hackaro::HackAroEnergyCreator , core::scoring::hackelec::HackElecEnergyAroAllCreator , core::scoring::hackelec::HackElecEnergyAroAroCreator , core::scoring::hackelec::HackElecEnergyCreator , core::scoring::hackelec::RNAHackElecEnergyCreator , core::scoring::hbonds::HBondEnergyCreator , core::scoring::interface::DDPscoreCreator , core::scoring::methods::BurialEnergyCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::ChainbreakEnergyCreator , core::scoring::methods::ChemicalShiftAnisotropyEnergyCreator , core::scoring::methods::ContactOrderEnergyCreator , core::scoring::methods::CustomAtomPairEnergyCreator , core::scoring::methods::dfire::DFIRE_EnergyCreator , core::scoring::methods::DipolarCouplingEnergyCreator , core::scoring::methods::DirectReadoutEnergyCreator , core::scoring::methods::DistanceChainbreakEnergyCreator , core::scoring::methods::DNA_BaseEnergyCreator , core::scoring::methods::EnergyMethodCreator , core::scoring::methods::EnvEnergyCreator , core::scoring::methods::EnvSmoothEnergyCreator , core::scoring::methods::Fa_MbenvEnergyCreator , core::scoring::methods::Fa_MbsolvEnergyCreator , core::scoring::methods::GaussianOverlapEnergyCreator , core::scoring::methods::GenBornEnergyCreator , core::scoring::methods::HybridVDW_EnergyCreator , core::scoring::methods::LinearChainbreakEnergyCreator , core::scoring::methods::LK_BallEnergyCreator , core::scoring::methods::LK_CosThetaEnergyCreator , core::scoring::methods::LK_hackCreator , 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::MMBondAngleEnergyCreator , core::scoring::methods::MMBondLengthEnergyCreator , core::scoring::methods::MMLJEnergyInterCreator , core::scoring::methods::MMLJEnergyIntraCreator , core::scoring::methods::MMTorsionEnergyCreator , core::scoring::methods::NMerPSSMEnergyCreator , core::scoring::methods::NMerRefEnergyCreator , core::scoring::methods::OmegaTetherEnergyCreator , core::scoring::methods::P_AA_EnergyCreator , core::scoring::methods::P_AA_pp_EnergyCreator , core::scoring::methods::PackStatEnergyCreator , core::scoring::methods::PairEnergyCreator , core::scoring::methods::PeptideBondEnergyCreator , core::scoring::methods::pHEnergyCreator , core::scoring::methods::PoissonBoltzmannEnergyCreator , core::scoring::methods::ProClosureEnergyCreator , core::scoring::methods::RamachandranEnergy2BCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::ReferenceEnergyCreator , core::scoring::methods::ReferenceEnergyNoncanonicalCreator , core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator , core::scoring::methods::ResidualDipolarCouplingEnergyCreator , core::scoring::methods::RG_Energy_FastCreator , core::scoring::methods::RMS_EnergyCreator , core::scoring::methods::SA_EnergyCreator , core::scoring::methods::SecondaryStructureEnergyCreator , core::scoring::methods::SequenceDependentRefEnergyCreator , core::scoring::methods::SmoothCenPairEnergyCreator , core::scoring::methods::SmoothEnvEnergyCreator , core::scoring::methods::SuckerEnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::VDW_EnergyCreator , 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::RG_Energy_RNACreator , core::scoring::rna::RNA_BulgeEnergyCreator , core::scoring::rna::RNA_DataBackboneEnergyCreator , core::scoring::rna::RNA_FullAtomStackingEnergyCreator , core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator , core::scoring::rna::RNA_LJ_BaseEnergyCreator , core::scoring::rna::RNA_Mg_EnergyCreator , core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator , core::scoring::rna::RNA_SugarCloseEnergyCreator , core::scoring::rna::RNA_TorsionEnergyCreator , core::scoring::rna::RNA_VDW_EnergyCreator , core::scoring::saxs::FastSAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symECreator , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::scoring::methods::EnsembleEnergyCreator , protocols::scoring::methods::InterchainEnvEnergyCreator , protocols::scoring::methods::InterchainPairEnergyCreator , protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator , protocols::scoring::methods::pcs2::PcsEnergyCreator , 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::constraints::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::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• 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::CDRH3Modeler , protocols::antibody2::H3PerturbCCD
• 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::simple_filters::ScoreEvaluator
• ScoreEValuator() : protocols::frag_picker::scores::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 , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::PDBOutput , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , 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 , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::Revert , 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::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , core::scoring::ScoreFunction
• scorefunction() : core::pack::interaction_graph::SimpleInteractionGraph , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• scorefunction_ : protocols::docking::DockingHighResFilter
• scorefunction_initialized : protocols::simple_moves::ShakeStructureMover
• ScoreFunctionCOP : protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FlxbbDesignPack , protocols::forge::remodel::RemodelAccumulator , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::Revert , 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::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover
• 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::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_Normal , protocols::flxbb::DesignTask_Layer , 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::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::Revert , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::RepackMinimize , 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::rna::RNA_HelixAssembler , protocols::simple_moves::ShakeStructureMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::flxbb::DesignTask , protocols::jd2::archive::EvaluatedArchive , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::multistate_design::MultiStateFitnessFunction , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::Splice , protocols::seeded_abinitio::SeedFoldTree , protocols::simple_filters::AlaScan , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SwitchChainOrderMover , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• scorefxn_ : protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::RefineOneCDRLoop , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::ddg::ddGMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::docking::DockingSlideIntoContact , protocols::docking::FaDockingSlideIntoContact , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::features::helixAssembly::HelixBundleFeatures , 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::hybridization::CartesianSampler , protocols::hybridization::DomainAssembly , protocols::hybridization::FoldTreeHybridize , protocols::jd2::archive::EvaluatedArchive , protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::LoopRebuild , protocols::motifs::MotifDnaPacker , protocols::moves::JumpOutMover , protocols::moves::RampingMover , protocols::multistate_design::MultiStateFitnessFunction , protocols::pmut_scan::PointMutScanDriver , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::Revert , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , 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::Splice , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , protocols::relax::WorkUnit_BatchRelax , protocols::rna::RNA_Minimizer , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , 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_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::ddG , protocols::simple_moves::DumpPdb , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SymmetrySlider , protocols::surface_docking::SlideIntoSurface , protocols::surface_docking::FaSlideIntoSurface , protocols::surface_docking::FaSlideAwayFromSurface , protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_O2StarMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::RigidBodySampler , protocols::swa::rna::RNA_AnalyticLoopCloser , protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWiseResidueSampler , 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::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• scorefxn_cen_cst : protocols::loophash::LoopHashLibrary , protocols::loophash::LocalInserter_SimpleMin
• scorefxn_cen_cst_ : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashDiversifier
• scorefxn_centroid_ : protocols::abinitio::Protocol
• 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_low() : protocols::docking::DockingEnsemble
• scorefxn_low_ : protocols::docking::DockingEnsemble
• scorefxn_lowres_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::symmetric_docking::SymDockBaseProtocol
• 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_non_const() : protocols::jd2::archive::EvaluatedArchive
• scorefxn_pack() : protocols::docking::DockingHighRes
• scorefxn_pack_ : protocols::antibody2::GraftCDRLoopsProtocol , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scorefxn_packing() : protocols::docking::DockMCMProtocol
• scorefxn_rama_cst : protocols::loophash::LoopHashLibrary , protocols::loophash::LocalInserter_SimpleMin
• 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_weights_ : core::scoring::Energies
• scorefxns() : protocols::comparative_modeling::LoopRelaxMover
• ScoreIterator : core::fragment::picking_old::vall::VallLibrarian
• 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 >
• ScoreMover() : protocols::simple_moves::ScoreMover
• scorename_ : protocols::filters::Filter
• ScoreOnlyJobOutputter() : protocols::jd2::ScoreOnlyJobOutputter
• scorer_ : protocols::nonlocal::SmoothPolicy
• scoreRepacks : core::scoring::electron_density::PattersonCorrEnergy
• Scores : core::fragment::picking_old::vall::VallLibrarian , protocols::sic_dock::RigidScore
• scores() : core::fragment::picking_old::vall::VallLibrarian , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::sequence::SequenceAlignment
• scores_ : core::import_pose::atom_tree_diffs::AtomTreeDiff , 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
• ScoreStruct() : core::io::raw_data::ScoreStruct
• ScoreType : core::scoring::Energies , protocols::simple_moves::ddG
• 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::OptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , 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_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• screen_verbose_ : protocols::swa::rna::StepWiseRNA_Minimizer
• script_ : protocols::relax::FastRelax
• script_max_accept_ : protocols::relax::FastRelax
• 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::constraints::CircularHarmonicFunc , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::MinMultiHarmonicFunc , protocols::simple_moves::symmetry::SetupNCSMover
• SD_ : core::scoring::ResidualDipolarCoupling
• sd_ : core::scoring::constraints::BoundFunc , core::scoring::constraints::CircularHarmonicFunc , core::scoring::constraints::CircularPowerFunc , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::GaussianFunc , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::KarplusFunc , core::scoring::constraints::MinMultiHarmonicFunc , protocols::simple_moves::symmetry::SetupNCSMover
• 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::constraints::SoedingFunc
• sdev2_ : core::scoring::constraints::SoedingFunc
• sdev_ : core::chemical::AddChiRotamer , core::scoring::constraints::BigBinConstraint
• sdevs_ : core::scoring::constraints::SOGFunc_Impl
• SDFParser() : core::chemical::sdf::SDFParser
• sds_ : core::scoring::disulfides::Cb_Distance_Func
• 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_rotations_and_translations() : protocols::swa::RigidBodySampler
• search_stubs_ : protocols::hotspot_hashing::SearchPatternRotSetOp
• search_translations() : protocols::swa::RigidBodySampler
• SearchPatternExpansion() : protocols::hotspot_hashing::SearchPatternExpansion
• SearchPatternRotSetOp() : protocols::hotspot_hashing::SearchPatternRotSetOp
• SearchPatternTransform() : protocols::hotspot_hashing::SearchPatternTransform
• Searchpoints() : protocols::hotspot_hashing::SearchPattern , protocols::hotspot_hashing::ConstPattern , protocols::hotspot_hashing::TestPattern , protocols::hotspot_hashing::LSMSearchPattern , protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SphericalRotationSearchPattern , protocols::hotspot_hashing::CartesianSearchPattern , protocols::hotspot_hashing::PartitionedSearchPattern , protocols::hotspot_hashing::ComposeSearchPatterns , protocols::hotspot_hashing::SearchPatternTransform , protocols::hotspot_hashing::SearchPatternExpansion , protocols::hotspot_hashing::SICPatternAtTransform , protocols::hotspot_hashing::SurfaceSearchPattern
• searchpoints_ : protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SphericalRotationSearchPattern , protocols::hotspot_hashing::CartesianSearchPattern
• sec_matcher_ : protocols::match::downstream::SecondaryMatchUpstreamResProcessor
• sec_shift_data_ : protocols::frag_picker::VallResidue
• sec_str() : protocols::hybridization::TMalign
• 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::Hit , protocols::match::downstream_hit
• second_ : protocols::match::Hit , protocols::match::downstream_hit
• second_atom_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• second_generator_ : protocols::swa::StepWiseCombineSampleGenerator
• 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
• SecondaryStructureEnergy() : core::scoring::methods::SecondaryStructureEnergy
• SecondaryStructureFilter() : protocols::fldsgn::filters::SecondaryStructureFilter
• SecondaryStructureMPM() : protocols::match::SecondaryStructureMPM
• SecondaryStructurePool() : protocols::frag_picker::quota::SecondaryStructurePool
• SecondaryStructurePotential() : core::scoring::SecondaryStructurePotential
• SecondaryStructureSegmentFeatures() : protocols::features::SecondaryStructureSegmentFeatures
• SecondaryStructureSegmentFeaturesCreator() : protocols::features::SecondaryStructureSegmentFeaturesCreator
• SecondaryStructureWeights() : core::scoring::SecondaryStructureWeights
• secondlib_extra_ : protocols::loophash::EXCN_bbdb_Merge_Failed
• SecondLoop() : core::scoring::sc::MolecularSurfaceCalculator
• seconds() : protocols::simple_filters::ExpiryFilter
• seconds_ : protocols::simple_filters::ExpiryFilter
• seconds_to_keep_files_alive_ : protocols::jd2::MpiFileBuffer
• secstruct : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::rna::TorsionSet , core::conformation::Conformation , core::fragment::FragData , core::fragment::SecondaryStructure , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::io::raw_data::DecoyStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pose::Pose , core::scoring::packing::PoseBalls , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::SS_Info2 , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• secstruct_ : core::conformation::Conformation , core::fragment::SecstructSRFD , core::io::raw_data::DecoyStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::scoring::packing::PoseBalls , protocols::abinitio::TemplateJumpSetup , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , 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::swa::StepWisePoseSetup , protocols::viewer::ConformationViewer
• SecStruct_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• secstruct_defined_ : protocols::rna::RNA_StructureParameters
• secstruct_input_ : protocols::fldsgn::filters::SheetTopologyFilter
• SecStructGen() : core::fragment::picking_old::vall::gen::SecStructGen
• 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 , protocols::frag_picker::VallResidue
• section_index_ : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• sections() : core::fragment::picking_old::vall::VallLibrary
• secx : protocols::hybridization::TMalign
• secy : protocols::hybridization::TMalign
• 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
• seg_len_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::swa::protein::StepWiseProteinLoopBridger
• seg_type : protocols::rbsegment_relax::RBResidueRange
• seg_vector_ : protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SegmentHybridizer
• segment() : protocols::backrub::BackrubMover
• Segment : core::pose::datacache::SpecialSegmentsObserver
• segment_ : protocols::rbsegment_relax::RBSegmentMover
• segment_definitions_ : protocols::scoring::ResidualDipolarCouplingRigidSegments
• segment_id : protocols::features::SecondaryStructureSegment , protocols::backrub::BackrubMover
• segment_length() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• segment_type_ : protocols::protein_interface_design::movers::Splice
• SegmentHybridizer() : protocols::seeded_abinitio::SegmentHybridizer
• SegmentInsert() : protocols::forge::build::SegmentInsert
• SegmentRebuild() : protocols::forge::build::SegmentRebuild
• segments() : core::pose::datacache::SpecialSegmentsObserver
• segments_ : core::pose::datacache::SpecialSegmentsObserver , protocols::backrub::BackrubMover , protocols::rbsegment_relax::RBSegment
• SegmentSwap() : protocols::forge::build::SegmentSwap
• select() : core::chemical::ResidueSelector
• select_core_loops() : protocols::abinitio::DoubleLayerKinematicAbinitio
• select_final_loop() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• 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::SymmetrySlider , protocols::simple_moves::symmetry::SequentialSymmetrySlider , protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider , protocols::simple_moves::symmetry::RandomSymmetrySlider
• select_loops() : protocols::abinitio::LoopJumpFoldCst , protocols::loops::loop_mover::IndependentLoopMover
• select_one_loop() : protocols::LoopRebuild
• select_orient_atoms() : core::chemical::ResidueType , core::conformation::Residue
• select_parts() : protocols::topology_broker::RigidChunkClaimer
• select_random() : protocols::jumping::JumpSelector
• select_relevant_states() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::MultistateAggregateFunction
• select_residues() : core::chemical::ResidueTypeSet
• select_rotamer_subset() : protocols::pack_daemon::PackDaemon
• select_score() : protocols::jd2::archive::EvaluatedArchive
• select_weights_ : protocols::jd2::archive::EvaluatedArchive
• SelectBySASAOperation() : protocols::toolbox::task_operations::SelectBySASAOperation
• selected_ : core::scoring::SelectedResPredicate
• selected_boundary_residues() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• selected_boundary_residues_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• selected_core_residues() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• selected_core_residues_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• selected_surface_residues() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• selected_surface_residues_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• SelectedResPredicate() : core::scoring::SelectedResPredicate
• SelectGdtEvaluator() : protocols::simple_filters::SelectGdtEvaluator
• selection_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::TruncatedScoreEvaluator
• selection_from_segment_cache_ : protocols::protein_interface_design::filters::RmsdFilter
• SelectMaxsubEvaluator() : protocols::simple_filters::SelectMaxsubEvaluator
• selector() : core::chemical::PatchCase
• selector_ : core::chemical::PatchCase , core::chemical::Patch , protocols::frag_picker::FragmentPicker
• Selector_AA() : core::chemical::Selector_AA
• Selector_CMDFLAG() : core::chemical::Selector_CMDFLAG
• Selector_MATCH_VARIANTS() : core::chemical::Selector_MATCH_VARIANTS
• Selector_NAME1() : core::chemical::Selector_NAME1
• Selector_NAME3() : core::chemical::Selector_NAME3
• Selector_NO_VARIANTS() : core::chemical::Selector_NO_VARIANTS
• Selector_PROPERTY() : core::chemical::Selector_PROPERTY
• Selector_VARIANT_TYPE() : core::chemical::Selector_VARIANT_TYPE
• selectors_ : core::chemical::ResidueSelector , protocols::frag_picker::CompositeFragmentSelector
• SelectRDC_Evaluator() : protocols::simple_filters::SelectRDC_Evaluator
• SelectResiduesByLayer() : protocols::toolbox::SelectResiduesByLayer
• 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::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• self_transition_ : protocols::canonical_sampling::SimulatedTempering
• selfmerge() : core::scoring::dssp::StrandPairingSet
• selfneigh() : core::scoring::FACTSResidueInfo
• selfneigh_ : core::scoring::FACTSResidueInfo
• 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
• SemiRotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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::DynamicAggregateFunction
• send_job_to_slave() : protocols::jd2::MPIFileBufJobDistributor
• 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
• 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_spin_down_signal() : protocols::pack_daemon::MPIMultistateFitnessFunction
• send_status_request() : protocols::wum2::EndPoint
• send_stop_to_jobdistributor() : protocols::jd2::archive::ArchiveManager
• send_success_message_to_remote_daemon_set() : protocols::pack_daemon::DynamicAggregateFunction
• 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
• sentCount_ : protocols::moves::UDPSocketClient
• sep : core::scoring::sc::MolecularSurfaceCalculator
• sep_ss() : core::scoring::packing::HolesParams
• sep_ss_ : core::scoring::packing::HolesParams
• separate_protein_and_ligand() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• separated_interface_energy_ : protocols::analysis::InterfaceAnalyzerMover
• separated_interface_energy_ratio_ : protocols::analysis::InterfaceAnalyzerMover
• 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::seeded_abinitio::GrowPeptides
• seq_dist_ : Entry , core::coarse::CoarseEtable
• seq_end() : protocols::features::helixAssembly::HelicalFragment
• seq_from_file() : core::sequence::SequenceFactory
• seq_num : core::scoring::rna::chemical_shift::ChemicalShiftData , protocols::swa::rna::Residue_info
• seq_recovery_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• seq_sep : protocols::jumping::DisulfPairing
• seq_sep_ : core::scoring::hbonds::HBEvalTuple
• 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
• seqmap() : protocols::forge::remodel::RemodelConstraintGenerator
• seqmap_ : protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelConstraintGenerator
• seqpos() : core::conformation::Residue , core::fragment::Frame , core::fragment::NonContinuousFrame , core::io::PositionDdGInfo::PositionDdGInfo , core::pack::interaction_graph::RotamerDots , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::contact_map::ContactPartner , protocols::motifs::BuildPosition
• 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::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::contact_map::ContactPartner , protocols::motifs::BuildPosition , protocols::pockets::PocketConstraint , protocols::simple_moves::HelicalPeptideLengthMover , protocols::simple_moves::PeptideStapleMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• seqpos_aa_vals_vec_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• 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
• Sequence() : core::sequence::Sequence
• sequence : protocols::forge::remodel::RemodelData , protocols::forge::remodel::WorkingRemodelSet , protocols::loophash::BBExtraData , protocols::sparta::Sparta::SpartaLib , core::fragment::FragData , core::fragment::SingleResidueFragData , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::silent::SimpleSequenceData , core::io::silent::SilentStruct , core::pose::MiniPose , core::pose::Pose , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::frag_picker::FragmentCandidate , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::ResonanceList , protocols::simple_moves::ExtendedPoseMover , protocols::swa::StepWiseJobParameters
• SEQUENCE : protocols::topology_broker::DofClaim
• sequence_ : core::fragment::SingleResidueFragData , core::io::raw_data::RawFileData , core::io::raw_data::RawStruct , core::io::silent::SimpleSequenceData , core::io::silent::SilentStruct , 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::VallData , protocols::jd2::parser::BluePrint , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::ResonanceList , protocols::simple_moves::ExtendedPoseMover , protocols::swa::StepWiseJobParameters , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::SequenceClaimer
• sequence_alignment_ : protocols::hybridization::InsertChunkMover
• sequence_alignment_local_ : protocols::hybridization::InsertChunkMover
• sequence_alignments_ : protocols::hybridization::ChunkTrialMover
• sequence_chunks_ : protocols::seeded_abinitio::GrowPeptides
• sequence_claims_ : protocols::topology_broker::TopologyBroker
• sequence_coupling() : protocols::constraints_additional::SequenceCouplingConstraint
• sequence_coupling_ : protocols::constraints_additional::SequenceCouplingConstraint
• sequence_indexer_ : protocols::match::output::SameSequenceGrouper
• sequence_indices() : core::sequence::SequenceAlignment
• sequence_length_ : protocols::frag_picker::JCouplingIO
• sequence_mapping() : core::sequence::SequenceAlignment , protocols::forge::build::BuildManager
• sequence_matches() : core::conformation::Conformation
• sequence_pos_map_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• SEQUENCE_PROFILE : core::pose::datacache::CacheableDataType
• sequence_profile() : core::scoring::constraints::SequenceProfileConstraint , protocols::protein_interface_design::movers::SpliceSegment
• sequence_profile_ : core::scoring::constraints::SequenceProfileConstraint , protocols::protein_interface_design::movers::SpliceSegment
• 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
• SequenceClaim() : protocols::topology_broker::SequenceClaim
• SequenceClaimer() : protocols::topology_broker::SequenceClaimer
• SequenceComparison() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• SequenceCoupling : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , core::sequence::SequenceCoupling
• 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::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::forge::build::BuildManager , core::id::SequenceMapping
• SequenceMappingCOP : protocols::forge::build::BuildManager
• SequenceMappingOP : protocols::forge::build::BuildManager
• SequenceMover() : protocols::moves::SequenceMover
• 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::sequence::SequenceAlignment , protocols::toolbox::task_operations::JointSequenceOperation
• sequences_are_in_frame() : core::sequence::SequenceAlignment
• SequenceShiftMover() : protocols::rbsegment_relax::SequenceShiftMover
• sequential_order() : protocols::loops::Loops
• SequentialSymmetrySlider() : protocols::simple_moves::symmetry::SequentialSymmetrySlider
• seqx : protocols::hybridization::TMalign
• seqy : protocols::hybridization::TMalign
• serial : core::io::pdb::AtomInformation
• serial_data() : protocols::wum::WorkUnitBase
• serial_data_ : protocols::wum::WorkUnitBase
• serialize() : core::grid::CartGrid< T > , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeAtom , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::RepGrid , 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::WorkUnitBase , protocols::wum::WorkUnit_SilentStructStore
• serialize_to_file() : protocols::wum::SilentStructStore
• serialize_weights() : core::scoring::ScoreFunction
• serialized_ : core::chemical::ResidueType
• serialized_size() : protocols::wum2::WUQueue
• SerializedLoopList : protocols::loops::Loops
• set() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::kinematics::MoveMap , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pose::datacache::ObserverCache , core::scoring::EMapVector , protocols::hybridization::TemplateHistory , protocols::jobdist::BasicJob , protocols::toolbox::AllowInsert
• set_A_index() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• set_aa() : core::chemical::ResidueSelector
• set_aa_periodicity() : protocols::optimize_weights::IterativeOptEDriver
• 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_abego() : protocols::forge::components::VarLengthBuild
• set_abgar() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcs2::PcsTensor
• set_abort_on_failed_loop() : protocols::LoopRebuild
• 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_hetatm() : protocols::hybridization::FoldTreeHybridize
• set_add_lead_zero_to_tag() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_add_ligand_to_pose() : protocols::forge::constraints::InvrotTreeRCG
• set_add_non_init_chunks() : protocols::hybridization::FoldTreeHybridize
• set_add_peptide_plane() : protocols::swa::protein::StepWiseProteinPoseSetup
• set_add_peptide_plane_variants() : protocols::swa::StepWisePoseSetup
• set_add_target_to_pose() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• set_add_virt_res_as_root() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_additional_task_operarations() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• set_adduct_flag() : core::chemical::ResidueType
• set_Aform_torsions() : protocols::rna::RNA_HelixAssembler
• set_aggregate_function() : protocols::multistate_design::MultiStateFitnessFunction
• set_akash_dyepos() : protocols::anchored_design::AnchorMoversData
• set_align_file() : protocols::swa::StepWisePoseSetup
• set_align_only_over_base_atoms() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_align_to_native() : protocols::swa::rna::StepWiseRNA_PoseSetup
• set_aligned_chunk() : protocols::hybridization::InsertChunkMover
• set_alignment_res() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_all_bb() : protocols::ligand_docking::MoveMapBuilder
• set_all_chi() : core::conformation::Residue , protocols::ligand_docking::MoveMapBuilder
• set_all_energies() : protocols::toolbox::DecoySetEvaluation
• set_all_extra_parameters() : core::chemical::AtomType
• set_all_jumps_minimizable() : protocols::enzdes::EnzdesBaseProtocol
• set_all_rna_fragments_file() : protocols::rna::RNA_DeNovoProtocol
• 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::swa::rna::StepWiseRNA_ResidueSampler
• set_allow_bulge_at_chainbreak() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_allow_chain_boundary_jump_partner_right_at_fixed_BP() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_allow_consecutive_bulges() : protocols::rna::RNA_DeNovoProtocol
• set_allow_deletion_of_last_residue() : protocols::swa::monte_carlo::RNA_AddOrDeleteMover
• set_allow_fixed_res_at_moving_res() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_allow_insert() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::rna::RNA_ChunkLibrary , protocols::rna::RNA_Minimizer , protocols::rna::RNA_StructureParameters
• set_allow_scoring() : core::scoring::MembraneTopology
• set_allow_syn_pyrimidine() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_allow_tmh_scoring() : core::scoring::MembraneTopology
• set_allowed_bulge_res() : protocols::rna::RNA_DeNovoProtocol
• set_allowed_failure_before_extend() : protocols::LoopRebuild
• set_allowed_failure_before_stop() : protocols::LoopRebuild
• set_allowed_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• set_AllowInsert() : protocols::simple_moves::ConstrainToIdealMover
• set_alpha() : core::pose::Pose
• set_alpha_increment() : protocols::swa::RigidBodySampler
• set_alpha_max() : protocols::swa::RigidBodySampler
• set_alpha_min() : protocols::swa::RigidBodySampler
• 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_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_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() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• 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
• set_angle_sigma2() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_angle_tolerance() : protocols::fldsgn::SheetConstraintsRCG
• set_angle_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_angles() : protocols::simple_moves::BackboneMover , protocols::simple_moves::SmallMover , protocols::simple_moves::ShearMover
• set_antibody_info() : protocols::antibody2::SnugDock
• set_antiparallel_weight() : core::scoring::SecondaryStructureWeights
• set_apply_vdw_cut() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_apply_virtual_res_variant_at_dinucleotide() : protocols::swa::rna::StepWiseRNA_PoseSetup
• set_approved() : protocols::topology_broker::DofClaim
• set_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• set_array() : core::graph::NegSpaceElement< T >
• set_array_size() : core::graph::ArrayPool< T >
• set_assert_no_virt_ribose_sampling() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_assign_state_to_all_nodes_immediately() : core::pack::annealer::RotamerAssigningAnnealer
• set_assign_WC_edges() : protocols::swa::RigidBodySampler
• set_atom_base() : core::chemical::ResidueType
• set_atom_type() : core::chemical::ResidueType , core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser
• set_atrdist_params_helix_strands() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_auto_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_auto_tune() : protocols::swa::StepWiseClusterer
• set_auto_update() : core::scoring::NeighborList
• set_autofilter() : protocols::rna::RNA_DeNovoProtocol
• 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_backbone_acceptor() : core::scoring::hbonds::HBondSet
• set_backbone_backbone_donor() : core::scoring::hbonds::HBondSet
• set_backbone_burial() : core::scoring::rna::RNA_DataInfo
• set_backbone_exposed() : core::scoring::rna::RNA_DataInfo
• set_backbone_heavyatom() : core::chemical::ResidueType
• set_backbone_only() : protocols::swa::InputStreamWithResidueInfo
• set_background_residue_rotamer_dots() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• set_bad() : protocols::jd2::InnerJob , protocols::jd2::Job
• set_bad_nter() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::ModelCDRH3
• set_base_and_pucker_state() : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• set_base_centroid_screener() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• set_base_pairing_only_screen() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• set_batch_id() : protocols::jd2::JobDistributor
• set_bb() : core::kinematics::MoveMap , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::simple_moves::symmetry::SetupNCSMover
• set_bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• set_bb_bbE() : core::pack::interaction_graph::SimpleEdge
• set_bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• set_bb_dihedral_tolerance() : protocols::fldsgn::SheetConstraintsRCG
• 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_true_range() : core::kinematics::MoveMap
• set_bb_xyz_aligned() : protocols::hybridization::InsertChunkMover
• set_BenchMark() : protocols::antibody2::AntibodyModelerProtocol
• set_benchmark() : protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::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
• set_bIdealLoopClosing() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_big_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_bin_size() : protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_bin_width() : protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid
• set_binary_rna_output() : protocols::rna::RNA_DeNovoProtocol
• set_bInitDofs() : protocols::topology_broker::FragmentClaimer
• set_block_size() : core::graph::ArrayPool< T >
• set_blueprint() : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::flxbb::FlxbbDesign
• set_boltz_rank() : protocols::simple_moves::GenericMonteCarloMover
• set_bond_angle() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_bond_count() : core::chemical::sdf::atomTyper
• set_bond_length() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_bootstrap() : protocols::rbsegment_relax::RBSegmentRelax
• set_boundary() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , 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_bRama_check() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• set_bridge_res() : protocols::swa::StepWisePoseSetup
• set_broker() : protocols::topology_broker::TopologyClaimer
• set_buffer_length() : protocols::simple_moves::WobbleMover
• set_build_all_loops_() : protocols::loops::loop_mover::IndependentLoopMover
• set_build_attempts_() : protocols::loops::loop_mover::IndependentLoopMover
• set_bulge_res() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• set_bump_check() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• set_bump_overlap_factor() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_bump_tolerance() : protocols::match::Matcher
• set_c_terminus() : protocols::swa::protein::StepWiseProteinPoseSetup
• set_cacb_dihedral_tolerance() : protocols::fldsgn::SheetConstraintsRCG
• set_cache_size() : protocols::match::output::UpstreamHitCacher
• set_calc_hbond_sasaE() : protocols::analysis::InterfaceAnalyzerMover
• set_calc_rms_res() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::StepWiseClusterer , protocols::swa::StepWisePoseSetup
• 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_calculator_by_name() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• set_camelid() : protocols::antibody::CDRH3Modeler , protocols::antibody::GraftMover , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::ModelCDRH3
• set_camelid_constraints() : protocols::antibody2::GraftCDRLoopsProtocol
• set_candidates_collector() : protocols::frag_picker::FragmentPicker
• set_cartesian() : core::pack::RTMin , protocols::relax::CentroidRelax , protocols::rotamer_recovery::RRProtocolRTMin
• set_cartesian_bonded_linear() : core::scoring::methods::EnergyMethodOptions
• set_cartesian_bonded_parameters() : core::scoring::methods::EnergyMethodOptions
• set_cartfrag_overlap() : protocols::hybridization::CartesianHybridize
• set_catalytic_atoms() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_ccd_close_res() : protocols::swa::protein::StepWiseProteinCCD_Closer
• set_ccd_cycles() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• set_cell_a() : core::conformation::symmetry::SymmData
• set_cell_alfa() : core::conformation::symmetry::SymmData
• set_cell_b() : core::conformation::symmetry::SymmData
• set_cell_beta() : core::conformation::symmetry::SymmData
• set_cell_c() : core::conformation::symmetry::SymmData
• set_cen_dist() : protocols::MakeRotLib::RotData
• set_cen_scorefunction() : protocols::grafting::AnchoredGraftMover , protocols::grafting::GraftMoverBase
• set_cen_scorefxn() : protocols::floppy_tail::FloppyTailMover
• set_center() : core::scoring::MembraneEmbed , protocols::docking::DockingInitialPerturbation , protocols::qsar::scoring_grid::SingleGrid
• set_centroid() : core::import_pose::ImportPoseOptions , protocols::topology_broker::ConstraintClaimer
• set_centroid_loop_building() : protocols::antibody::CDRH3Modeler
• set_centroid_score_diff_cut() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_centroid_scorefunction() : protocols::anchored_design::AnchorMoversData
• set_centroid_scorefxn() : protocols::abinitio::Protocol , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_centroid_screen() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWiseScreener
• set_chain() : 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::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• 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_weight() : protocols::anchored_design::AnchorMoversData , protocols::rna::RNA_DeNovoProtocol
• set_chains() : core::pose::PDBInfo
• set_chains_whose_residues_are_separate_chemical_entities() : core::io::pdb::FileDataOptions
• set_change_chi_without_replacing_residue() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• set_charged_residues_map() : core::scoring::methods::PBLifetimeCache
• set_check_if_residues_are_Ctermini() : core::io::pdb::FileDataOptions
• set_check_if_residues_are_Ntermini() : core::io::pdb::FileDataOptions
• set_check_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• set_check_ss() : protocols::simple_moves::ClassicFragmentMover
• set_checkpoint_gzip() : protocols::genetic_algorithm::GeneticAlgorithm
• set_checkpoint_prefix() : protocols::genetic_algorithm::GeneticAlgorithm
• set_checkpoint_rename() : protocols::genetic_algorithm::GeneticAlgorithm
• set_checkpoint_write_interval() : protocols::genetic_algorithm::GeneticAlgorithm
• 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_chunk_pdb_files() : protocols::rna::RNA_DeNovoProtocol
• set_chunk_silent_files() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_ciBR_only() : core::pack::annealer::FASTERAnnealer , protocols::pack_daemon::FASTER_IG_Repacker
• set_claim_right() : protocols::topology_broker::FragmentClaimer
• set_clash_check_types() : protocols::match::downstream::TargetRotamerCoords
• set_clash_checking() : protocols::match::downstream::TargetRotamerCoords
• set_close_loops() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_close_loops_after_each_move() : protocols::rna::RNA_DeNovoProtocol
• set_closest_states_on_other_bbs() : protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_cluster() : protocols::toolbox::KClusterElement
• set_cluster_by_all_atom() : protocols::cluster::GatherPosesMover
• set_cluster_by_all_atom_rmsd() : protocols::swa::StepWiseClusterer
• set_cluster_by_protein_backbone() : protocols::cluster::GatherPosesMover
• set_cluster_num() : protocols::MakeRotLib::RotData
• set_cluster_radius() : protocols::cluster::ClusterBase , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• set_cluster_rmsd() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_combine_long_loop_mode() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_combine_ratio() : protocols::constraints_additional::ConstraintEvaluator , protocols::topology_broker::ConstraintClaimer
• set_command() : protocols::simple_filters::ExternalEvaluator
• set_comp_constraint_aa() : protocols::fldsgn::potentials::AACompositionEnergy
• set_comparer_info() : protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , 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
• set_compute_separated_sasa() : protocols::analysis::InterfaceAnalyzerMover
• set_conformational_data() : core::scoring::methods::PBLifetimeCache
• set_conserved() : core::pose::datacache::PositionConservedResiduesStore
• set_considering_alternate_state() : protocols::flexpack::interaction_graph::FlexbbNode
• set_constrain_cter() : protocols::antibody2::AntibodyModelerProtocol
• set_constrain_dist_only() : protocols::fldsgn::SheetConstraintsRCG
• set_constrain_vlvh_qq() : protocols::antibody2::AntibodyModelerProtocol
• set_constraint_file() : protocols::fldsgn::BluePrintBDR , protocols::hybridization::FoldTreeHybridize
• set_constraint_func() : protocols::forge::constraints::InverseRotamersRCG
• set_constraint_weight() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• set_constraints() : core::scoring::constraints::CstMinimizationData , protocols::simple_filters::ConstraintScoreCutoffFilter
• set_constraints_NtoC() : protocols::fldsgn::BluePrintBDR
• set_contact_cutoff() : protocols::swa::RigidBodySampler
• set_contents() : protocols::checkpoint::FileBuffer
• set_context_pose() : protocols::flexpack::OtherContextScoreFunction
• set_coord_cst_weight_array() : protocols::abinitio::LoopJumpFoldCst
• set_coordinate_cacher() : protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• 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_residues() : protocols::features::ProteinResidueConformationFeatures
• set_copy_DOF() : protocols::swa::rna::StepWiseRNA_PoseSetup
• set_core_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• set_cosbeta_increment() : protocols::swa::RigidBodySampler
• set_cosbeta_max() : protocols::swa::RigidBodySampler
• set_cosbeta_min() : protocols::swa::RigidBodySampler
• set_couplings() : core::pack::task::operation::SetRotamerCouplings
• set_cp_weighting_during_minimization() : core::conformation::symmetry::SymmetryInfo
• set_create_db() : protocols::loophash::LoopHashLibrary
• set_crossover() : core::scoring::etable::count_pair::CountPairGeneric
• 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::swa::StepWisePoseSetup , protocols::topology_broker::ConstraintClaimer
• set_cst_file_name() : protocols::simple_moves::SequenceProfileMover
• set_cst_root() : protocols::topology_broker::CoordConstraintClaimer
• set_cst_source() : protocols::constraints_additional::ConstraintEvaluator
• set_cst_weight() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::GraftCDRLoopsProtocol , protocols::docking::DockingProtocol , protocols::rbsegment_relax::RBSegmentRelax
• set_cst_width() : protocols::rbsegment_relax::RBSegmentRelax
• set_cstAtoms() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• set_cstfile() : protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::InvrotTreeRCG
• set_cstid_list() : protocols::enzdes::RepackWithoutLigandFilter
• set_cstInfo() : protocols::jumping::ResiduePairJump
• set_cstio() : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::EnzdesScorefileFilter
• set_CterInsert() : protocols::antibody2::AntibodyModelerProtocol
• 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_job() : protocols::moves::Mover
• set_current_jump() : protocols::simple_moves::symmetry::SymmetrySlider
• set_current_no_E_update() : core::pack::interaction_graph::SimpleNode
• set_current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• set_current_tag() : protocols::moves::_BoolMover , protocols::moves::Mover
• set_current_temp() : protocols::canonical_sampling::TemperingBase
• set_current_weight() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• set_cut() : protocols::loops::Loop
• set_cutoff() : protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ScoreCutoffFilter
• set_cutoff_distance() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• set_cutoff_lr() : core::scoring::CenHBPotential
• set_cutoff_sr() : core::scoring::CenHBPotential
• set_cutpoint_closed_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_cycle() : protocols::noesy_assign::PeakAssignmentParameters
• set_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::LoopClosure
• set_d() : core::conformation::Residue , core::pack::scmin::ResidueAtomTreeCollection
• set_data() : core::scoring::ResSingleMinimizationData , core::scoring::ResPairMinimizationData
• 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
• set_debug_eplison_south_sugar_mode() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_decoy_compatibility() : protocols::noesy_assign::PeakAssignment
• set_decoy_tag() : core::io::silent::SilentStruct
• set_decoys_returned() : protocols::jd2::archive::Batch
• set_default() : protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::antibody::GraftMover , protocols::antibody::GraftOneMover , protocols::antibody::CloseOneMover , protocols::antibody::LoopRlxMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::Ab_TemplateInfo , protocols::antibody2::AntibodyInfo , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CloseOneCDRLoop , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::H3CterInsert , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::RefineOneCDRLoopCentroid , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::docking::DockTaskFactory , protocols::docking::SidechainMinMover , protocols::docking::InterfaceSidechainMinMover , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol
• set_default_cen_scorefunction() : protocols::grafting::AnchoredGraftMover , protocols::grafting::GraftMoverBase
• set_default_coordinate_settings() : protocols::relax::RelaxProtocolBase
• set_default_fa_scorefunction() : protocols::grafting::GraftMoverBase
• 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_move_map() : protocols::symmetric_docking::SymDockingLowRes
• set_default_movemap() : protocols::grafting::GraftMoverBase , 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_options() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::symmetric_docking::SymSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• set_default_protocol() : protocols::symmetric_docking::SymDockingLowRes
• 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::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• set_default_settings() : protocols::loop_build::LoopMover_SlidingWindow , 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 , protocols::LoopRebuild
• set_defaults() : core::scoring::constraints::SOGFunc_Impl , protocols::abinitio::AbrelaxMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::antibody::Antibody , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::grafting::AnchoredGraftMover , 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::relax::CentroidRelax , protocols::relax::RelaxProtocolBase , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_moves::ClassicFragmentMover , 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::symmetry::SetupNCSMover , protocols::simple_moves::WobbleMover , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::RigidChunkClaimer , 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 , protocols::moves::CanonicalSamplingMover
• set_defeat_purpose() : protocols::abinitio::JumpingFoldConstraints
• 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_deriv_check_result() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• set_derivative_graph() : core::scoring::symmetry::SymmetricEnergies
• set_design() : protocols::docking::DockingProtocol , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzRepackMinimize
• set_design_chains() : protocols::docking::DockTaskFactory
• set_design_layer() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• set_design_loop() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• set_design_shell() : protocols::design_opt::PointMutationCalculator
• set_design_target_res() : protocols::enzdes::DetectProteinLigandInterface
• set_design_taskset() : protocols::flxbb::FlxbbDesign
• set_designable_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• set_direction() : protocols::features::strand_assembly::StrandFragment
• 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_disabled() : protocols::checkpoint::CheckPointer
• set_disallow_quench() : core::pack::annealer::SimAnnealerBase
• 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_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::GenericResidueConnectionData , core::scoring::etable::etrie::CountPairDataGeneric
• set_dist_wts() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• set_distance() : protocols::fldsgn::SheetConstraintsRCG , protocols::forge::constraints::NtoC_RCG , 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_distinguish_pucker() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_disulfide_file() : protocols::swa::StepWisePoseSetup
• set_dlig_nmeg_limit() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• set_do_add_delete() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• set_do_dump_pdb() : protocols::rna::RNA_Minimizer
• set_do_not_sample_multiple_virtual_sugar() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_do_prepack() : protocols::swa::protein::StepWiseProteinResidueSampler
• set_do_sfxn_eval_every_iteration() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_dock_jump() : protocols::antibody2::LHRepulsiveRamp
• 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_ppk() : protocols::docking::DockingPrepackProtocol , protocols::symmetric_docking::SymDockProtocol
• set_dock_ppk_protocol() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_dock_rtmin() : protocols::symmetric_docking::SymDockProtocol
• set_dock_score_func() : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::RefineBetaBarrel
• set_docking_highres_mover() : protocols::docking::DockingProtocol
• set_docking_local_refine() : protocols::docking::DockingProtocol
• set_docking_pose() : protocols::enzdes::PredesignPerturbMover
• set_DOF() : protocols::simple_moves::TorsionDOFMover
• set_dof() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pose::Pose
• set_dof_moved() : core::conformation::Conformation
• set_dofs() : core::conformation::symmetry::SymmetryInfo
• set_domain() : protocols::toolbox::AllowInsert
• set_domain_assembly() : protocols::hybridization::FoldTreeHybridize
• 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::UpstreamDownstreamCollisionFilter , protocols::match::output::SingleDownstreamResidueWriter
• 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_drop_random_rate() : protocols::topology_broker::ConstraintClaimer
• set_dry_run() : protocols::relax::RelaxProtocolBase
• set_ds_atom_ids_needed() : protocols::match::downstream::TargetRotamerCoords
• set_ds_coords_needed() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_dsbuilder() : protocols::match::downstream::DownstreamAlgorithm
• set_dswriter() : protocols::match::output::WriteUpstreamHitKinemage
• set_dump() : protocols::swa::StepWisePoseSetup
• set_dump_pdb() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• 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_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::FASTEREdge , core::pack::interaction_graph::EdgeBase , 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_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_end() : protocols::loophash::WorkUnit_LoopHash , protocols::rbsegment_relax::RBResidueRange
• set_end_bias() : protocols::simple_moves::ClassicFragmentMover
• set_energy() : protocols::MakeRotLib::RotData
• set_energy_method_options() : core::scoring::ScoreFunction
• set_energy_state() : core::scoring::methods::PBLifetimeCache
• set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• 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::GeneticAlgorithm
• set_enumerate_ligand_rotamers() : protocols::match::MatcherTask
• 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_epsilon() : core::pose::Pose , protocols::MakeRotLib::RotData
• set_epsilon_range() : protocols::swa::rna::RNA_LoopCloseSampler
• set_equiv() : core::pack::rotamer_set::RotamerLinks
• set_errorfull_deltaE_threshold() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• set_etable() : core::scoring::ScoreFunction
• set_euler_bin_widths() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_evaluate_local() : protocols::jd2::archive::EvaluatedArchive
• set_evaluation() : protocols::abinitio::Protocol , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• set_evaluator() : protocols::match::output::MatchConsolidator
• set_evaluators() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• set_exclude_alpha_beta_gamma_sampling() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_excluded_positions() : 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::pdb::FileDataOptions
• set_experimental_ddg() : protocols::optimize_weights::DDGMutationOptEData
• set_experimental_ddg_bind() : protocols::optimize_weights::DDGBindOptEData
• 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_anti_chi() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_extra_anti_chi_rotamer() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_extra_beta() : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_extra_beta_rotamer() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_extra_epsilon() : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_extra_epsilon_rotamer() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_extra_minimize_res() : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Minimizer
• set_extra_parameter() : core::chemical::AtomType
• set_extra_samples() : core::pack::rotamer_set::RotamerSet_
• set_extra_syn_chi() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_extra_syn_chi_rotamer() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_fa_dun_cutoff() : protocols::match::upstream::BuildSet
• set_fa_dun_cutoff_for_constraint() : protocols::match::Matcher
• set_fa_rep_cutoff() : protocols::swa::RigidBodySampler
• set_fa_score_function() : protocols::relax::CentroidRelax
• set_fa_scorefunction() : protocols::grafting::GraftMoverBase
• set_fa_scorefxn() : protocols::floppy_tail::FloppyTailMover
• set_facet_alpha() : protocols::match::Bool3DGridKinemageWriter
• set_facet_color() : protocols::match::Bool3DGridKinemageWriter
• set_facet_master() : protocols::match::Bool3DGridKinemageWriter
• set_farray_from_sso() : core::pose::datacache::SpecialSegmentsObserver
• set_fast() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• 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_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
• set_filter_by_lj() : protocols::match::output::MatchCollisionFilter
• set_filter_by_phipsi() : protocols::loophash::LoopHashSampler
• set_filter_chain_closure() : protocols::rna::RNA_DeNovoProtocol
• set_filter_chain_closure_distance() : protocols::rna::RNA_DeNovoProtocol
• set_filter_chain_closure_halfway() : protocols::rna::RNA_DeNovoProtocol
• set_filter_during_design() : protocols::flxbb::FlxbbDesign
• set_filter_for_previous_clash() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• set_filter_for_previous_contact() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• set_filter_lores_base_pairs() : protocols::rna::RNA_DeNovoProtocol
• set_filter_lores_base_pairs_early() : protocols::rna::RNA_DeNovoProtocol
• set_filter_native_big_bins() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_filter_off() : protocols::flxbb::FilterStructs
• set_filter_omega() : protocols::anchored_design::AnchoredDesignMover
• set_filter_on() : protocols::flxbb::FilterStructs
• 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_user_alignment_res() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_filter_virtual_res_list() : protocols::swa::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_number() : protocols::swa::protein::StepWiseProteinFilterer , protocols::swa::StepWiseFilterer
• set_finer_sampling_at_chain_closure() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_finish_stage() : protocols::abinitio::IterativeBase
• set_first() : core::scoring::packstat::trace
• set_first_chain_break_res() : protocols::swa::StepWiseJobParameters
• set_first_cycle() : protocols::docking::DockMCMProtocol
• set_fitness() : protocols::genetic_algorithm::Entity
• set_five_prime_chain_break_res() : protocols::swa::rna::StepWiseRNA_JobParameters
• 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_res() : protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• set_fixed_residues() : protocols::swa::protein::StepWiseProteinScreener
• set_fixed_stub() : core::scoring::constraints::LocalCoordinateConstraint
• set_flags() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• set_flank_relax() : protocols::antibody2::RefineOneCDRLoop
• set_flank_residue_min() : protocols::antibody2::AntibodyModelerProtocol , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_flank_residue_size() : protocols::antibody2::AntibodyModelerProtocol
• set_flank_size() : protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::RefineOneCDRLoop
• set_flexseg_considering_alt_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_floating_base() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_focused_geomcst_id() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• set_fold_tree() : core::io::silent::BinaryRNASilentStruct , core::io::silent::RNA_SilentStruct , protocols::rigid::RigidBodyMotionMover , protocols::swa::rna::StepWiseRNA_JobParameters
• 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
• set_folding_window() : protocols::noesy_assign::CrossPeakInfo
• set_foldtree() : protocols::seeded_abinitio::SeedFoldTree
• set_force_align() : protocols::swa::StepWiseClusterer
• set_force_ideal_chainbreak() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::toolbox::AllowInsert
• set_force_nonideal() : protocols::relax::FastRelax
• set_force_north_ribose_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_force_south_ribose_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_force_syn_chi_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• set_format_from_peak() : protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• set_frac_by_recomb() : protocols::genetic_algorithm::GeneticAlgorithm
• 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_size() : protocols::rna::RNA_FragmentMover
• set_frag_weight_aligned() : protocols::hybridization::FoldTreeHybridize
• set_fragments() : protocols::jd2::parser::FragmentReader , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign , protocols::simple_moves::FragmentMover
• set_frags() : protocols::anchored_design::AnchorMoversData
• set_fragset() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• 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_full_length_loop_rmsd_clustering() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_full_repack() : protocols::relax::ClassicRelax
• set_full_sequence() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_full_to_sub() : protocols::swa::InputStreamWithResidueInfo , protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_fullatom() : protocols::symmetric_docking::SymDockProtocol , protocols::topology_broker::ConstraintClaimer
• set_fullatom_loop_building() : protocols::antibody::CDRH3Modeler
• set_fullatom_pose() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• set_fullatom_scorefunction() : protocols::anchored_design::AnchorMoversData
• set_fullatom_scorefxn() : protocols::abinitio::Protocol
• set_func() : protocols::genetic_algorithm::GeneticAlgorithm
• set_func_for_weight() : protocols::moves::RampingMover
• set_Fv() : protocols::antibody::Antibody
• set_gamma() : core::pose::Pose
• set_gamma_increment() : protocols::swa::RigidBodySampler
• set_gamma_max() : protocols::swa::RigidBodySampler
• set_gamma_min() : protocols::swa::RigidBodySampler
• set_gap_size() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_gaussian() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• set_general_overlap_tolerance() : protocols::match::BumpGrid
• set_generator() : protocols::forge::constraints::RemoveCsts
• set_genericRBMoveStepsize() : protocols::rbsegment_relax::RBSegmentRelax
• set_geomcst_for_superposition_from_enz_io() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• set_ghost_loops() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_global_sample_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_GlyCorrection_values() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• set_GlyCorrection_values_for_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• set_graft_h1() : protocols::antibody2::GraftCDRLoopsProtocol
• set_graft_h2() : protocols::antibody2::GraftCDRLoopsProtocol
• set_graft_h3() : protocols::antibody2::GraftCDRLoopsProtocol
• set_graft_l1() : protocols::antibody2::GraftCDRLoopsProtocol
• set_graft_l2() : protocols::antibody2::GraftCDRLoopsProtocol
• set_graft_l3() : protocols::antibody2::GraftCDRLoopsProtocol
• set_grid_param() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• 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::antibody2::RefineOneCDRLoop
• set_h3_stem_graft() : protocols::antibody2::GraftCDRLoopsProtocol
• set_H3Filter() : protocols::antibody2::AntibodyModelerProtocol
• set_H3Filter_Tolerance() : protocols::antibody2::AntibodyModelerProtocol
• set_half_width() : core::scoring::constraints::LinearPenaltyFunction
• set_handedness_score_flag() : core::scoring::SecondaryStructureWeights
• set_hardsphere_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• 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_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::CDRH3Modeler , protocols::antibody2::H3RefineCCD
• 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_history_size() : protocols::pack_daemon::MultistateFitnessFunction
• set_hit_cacher() : protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameSequenceGrouper
• set_hpairset() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential
• 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_icodes() : core::pose::PDBInfo
• set_icoor() : core::chemical::ResidueType
• set_id() : core::optimization::DOF_Node , protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::scores::FragmentScoringMethod , protocols::jd2::archive::Batch , protocols::optimize_weights::OptEVariableExpression
• set_ideal_xyz() : core::chemical::ResidueType
• set_idealize_loop_first() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_ident_string() : protocols::loophash::MPI_LoopHashRefine
• 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::swa::rna::StepWiseRNA_Clusterer
• set_ignore_FARFAR_no_auto_bulge_tag() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_ignore_negative_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• set_ignore_o2star_hbonds_in_filter() : protocols::swa::RigidBodySampler
• set_ignore_pose_profile_length_mismatch() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• set_ignore_unmatched_virtual_res() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_ignore_unrecognized_res() : core::io::pdb::FileDataOptions , protocols::rotamer_recovery::RotamerRecovery
• set_ignore_waters() : core::io::pdb::FileDataOptions
• set_ignore_zero_occupancy() : core::io::pdb::FileDataOptions
• set_include_backbone_atoms() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• set_include_background_energies() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• set_include_default_linear_chainbreak() : protocols::rna::RNA_Minimizer
• set_include_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• set_include_syn_chi() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_include_torsion_value_in_tag() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_increase_cycles() : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• 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_initial_decoy_stddev() : protocols::optimize_weights::PNatStructureOptEData
• set_initial_pose() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged , protocols::vip::VIP_Mover
• set_initial_values() : protocols::qsar::qsarOptFunc
• set_initialized() : protocols::rna::RNA_SecStructInfo
• set_inner_cycles() : protocols::docking::DockingLowRes , protocols::docking::DockingProtocol
• set_inp_chi() : protocols::MakeRotLib::RotData
• set_input_code() : protocols::sparta::ANN
• set_input_pose() : protocols::moves::_BoolMover , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::TrialMover
• set_input_pose_is_fa() : protocols::abinitio::KinematicTaskControl
• set_input_res() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_input_res_vectors() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_input_tags() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_PoseSetup
• 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_integration_test_mode() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_intensity() : protocols::noesy_assign::Resonance
• set_inter_atr() : protocols::MakeRotLib::RotData
• set_inter_rep() : protocols::MakeRotLib::RotData
• set_interface_definition_task_operation() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• set_interface_dist() : protocols::docking::InterfaceSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• 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::swa::monte_carlo::RNA_AddMover
• set_interval() : protocols::checkpoint::Timer
• set_interval_data_dump() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• set_interval_pose_dump() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• set_intra_atr() : protocols::MakeRotLib::RotData
• set_intra_rep() : protocols::MakeRotLib::RotData
• set_invert_task() : protocols::simple_moves::ConsensusDesignMover
• set_invrots_for_listnum() : protocols::toolbox::match_enzdes_util::InvrotCollector
• set_Is_internal() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_is_moving_res() : protocols::swa::StepWiseJobParameters
• set_Is_prepend() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_Is_prepend_map() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_is_properly_initialized() : protocols::simple_moves::ShakeStructureMover
• set_Is_simple_full_length_job_params() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_is_working_res() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_job_outputter() : protocols::jd2::JobDistributor
• set_job_parameters() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_job_parameters_exist() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_jump() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::DownJumpSRFD , core::kinematics::AtomTree , core::kinematics::MoveMap , core::pose::Pose
• set_jump_atom() : protocols::topology_broker::JumpClaim
• set_jump_atom_stub_id() : core::conformation::Conformation , core::kinematics::AtomTree
• set_jump_atoms() : core::kinematics::FoldTree
• set_jump_def() : protocols::topology_broker::JumpClaimer
• set_jump_library() : protocols::rna::RNA_StructureParameters
• set_jump_library_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_jump_mover() : protocols::abinitio::KinematicControl
• set_jump_name() : core::conformation::symmetry::SymmetryInfo
• set_jump_now() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose
• set_jump_point_pair_list() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_jump_res() : protocols::swa::StepWisePoseSetup
• set_jump_sample() : protocols::jumping::JumpSetup
• set_jumpAtoms() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• set_jumps_manually : protocols::seeded_abinitio::SeedFoldTree
• set_just_output_score() : protocols::swa::rna::RNA_LoopCloseSampler
• set_keep_covalent() : protocols::enzdes::AddOrRemoveMatchCsts
• set_keep_input_foldtree() : protocols::forge::remodel::RemodelLoopMover
• set_keep_input_protonation_state() : core::io::pdb::FileDataOptions
• set_keep_jumps_from_input_pose() : protocols::topology_broker::JumpClaimer
• set_keep_pose_in_memory() : protocols::swa::rna::StepWiseRNA_Clusterer
• 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::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• set_label() : protocols::noesy_assign::CrossPeakInfo , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::TopologyClaimer
• set_last_accepted() : protocols::canonical_sampling::MetropolisHastingsMover
• set_last_accepted_pose() : protocols::moves::MonteCarlo
• 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_lib_chi_val() : protocols::MakeRotLib::RotData
• set_ligand() : protocols::enzdes::PredesignPerturbMover
• set_ligand_rings() : protocols::qsar::scoring_grid::AtrGrid
• set_ligres() : protocols::match::MatcherMover
• set_limit() : protocols::simple_moves::symmetry::SetupNCSMover
• set_limit_for_rotamer_combo() : protocols::match::output::LimitHitsPerRotamerFilter
• set_line_color() : protocols::match::Bool3DGridKinemageWriter
• set_line_continuation() : core::io::pdb::HeaderInformation
• set_linear_chainbreak_weight() : protocols::rna::RNA_DeNovoProtocol
• set_linecount_offset() : protocols::loops::PoseNumberedLoopFileReader , protocols::loops::JSONFormattedLoopsFileReader
• 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_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::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::swa::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_mover() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• 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::toolbox::task_operations::RestrictToLoopsAndNeighbors
• set_loops_and_anchor() : protocols::anchored_design::AnchorMoversData
• set_loops_from_pose_observer_cache() : protocols::loops::loop_mover::LoopMover
• set_loops_pointer() : protocols::loops::GuardedLoopsFromFile
• set_loops_to_virt_ala() : protocols::hybridization::FoldTreeHybridize
• set_lores_scorefxn() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_low_res_protocol_only() : protocols::docking::DockingProtocol
• set_lower_connect_atom() : core::chemical::ResidueType
• set_lower_threshold() : protocols::filters::IfThenFilter
• set_lowest_score_pose() : protocols::moves::MonteCarlo
• set_lowres_score_func() : protocols::antibody::CDRH3Modeler , protocols::antibody2::H3PerturbCCD , protocols::antibody2::ModelCDRH3
• 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
• set_manager() : protocols::abinitio::IterativeAbrelax , protocols::jd2::archive::AbstractArchiveBase
• set_map_cst_from_centroid_to_fa() : protocols::abinitio::ResolutionSwitcher
• set_mapreso() : core::scoring::electron_density::ElectronDensityOptions
• set_master() : protocols::match::Bool3DGridKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• set_match_algorithm() : protocols::match::output::WriteUpstreamCoordinateKinemage
• set_match_positions() : protocols::match::MatcherMover
• 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_bbrms() : protocols::loophash::LoopHashSampler
• set_max_context_neighbor_cutoff() : core::scoring::Energies
• set_max_decoys() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::StepWiseClusterer
• set_max_frag_length() : core::fragment::FragSet
• set_max_generations() : protocols::genetic_algorithm::GeneticAlgorithm
• set_max_kic_build_attempts() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• set_max_lib_size() : protocols::loophash::MPI_LoopHashRefine
• set_max_nstruct() : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashSampler
• set_max_pop_size() : protocols::genetic_algorithm::GeneticAlgorithm
• set_max_pos() : core::fragment::FragSet
• set_max_radius() : protocols::loophash::LoopHashSampler
• set_max_rama_score_increase() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• set_max_registry_shift() : 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_seq_sep() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::constraints_additional::MaxSeqSepConstraintSet
• set_max_small_angle() : protocols::simple_moves::oop::OopRandomSmallMover
• set_max_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_max_struct() : protocols::loophash::LoopHashSampler
• set_max_struct_per_radius() : protocols::loophash::LoopHashSampler
• set_max_surface_deltaE() : core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• set_max_total_delta() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• 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::MonteCarloTest
• 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_medium_fast() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_memory_limit() : protocols::wum::WorkUnitQueue
• set_memory_max_for_rpes() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• 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_middle_pack_min() : protocols::antibody2::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::MakeRotLib::RotData
• set_min_cst() : protocols::ddg::ddGMover
• set_min_epsilon() : protocols::MakeRotLib::RotData
• set_min_frag_length() : protocols::simple_moves::ClassicFragmentMover
• set_min_hbonds() : protocols::swa::RigidBodySampler
• set_min_lig() : protocols::enzdes::EnzRepackMinimize
• set_min_max_angles() : protocols::rigid::RollMover
• set_min_move() : protocols::abinitio::FoldConstraints
• set_min_num_contacts() : protocols::swa::RigidBodySampler
• set_min_num_south_ribose_filter() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_min_omega() : protocols::MakeRotLib::RotData
• 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::simple_moves::ShakeStructureMover
• set_min_tolerance() : protocols::docking::DockMinMover , protocols::swa::protein::StepWiseProteinPoseMinimizer
• set_min_type() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::relax::CentroidRelax , protocols::relax::RelaxProtocolBase , protocols::rna::RNA_Minimizer , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::symmetric_docking::SymDockingHiRes
• set_min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
• set_minimization_graph() : core::scoring::Energies
• set_minimization_score_function() : protocols::ddg::ddGMover
• set_minimize_all() : protocols::rna::RNA_HelixAssembler
• set_minimize_and_score_sugar() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_minimize_options() : protocols::enzdes::EnzdesBaseProtocol
• set_minimize_with_cst() : protocols::simple_moves::ShakeStructureMover
• set_minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• set_minmover() : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
• set_mintype() : protocols::grafting::AnchoredGraftMover
• set_mm_atom_type() : core::chemical::ResidueType
• set_model_and_remove_capping_residues() : protocols::rna::RNA_HelixAssembler
• set_ModelH3() : protocols::antibody2::AntibodyModelerProtocol
• set_mol_data() : core::chemical::ResidueType
• set_monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController
• set_monte_carlo_cycles() : protocols::rna::RNA_DeNovoProtocol
• set_motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• set_movable_jumps() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::InterfaceTaskOperation
• set_move_first_rigid_body() : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Minimizer
• set_move_jumps_between_chains() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• set_move_map() : protocols::antibody2::CDRsMinPackMin , protocols::antibody2::LHRepulsiveRamp , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::symmetric_docking::SymDockingHiRes
• set_move_map_list() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_move_takeoff_torsions() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• 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::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::relax::RelaxProtocolBase , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::FragmentMover
• set_movemap_from_kic_segment() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• set_movemaps() : protocols::grafting::AnchoredGraftMover
• set_movement() : protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::RBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::StrandTwistingMover
• set_mover() : protocols::flxbb::DesignTask , protocols::moves::FilterMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• set_mover_tag() : protocols::topology_broker::FragmentClaimer
• set_mover_weight() : protocols::topology_broker::TopologyClaimer
• set_moves() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• set_moving_pos() : protocols::swa::StepWiseJobParameters
• set_moving_res() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_moving_res_list() : protocols::swa::monte_carlo::SubToFullInfo
• set_moving_residues() : protocols::swa::protein::StepWiseProteinScreener
• set_mpi_feedback() : protocols::loophash::MPI_LoopHashRefine
• set_multicomponent_info() : core::conformation::symmetry::SymmetryInfo
• set_multifunc() : protocols::optimize_weights::WrapperOptEMultifunc
• set_mut_aa() : protocols::optimize_weights::DDGMutationOptEData
• set_mut_unfolded_energies_emap() : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• set_mutate_to_glycine() : protocols::simple_moves::RepulsiveOnlyMover
• set_mutation_rate() : protocols::genetic_algorithm::EntityRandomizer
• set_n_atom() : protocols::toolbox::DecoySetEvaluation
• set_n_chi_bins() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• set_n_downstream_to_output() : protocols::match::output::WriteUpstreamCoordinateKinemage
• set_n_geomcst() : protocols::match::output::WriteKinemageOutputter
• set_n_geometric_constraints() : protocols::match::Matcher , protocols::match::MatchCounter , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper
• set_n_max_cluster() : protocols::toolbox::ClusterPhilStyle
• set_n_sample() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_n_sample_alpha_full_range() : protocols::swa::RigidBodySampler
• set_n_sample_cosbeta_full_range() : protocols::swa::RigidBodySampler
• set_n_sample_gamma_full_range() : protocols::swa::RigidBodySampler
• set_n_samples_per_side_of_nrchi_bin() : protocols::match::upstream::SampleStrategyData
• set_n_samples_wi_sd_range() : protocols::match::upstream::SampleStrategyData
• set_n_terminus() : protocols::swa::protein::StepWiseProteinPoseSetup
• set_n_to_output_per_group() : protocols::match::output::MatchConsolidator
• set_n_worker() : protocols::jd2::MPIFileBufJobDistributor
• set_name() : core::grid::CartGrid< T > , protocols::jd2::archive::AbstractArchiveBase
• set_name1() : core::chemical::ResidueSelector
• 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::rotamer_recovery::PerNativeRRReporterHuman
• set_native_aa() : protocols::optimize_weights::PNatAAOptEPositionData
• set_native_alignment() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_native_alignment_res() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_native_chi_periodicity() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_distance_viol() : protocols::noesy_assign::PeakAssignment
• set_native_edensity_score_cutoff() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_native_flag() : protocols::match::upstream::ProteinUpstreamBuilder
• set_native_pose() : protocols::abinitio::JumpingFoldConstraints , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::moves::_BoolMover , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::TrialMover , protocols::relax::WorkUnit_BatchRelax , protocols::swa::RigidBodySampler
• set_native_rmsd_screen() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_native_rotamer_chi() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_rotamer_index() : protocols::optimize_weights::PNatRotOptEPositionData
• set_native_screen_rmsd_cutoff() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• 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::swa::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 , core::scoring::symmetry::NBListCache
• set_nbrs() : core::scoring::hbonds::HBondSet
• set_ncaa_rotlib_n_bin_per_rot() : core::chemical::ResidueType
• set_ncaa_rotlib_n_rotameric_bins() : core::chemical::ResidueType
• set_ncaa_rotlib_path() : core::chemical::ResidueType
• set_nchi() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_ncluster() : protocols::toolbox::KCluster
• set_ncopies() : core::fragment::FragmentIO
• set_ncycle() : protocols::flxbb::DesignTask
• set_ncycles() : protocols::flxbb::FlxbbDesign , protocols::hybridization::CartesianSampler , protocols::rbsegment_relax::RBSegmentRelax
• set_neighbor_count() : protocols::optimize_weights::PNatAAOptEPositionData
• 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::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• set_new_chain_order() : core::io::pdb::PDB_DReaderOptions
• set_new_conformation() : core::pose::Pose
• set_new_energies_object() : core::pose::Pose
• 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_segment_id() : protocols::backrub::BackrubMover
• set_next_size() : boost::unordered_object_pool< T, UserAllocator >
• set_nhits_per_match() : protocols::match::HitHasher
• set_nmoves() : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• set_nneighbors() : core::scoring::hbonds::HBondResidueMinData
• 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_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_nonideal() : core::pack::RTMin , core::pack::scmin::SCMinMinimizerMap , protocols::loophash::LoopHashSampler , protocols::rotamer_recovery::RRProtocolRTMin
• 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 >
• set_nonrotameric_chi_bbind_scoring_step_size() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• set_nonrotameric_chi_start_angle() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• set_norepack1() : protocols::docking::DockTaskFactory
• set_norepack2() : protocols::docking::DockTaskFactory
• set_normal() : core::scoring::MembraneEmbed
• set_normalize_decoy_stddev() : protocols::optimize_weights::PNatStructureOptEData
• set_normalized() : protocols::qsar::scoring_grid::GridManager
• 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 >
• 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_nres() : core::scoring::electron_density::ElectronDensity
• set_nres_mono() : core::scoring::hackelec::HackElecEnergy
• 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_nstruct() : protocols::jd2::archive::ArchiveBase
• set_nstruct_centroid() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• set_ntrial() : protocols::flxbb::FilterStructs
• set_ntrials() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• 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_chi() : protocols::MakeRotLib::RotData
• set_num_clusters() : protocols::MakeRotLib::RotData
• set_num_cycles() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• 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::antibody2::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 , core::scoring::PeptideBondedEnergyContainer
• 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::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_num_pose_minimize() : protocols::swa::rna::StepWiseRNA_Minimizer
• 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::GeneticAlgorithm
• 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_o2star_screen() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• set_o2star_trials() : protocols::swa::RigidBodySampler
• set_obey_ENDMDL() : core::io::pdb::PDB_DReaderOptions
• set_observed_sufficient_boolean_true() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< 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 , protocols::topology_broker::SequenceClaim
• set_omega() : core::pose::Pose , protocols::MakeRotLib::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_memory_usage() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_options() : protocols::wum::WorkUnitBase
• set_options_from_cmdline() : protocols::noesy_assign::PeakAssignmentParameters
• set_orb_weights() : core::scoring::orbitals::OrbitalsLookup
• 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_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_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_outer_cycles() : protocols::docking::DockingLowRes , protocols::docking::DockingProtocol
• set_output_before_o2star_pack() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_output_extra_RMSDs() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_output_file_name() : protocols::jobdist::BasicJob
• set_output_filename() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_output_filters() : protocols::rna::RNA_DeNovoProtocol
• set_output_level() : protocols::rotamer_recovery::RRReporterSQLite
• set_output_name() : protocols::canonical_sampling::MetropolisHastingsMover
• set_output_pdb() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• set_output_period() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• set_output_prefix() : protocols::contact_map::ContactMap
• set_output_writer() : protocols::match::output::MatchProcessor
• set_overall_cstfilter_weight() : protocols::abinitio::IterativeBase
• set_overhang() : protocols::grafting::GraftMoverBase
• set_overlap() : protocols::hybridization::CartesianSampler
• set_owner() : core::scoring::Energies , protocols::flexpack::rotamer_set::FlexbbRotamerSet
• set_pack() : protocols::scoring::Interface
• set_pack_input() : protocols::analysis::InterfaceAnalyzerMover
• set_pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• set_pack_score_func() : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::RefineBetaBarrel
• set_pack_separated() : protocols::analysis::InterfaceAnalyzerMover
• set_packer() : protocols::docking::DockingEnsemble
• set_packer_default() : protocols::antibody::GraftMover
• set_packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• set_packertask() : protocols::flxbb::DesignTask
• set_packerTasks_target_and_seeds() : protocols::seeded_abinitio::SeedSetupMover
• set_packonly_after_graft() : protocols::antibody2::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
• set_param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• set_parameter() : core::chemical::AtomType , core::chemical::MMAtomType , core::chemical::orbitals::OrbitalType
• set_parameters() : protocols::fldsgn::potentials::SetAACompositionPotential
• 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_parent() : core::optimization::DOF_Node
• set_parin_favorite_output() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup
• set_partition_definition() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking
• set_pbp() : core::scoring::methods::PBLifetimeCache
• set_PBP_clustering_at_chain_closure() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_pdb_source() : protocols::features::strand_assembly::StrandFragment
• set_peak_id() : protocols::noesy_assign::CrossPeak
• set_penalty() : core::scoring::MembraneEmbed
• set_peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• set_perform_filters() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_perform_minimize() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_perform_minimizer_run() : protocols::rna::RNA_Minimizer
• set_perform_o2star_pack() : protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_perform_score_diff_cut() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_perform_VDW_rep_screen() : protocols::swa::rna::StepWiseRNA_Clusterer
• 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::antibody2::AntibodyModelerProtocol , protocols::antibody2::ModelCDRH3
• set_perturbed_state() : core::pack::interaction_graph::FASTERNode
• set_perturber() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_pH() : core::scoring::methods::pHEnergy
• set_phi() : core::pose::Pose , protocols::MakeRotLib::RotData , protocols::simple_moves::oop::OopMover
• set_phosphate() : protocols::toolbox::AllowInsert
• set_phosphate_domain() : protocols::toolbox::AllowInsert
• set_physical_pose_clash_dist_cutoff() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• set_picked_positions() : protocols::frag_picker::FragmentPicker
• set_piece() : protocols::grafting::GraftMoverBase
• set_pivot_atoms() : protocols::backrub::BackrubMover
• set_pivot_residues() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• set_pivots() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_placeholder() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• set_plaintext() : protocols::sparta::GDB
• set_point() : protocols::qsar::scoring_grid::SingleGrid
• set_polymeric_connection() : core::conformation::Conformation
• set_pool_name() : protocols::frag_picker::FragmentCandidate
• set_poolrmsd() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::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 , core::scoring::methods::PBLifetimeCache , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::jd2::InnerJob , protocols::pack_daemon::EntityCorrespondence
• set_pose_after_closure() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• set_pose_and_task() : protocols::pack_daemon::PackDaemon
• set_pose_filter() : protocols::swa::protein::StepWiseProteinPacker
• set_pose_info() : protocols::analysis::InterfaceAnalyzerMover
• set_pose_no_initialize() : core::pack::interaction_graph::SimpleInteractionGraph
• set_position() : 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::simple_filters::ScoreCutoffFilter
• set_pr_idx() : core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator
• set_preapply() : protocols::simple_moves::GenericMonteCarloMover
• set_precision() : protocols::frag_picker::scores::FragmentScoreManager , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• set_prefix() : protocols::match::output::PDBWriter
• set_prepack_only() : protocols::docking::DockTaskFactory
• set_presample_added_residue() : protocols::swa::monte_carlo::RNA_AddMover
• set_preserve_detailed_balance() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::rigid::RigidBodyMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• set_preserve_header() : core::io::pdb::FileDataOptions
• set_preserve_whole_input_tag() : protocols::jobdist::BasicJob
• set_prob() : core::pack::dunbrack::DunbrackRotamerSampleData
• set_prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• 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::MakeRotLib::RotData
• set_probe_atom_type() : protocols::qsar::scoring_grid::SolvationGrid
• 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_property() : core::chemical::AtomType , core::chemical::orbitals::OrbitalType , core::chemical::ResidueSelector
• 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::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• set_proton() : protocols::noesy_assign::CrossPeakInfo
• set_proton_chi() : core::chemical::ResidueType
• set_protonated_H1_adenosine_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_pseudobonds_to_residue() : core::conformation::Residue
• set_psi() : core::pose::Pose , protocols::MakeRotLib::RotData , protocols::simple_moves::oop::OopMover
• set_pssm_probabilities() : protocols::optimize_weights::PSSMOptEPositionData
• 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::swa::rna::StepWiseRNA_Clusterer
• set_quota_score() : protocols::frag_picker::scores::FragmentScoreMap
• set_radius() : protocols::toolbox::ClusterPhilStyle
• set_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• 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::GeneticAlgorithm
• set_random_confomer() : protocols::docking::ConformerSwitchMover
• set_random_loop_flag() : protocols::LoopRebuild
• 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::pdb::FileDataOptions
• set_ranges_unmodifiable() : core::kinematics::MoveMap
• set_rb_center() : core::kinematics::Jump
• set_rb_delta() : core::kinematics::Jump
• set_rb_deltas() : core::kinematics::Jump
• set_rbs_new_pair() : protocols::swa::rna::RNA_LoopCloseSampler
• set_read_annotation() : core::fragment::FragmentIO
• set_read_fold_tree() : core::import_pose::ImportPoseOptions
• set_rebuild_bulge_mode() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_recent_history_size() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• 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_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
• set_recover_sidechains_filename() : protocols::docking::DockingProtocol
• set_recovery_threshold() : protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• 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_energy() : core::pack::dunbrack::SingleLigandRotamerLibrary
• set_reference_pose() : protocols::dna::RestrictDesignToProteinDNAInterface , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::simple_moves::SuperimposeMover
• set_reference_round_task_factory() : protocols::simple_moves::GreenPacker
• set_reference_xyz() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• set_refine_CCD_off() : protocols::anchored_design::AnchoredRefineMover
• set_refine_cycles() : protocols::anchored_design::AnchoredRefineMover
• set_refine_h3() : protocols::antibody2::AntibodyModelerProtocol
• set_refine_input_loop() : protocols::antibody2::RefineOneCDRLoopCentroid
• set_refine_KIC_off() : protocols::anchored_design::AnchoredRefineMover
• set_refine_mode() : protocols::antibody2::RefineOneCDRLoop
• set_refine_only() : protocols::anchored_design::AnchoredDesignMover
• set_refine_repack_cycles() : protocols::anchored_design::AnchoredRefineMover
• set_refine_temp() : protocols::anchored_design::AnchoredRefineMover
• set_refine_type() : protocols::antibody2::AntibodyModelerProtocol
• set_region() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• set_regions_from_flexibility() : protocols::grafting::GraftMoverBase
• set_regions_from_movemap() : protocols::grafting::GraftMoverBase
• set_registry_shift() : protocols::hybridization::InsertChunkMover
• set_reinitialize_CCD_torsions() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_relevant_atom_ids() : protocols::match::output::SameSequenceAndDSPositionGrouper
• set_remember_unrecognized_res() : core::io::pdb::FileDataOptions
• set_remember_unrecognized_water() : core::io::pdb::FileDataOptions
• set_remove_cterminus_variant() : protocols::swa::StepWisePoseSetup
• set_remove_nterminus_variant() : protocols::swa::StepWisePoseSetup
• set_rename_tag() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_rename_tags() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• set_rep_cutoff() : protocols::swa::rna::RNA_LoopCloseSampler
• set_repack() : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• set_repack_list() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• set_repack_shell() : protocols::design_opt::PointMutationCalculator
• set_repeat_tail_length() : protocols::forge::remodel::RemodelLoopMover
• set_replacement_resid() : protocols::match::output::PoseInserter
• set_repldist_params_helix_sheet() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• set_reporting() : protocols::docking::DockingProtocol
• set_representative_target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget
• 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_data() : core::scoring::hbonds::HBondResPairMinData
• set_res2_data() : core::scoring::hbonds::HBondResPairMinData
• set_res_inds() : core::scoring::disulfides::DisulfMinData
• set_rescoords() : core::pack::scmin::ResidueAtomTreeCollection
• set_rescore_only() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer
• set_reserve_size() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• 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::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_pair() : core::coarse::CoarseEtable
• 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_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_resinfo() : core::pose::PDBInfo
• set_resnum() : core::pack::task::operation::AppendResidueRotamerSet , protocols::protein_interface_design::movers::TryRotamers
• set_resolution() : protocols::qsar::scoring_grid::GridManager
• set_resonances() : protocols::noesy_assign::CrossPeak
• set_restrict_restypes() : protocols::flxbb::LayerDesignOperation
• set_restype() : protocols::match::downstream::TargetRotamerCoords , protocols::match::output::SingleDownstreamResidueWriter
• set_restype_index() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• 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_ring() : protocols::qsar::scoring_grid::SingleGrid
• set_rm_virt_phosphate() : protocols::swa::rna::StepWiseRNA_Minimizer
• set_rms_group_cutoff() : protocols::match::output::SameSequenceAndDSPositionGrouper
• set_rmsd() : protocols::anchored_design::AnchoredDesignMover
• set_rmsd_cutoff() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::RigidBodySampler , protocols::swa::StepWiseScreener
• set_RMSD_only_this() : protocols::anchored_design::AnchoredDesignMover
• set_rmsd_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_rmsd_target_tolerance() : protocols::simple_moves::ShakeStructureMover
• set_rna() : core::import_pose::ImportPoseOptions
• set_rna_data_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_rna_params_file() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• set_root() : protocols::jumping::ResiduePairJumpSetup
• set_root_at_first_rigid_body() : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_StructureParameters
• set_rot_mag() : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy
• set_rot_magnitude() : 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::AppendRotamerSet , core::pack::task::operation::AppendResidueRotamerSet
• 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_RotamerLibraryName() : core::chemical::ResidueType
• set_rotamers() : core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• set_rotation() : core::kinematics::Jump , core::kinematics::RT
• set_rotation_matrix() : core::conformation::symmetry::SymmData
• set_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::relax::CentroidRelax
• set_rsd_set() : protocols::swa::InputStreamWithResidueInfo , protocols::swa::StepWisePoseSetup
• set_rsd_type_set() : protocols::swa::StepWiseClusterer
• set_rt_min() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol
• set_rtmin() : protocols::docking::DockMCMCycle
• set_run_start() : protocols::wum::WorkUnitBase , protocols::wum2::WorkUnit
• set_run_stop() : protocols::wum::WorkUnitBase , protocols::wum2::WorkUnit
• 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_both_sugar_base_rotamer() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_sample_chi_torsion() : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_sample_extra_rotamers() : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• set_sample_junction() : protocols::swa::protein::StepWiseProteinPoseSetup
• set_sample_level() : protocols::match::upstream::SampleStrategyData
• set_sample_native_torsion() : protocols::swa::rna::RNA_LoopCloseSampler
• set_sample_nonpivot_torsions() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_sample_only() : protocols::swa::rna::RNA_LoopCloseSampler
• set_sample_ONLY_multiple_virtual_sugar() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_sample_range_large() : protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• set_sample_range_small() : protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• set_sample_startegy_for_constraint() : protocols::match::Matcher
• set_sample_strategy_for_chi() : protocols::match::upstream::BuildSet
• set_sampler() : protocols::match::upstream::ProteinUpstreamBuilder
• 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_sc_min() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::simple_moves::ShakeStructureMover , protocols::symmetric_docking::SymDockProtocol
• 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
• set_score_component() : protocols::frag_picker::scores::FragmentScoreMap
• set_score_cutoff() : protocols::docking::DockingHighResFilter , protocols::swa::RigidBodySampler
• set_score_diff_cut() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• set_score_file() : protocols::simple_moves::ScoreMover
• set_score_function() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::RefineOneCDRLoopCentroid , protocols::cluster::GatherPosesMover , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::relax::CentroidRelax , protocols::rna::RNA_Minimizer , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::swa::RigidBodySampler
• 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_type() : protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ScoreCutoffFilter
• 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::canonical_sampling::CanonicalSamplingMover , protocols::docking::DockingHighResFilter , protocols::features::DatabaseJobInputter , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::moves::CanonicalSamplingMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::GreenPacker , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• set_scorefxn() : protocols::abinitio::ResolutionSwitcher , protocols::antibody2::GraftOneCDRLoop , protocols::docking::DockingHighRes , protocols::docking::DockingLowRes , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::RepackWithoutLigandFilter , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::DesignTask , 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::multistate_design::MultiStateFitnessFunction , protocols::protein_interface_design::movers::TryRotamers , protocols::relax::RelaxProtocolBase , protocols::rna::RNA_HelixAssembler , protocols::simple_moves::DumpPdb , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RepackSidechainsMover , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWiseResidueSampler
• set_scorefxn_design() : protocols::flxbb::FlxbbDesign
• set_scorefxn_info() : core::scoring::Energies
• set_scorefxn_minimize() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• set_scorefxn_pack() : protocols::docking::DockingHighRes
• set_scorefxn_relax() : protocols::flxbb::FlxbbDesign
• set_scorefxn_repack() : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• set_scoretypes() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::EtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived >
• set_script_to_batchrelax_default() : protocols::relax::FastRelax
• set_sd() : protocols::simple_moves::symmetry::SetupNCSMover
• set_sd_range() : protocols::match::upstream::SampleStrategyData
• set_second_cycle() : protocols::docking::DockMCMProtocol
• set_secondary_structure() : protocols::star::Extender
• set_secstruct() : protocols::frags::TorsionFragment , core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::fragment::SecstructSRFD , core::io::silent::RNA_SilentStruct , core::pose::Pose , protocols::jumping::JumpSelector , protocols::rna::RNA_SecStructInfo , protocols::swa::StepWisePoseSetup
• set_seq_recovery_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• 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_seqmap() : protocols::forge::remodel::RemodelConstraintGenerator
• set_seqprof() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• set_sequence() : protocols::simple_moves::FavorSequenceProfile , core::fragment::FragData , core::fragment::SingleResidueFragData , core::io::silent::SimpleSequenceData , protocols::noesy_assign::FragsToAtomDist , protocols::swa::StepWiseJobParameters , 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_sf() : protocols::analysis::LoopAnalyzerMover
• set_sfxn() : protocols::flexpack::FlexPacker , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_shared_silent_data() : core::io::silent::SilentFileData
• set_sheet() : protocols::nonlocal::SheetTranslate
• set_sheet_number() : protocols::fldsgn::topology::SheetSet
• set_sheets() : protocols::hybridization::FoldTreeHybridize
• set_show_extended() : protocols::anchored_design::AnchoredDesignMover
• set_show_viol_level() : protocols::abinitio::FoldConstraints , protocols::abinitio::ConstraintFragmentSampler
• set_shrink_factor() : protocols::match::Bool3DGridKinemageWriter
• set_silent_file() : protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWiseResidueSampler , protocols::swa::StepWiseScreener
• set_silent_file_data() : core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::swa::RigidBodySampler , protocols::swa::StepWiseClusterer
• set_silent_file_name() : protocols::jd2::SilentFileJobOutputter
• set_silent_files_in() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_PoseSetup
• 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::swa::rna::StepWiseRNA_JobParameters_Setup
• set_size() : core::scoring::Energies , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• set_skip_clustering() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_skip_completely_buried_positions() : protocols::match::Bool3DGridKinemageWriter
• set_skip_complicated_stuff() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• set_skip_low_temp_phase() : protocols::simple_moves::ShakeStructureMover
• set_skip_lr() : protocols::rbsegment_relax::RBSegmentRelax
• set_skip_redundant() : protocols::topology_broker::ConstraintClaimer
• set_skip_reporting() : protocols::analysis::InterfaceAnalyzerMover
• 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::swa::InputStreamWithResidueInfo
• 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::constraints::LinearPenaltyFunction
• set_small_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• set_smallmovesize() : protocols::surface_docking::FullatomRelaxMover
• set_snugdock_foldtree() : protocols::antibody::AntibodyModeler
• set_SnugFit() : protocols::antibody2::AntibodyModelerProtocol
• set_snugfit() : protocols::antibody2::RefineOneCDRLoopCentroid
• set_solvation() : protocols::MakeRotLib::RotData
• set_sparse_aa_info() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , 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::OnTheFlyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph
• 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
• 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_stage2_cycles() : protocols::relax::ClassicRelax
• set_stage2_repack_period() : protocols::relax::ClassicRelax
• 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::rna::RNA_DeNovoProtocol
• set_standard_stub_atoms() : core::fragment::DownJumpSRFD
• set_start() : protocols::loops::Loop , protocols::loophash::WorkUnit_LoopHash , protocols::rbsegment_relax::RBResidueRange
• set_start_added_residue_in_aform() : protocols::swa::monte_carlo::RNA_AddMover
• set_start_rep_weight() : protocols::relax::ClassicRelax
• set_start_res() : protocols::loophash::LoopHashSampler
• set_starting_reference_energies() : protocols::optimize_weights::OptEMultifunc
• set_state() : protocols::forge::remodel::RemodelDesignMover
• set_state_for_node() : core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , 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_status() : protocols::frag_picker::quota::ABEGO_SS_Map
• set_status_prefix() : protocols::jd2::Job
• set_std_dev() : protocols::MakeRotLib::RotData
• set_step_size() : protocols::match::upstream::SampleStrategyData
• set_stepwise_pose_setup() : protocols::swa::StepWiseIdentitySampleGenerator , protocols::swa::StepWisePoseCombineSampleGenerator
• set_steric_dist_cutoff() : protocols::swa::RigidBodySampler
• set_stiffness() : core::scoring::dna::DNA_BasePotential
• set_stop() : protocols::loops::Loop
• set_stop_res() : protocols::loophash::LoopHashSampler
• set_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• set_strand_strand_weights() : core::scoring::methods::EnergyMethodOptions
• set_strategy() : 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
• set_struct_id1() : protocols::rotamer_recovery::RRReporterSQLite
• set_struct_id2() : protocols::rotamer_recovery::RRReporterSQLite
• set_struct_ids_from_sql() : protocols::features::DatabaseJobInputter
• set_struct_ids_from_strings() : protocols::features::DatabaseJobInputter
• set_stub_atoms() : core::fragment::DownJumpSRFD
• set_stub_transform() : core::conformation::Conformation , core::kinematics::AtomTree
• set_sub_to_full() : protocols::swa::monte_carlo::SubToFullInfo
• set_subunits() : core::conformation::symmetry::SymmData
• set_suite_cluster_radius() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_super_secret_fixed_interface_mode() : protocols::anchored_design::AnchorMoversData
• set_superimpose_res() : protocols::swa::StepWisePoseSetup
• set_suppress_bp_constraint() : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_StructureParameters
• set_surf() : core::scoring::packing::PoseBalls
• set_surface_score_weight() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• 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::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_sweep_step_size() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• set_symm() : protocols::simple_filters::SymmetricMotifFilter
• set_symm_transforms() : core::conformation::symmetry::SymmData
• 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::noesy_assign::PeakAssignment
• set_symmetry_name() : core::conformation::symmetry::SymmData
• set_symmetry_type() : core::conformation::symmetry::SymmData
• set_tag_from_pose() : core::io::silent::SilentStruct
• 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_and_tolerance() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• 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_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_filters::PackerNeighborGraphFilter
• set_task_factory() : protocols::anchored_design::AnchorMoversData , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineBetaBarrel , protocols::backrub::BackrubSidechainMover , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , 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::LoopRefineInnerCycleContainer , protocols::pack_daemon::DaemonSet , protocols::relax::RelaxProtocolBase , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::flexpack::FlexPacker , protocols::simple_moves::GreenPacker , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::CDRsMinPackMin
• set_task_scaling() : protocols::simple_moves::GenericMonteCarloMover
• set_temp() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover , protocols::multistate_design::PartitionAggregateFunction< T >
• set_temp_based_on_ens_diversity() : protocols::simple_moves::ShakeStructureMover
• set_temperature() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::docking::ConformerSwitchMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::moves::MonteCarlo , protocols::rbsegment_relax::RBSegmentRelax , protocols::rna::RNA_DeNovoProtocol , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , core::pack::annealer::SimAnnealerBase , protocols::simple_moves::GenericMonteCarloMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_temperature_observer() : protocols::canonical_sampling::MultiTemperatureTrialCounter
• 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::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• set_test_control_mode() : protocols::grafting::AnchoredGraftMover
• set_testing_phase() : protocols::simple_moves::ShakeStructureMover
• set_theta() : core::conformation::Residue , core::pack::scmin::ResidueAtomTreeCollection
• set_threshold() : protocols::toolbox::KMedoid , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster
• set_thresholds() : protocols::simple_filters::SymmetricMotifFilter
• set_tmh_inserted() : core::scoring::MembraneTopology
• set_tmh_jump() : protocols::jumping::PairingLibrary
• set_to_default() : protocols::relax::FastRelax
• set_to_quench() : core::pack::annealer::SimAnnealerBase
• set_tolerance() : protocols::relax::ClassicRelax , protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• set_tolerated_overlap() : protocols::match::output::MatchCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• set_top_frag_num() : core::fragment::FragmentIO
• set_top_n_big_frag() : protocols::hybridization::FoldTreeHybridize
• set_top_n_small_frag() : protocols::hybridization::FoldTreeHybridize
• 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::SymmetricConformation , core::fragment::BBTorsionSRFD , protocols::frags::TorsionFragment , core::pose::Pose
• set_torsion_angle() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree
• set_torsion_increment() : protocols::swa::rna::RNA_LoopCloseSampler
• set_torsion_range() : protocols::swa::rna::RNA_LoopCloseSampler
• set_total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• set_total_energy_current_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• 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_tracer() : protocols::analysis::InterfaceAnalyzerMover
• set_traits() : protocols::genetic_algorithm::Entity
• set_traits_size() : protocols::genetic_algorithm::Entity
• set_trans_mag() : protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy
• set_transition_threshold() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• set_translation() : core::kinematics::Jump , core::kinematics::RT
• set_translation_matrix() : core::conformation::symmetry::SymmData
• set_translation_sample() : protocols::swa::RigidBodySampler
• set_transparent_facets() : protocols::match::Bool3DGridKinemageWriter
• set_trial_positions() : protocols::enzdes::SecondaryMatchProtocol
• set_trials() : protocols::abinitio::hConvergenceCheck , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::seeded_abinitio::CloseFold , protocols::hybridization::hConvergenceCheck
• set_trivial_decoy_compatibility_score() : protocols::noesy_assign::CrossPeakList
• set_turnoff_minimization() : protocols::antibody2::CDRsMinPackMin
• set_twist() : protocols::MakeRotLib::RotData
• set_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge , core::pack::interaction_graph::PDEdge
• set_two_body_energy_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• set_two_stage_clustering() : protocols::swa::rna::StepWiseRNA_Clusterer
• set_type() : protocols::checkpoint::CheckPointer , protocols::qsar::scoring_grid::SingleGrid
• set_unbound_mode() : protocols::anchored_design::AnchorMoversData
• set_undercount_ribose_rotamers() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• set_unfolded_energy_emap_vector() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
• set_uniform_euler_angle_bin_width() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash
• set_uniform_trans() : protocols::docking::DockingInitialPerturbation
• set_uniform_xyz_bin_width() : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::OccupiedSpaceHash , protocols::match::MatchCounter
• 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::TreeBuilder , protocols::nonlocal::StarTreeBuilder
• set_up_atom_order() : protocols::frag_picker::CSTalosIO
• set_up_constraints() : protocols::relax::RelaxProtocolBase
• 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_update_boinc() : protocols::moves::MonteCarlo
• set_upper_connect_atom() : core::chemical::ResidueType
• set_upper_threshold() : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• set_upstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• set_use_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• set_use_constraints() : protocols::antibody2::AntibodyModelerProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::docking::DockingLowResFilter
• set_use_default_movemap_from_flexibility() : protocols::grafting::AnchoredGraftMover
• set_use_double_loop_double_CCD_arms() : protocols::grafting::AnchoredGraftMover
• set_use_double_loop_quad_CCD_arms() : protocols::grafting::AnchoredGraftMover
• set_use_green_packer() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• 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_loops_from_observer_cache() : protocols::loops::loop_mover::LoopMover
• set_use_nblist() : core::scoring::Energies
• set_use_ncaa_rotlib() : core::chemical::ResidueType
• set_use_packer_instead_of_rotamer_trials() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• set_use_phenix_geo() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• set_use_rama2b() : protocols::relax::CentroidRelax
• set_use_relevant_residues_as_loop_length() : protocols::features::LoopAnchorFeatures
• set_use_resfile() : protocols::analysis::InterfaceAnalyzerMover
• set_use_seqprof_constraints() : protocols::simple_moves::ConsensusDesignMover
• set_use_single_loop_double_CCD_arms() : protocols::grafting::AnchoredGraftMover
• set_use_single_residue_to_define_anchor_transfrom() : protocols::features::LoopAnchorFeatures
• set_use_smooth_centroid_settings() : protocols::grafting::AnchoredGraftMover
• set_use_symmetry() : core::conformation::symmetry::SymmetryInfo
• set_user_defined_name() : protocols::filters::Filter
• set_user_input_VDW_bin_screener() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• set_user_provided_movers() : protocols::forge::remodel::RemodelLoopMover
• set_valid() : core::fragment::FragData
• set_valid_energies() : core::io::silent::SilentStruct
• set_vall() : protocols::frag_picker::FragmentPicker
• set_vall_torsions_file() : protocols::rna::RNA_DeNovoProtocol
• set_value() : protocols::qsar::qsarPoint , protocols::filters::ContingentFilter
• set_value_for_bin() : protocols::match::Bool3DGrid
• set_vary_bond_geometry() : protocols::rna::RNA_DeNovoProtocol
• set_vary_bondangles() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• set_vary_ca_bond_angles() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• set_vary_cutpoints() : protocols::anchored_design::AnchoredDesignMover
• set_VDW_atr_rep_screen() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• set_vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• set_VDW_rep_alignment_RMSD_CUTOFF() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• set_VDW_rep_delete_matching_res() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• set_VDW_rep_screen_info() : protocols::swa::rna::StepWiseRNA_Clusterer
• 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
• set_vector_name_and_weight() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• set_verbose() : protocols::flxbb::LayerDesignOperation , protocols::rna::RNA_Minimizer , protocols::simple_moves::ScoreMover , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_Minimizer
• 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_res() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• set_vlb() : protocols::forge::remodel::RemodelConstraintGenerator
• set_volume() : protocols::noesy_assign::CrossPeak
• set_water_base_atm() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• set_weak_pointer_to_self() : core::kinematics::AtomTree
• set_weak_ptr_to_self() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• set_weight() : core::scoring::DC , core::scoring::ScoreFunction , protocols::abinitio::PairingStatEntry , protocols::fldsgn::SheetConstraintsRCG , protocols::forge::constraints::NtoC_RCG , protocols::jd2::archive::EvaluatedArchive , protocols::simple_moves::symmetry::SetupNCSMover , core::scoring::CSA , protocols::simple_moves::FavorSequenceProfile , protocols::enzdes::ProteinLigandInterfaceUpweighter
• set_weight_constraints_NtoC() : protocols::flxbb::FlxbbDesign
• set_weight_constraints_sheet() : protocols::flxbb::FlxbbDesign
• set_weights() : core::scoring::etable::EtableEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::moves::RampingMover , protocols::simple_filters::SymmetricMotifFilter , protocols::toolbox::DecoySetEvaluation
• set_weights_for_sfxn() : protocols::simple_moves::GreenPacker
• set_well_depth() : core::scoring::constraints::LinearPenaltyFunction
• set_which_chain_has_moving_res() : protocols::swa::StepWiseJobParameters
• set_width() : protocols::qsar::scoring_grid::GridManager , protocols::frag_picker::scores::FragmentScoreManager
• set_window() : protocols::noesy_assign::FoldResonance
• set_working_best_alignment() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_working_bridge_res() : protocols::swa::StepWiseJobParameters
• set_working_calc_rms_res() : protocols::swa::StepWiseJobParameters
• set_working_fixed_res() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_working_moving_partition_pos() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_working_moving_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_working_moving_suite_list() : protocols::swa::StepWiseJobParameters
• set_working_native_alignment() : protocols::swa::rna::StepWiseRNA_JobParameters
• set_working_native_pose() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_working_res_list() : protocols::swa::StepWiseJobParameters
• set_working_sequence() : protocols::swa::StepWiseJobParameters
• set_working_set_size() : protocols::boinc::Boinc
• set_working_superimpose_res() : protocols::swa::StepWiseJobParameters
• set_working_terminal_res() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• set_worst() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• set_wrapping_optE_multifunc() : protocols::optimize_weights::WrappedOptEExpressionCreator
• set_write_atom_names() : protocols::noesy_assign::PeakFileFormat
• 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_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_increment() : protocols::swa::RigidBodySampler
• set_x_max() : protocols::swa::RigidBodySampler
• set_x_middle() : core::scoring::constraints::LinearPenaltyFunction
• set_x_min() : protocols::swa::RigidBodySampler
• set_xyz() : core::conformation::Residue , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose , core::conformation::Conformation
• set_xyz_bin_widths() : protocols::match::HitHasher , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::match::HitNeighborFinder
• set_xyz_moved() : core::conformation::Conformation
• set_xyz_target() : core::scoring::constraints::LocalCoordinateConstraint
• set_y_increment() : protocols::swa::RigidBodySampler
• set_y_max() : protocols::swa::RigidBodySampler
• set_y_min() : protocols::swa::RigidBodySampler
• set_z_increment() : protocols::swa::RigidBodySampler
• set_z_max() : protocols::swa::RigidBodySampler
• set_z_min() : protocols::swa::RigidBodySampler
• set_zeta() : core::pose::Pose
• SetAACompositionPotential() : protocols::fldsgn::potentials::SetAACompositionPotential
• setall() : protocols::hybridization::TemplateHistory
• SetAtomicCharge() : core::chemical::SetAtomicCharge
• SetAtomTree() : protocols::protein_interface_design::movers::SetAtomTree
• SetAtomType() : core::chemical::SetAtomType
• SetBackboneHeavyatom() : core::chemical::SetBackboneHeavyatom
• setBase() : core::grid::CartGrid< T >
• setCartesianPositionsFromPose() : protocols::cartesian::MolecularDynamics
• SetCatalyticResPackBehavior() : protocols::enzdes::SetCatalyticResPackBehavior
• SetChiMover() : protocols::simple_moves::sidechain_moves::SetChiMover
• setData() : protocols::sparta::GDB
• setDefaultAnchors() : protocols::flexpep_docking::FlexPepDockingFlags
• setDihedralDerivatives() : protocols::cartesian::MolecularDynamics
• setDimensions() : core::grid::CartGrid< T >
• setEntry() : protocols::sparta::GDB
• setFullOccupied() : core::grid::CartGrid< T >
• SetICoor() : core::chemical::SetICoor
• SetIGTypeOperation() : protocols::toolbox::task_operations::SetIGTypeOperation
• setInitialSpeeds() : protocols::cartesian::MolecularDynamics
• SetIO_String() : core::chemical::SetIO_String
• setK() : core::scoring::constraints::KofNConstraint
• SetMMAtomType() : core::chemical::SetMMAtomType
• setNames() : core::io::sequence_comparation::DesignContrast
• SetNbrAtom() : core::chemical::SetNbrAtom
• SetNbrRadius() : core::chemical::SetNbrRadius
• setNeighbors() : core::io::sequence_comparation::DesignContrast
• SetOrientAtom() : core::chemical::SetOrientAtom
• setparent() : core::kinematics::Node
• setPdbCodes() : core::io::sequence_comparation::DesignContrast
• SetPolymerConnectAtom() : core::chemical::SetPolymerConnectAtom
• setPose() : protocols::match::downstream::ScoringSecMatchRPE
• setPoseExtraScores() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::relax::ClassicRelax
• setPosePositionsFromCartesian() : protocols::cartesian::MolecularDynamics
• setResidueRange() : protocols::rbsegment_relax::RBSegmentMover
• 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
• SetSecondayStruct() : protocols::surface_docking::SurfaceDockingProtocol
• setSecStruct() : core::io::sequence_comparation::DesignContrast
• SetSecStructEnergies() : protocols::fldsgn::potentials::SetSecStructEnergies
• SetTemperatureFactor() : protocols::protein_interface_design::movers::SetTemperatureFactor
• settings : core::scoring::sc::MolecularSurfaceCalculator
• setTop() : core::grid::CartGrid< T >
• SetTorsion() : protocols::simple_moves::SetTorsion
• setup() : core::optimization::CartesianMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , protocols::abinitio::AbrelaxApplication , protocols::canonical_sampling::mc_convergence_checks::PoolData , protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Normal , protocols::flxbb::DesignTask_Layer , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::NPDPropCalculator , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::swa::rna::SlicedPoseJobParameters , protocols::loophash::LoopHashMap , protocols::simple_moves::sidechain_moves::SidechainMCMover , core::scoring::NeighborList , core::optimization::MinimizerMap
• setup_additional_cutpoint_closed() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• setup_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• setup_approximate_vdw_radii() : core::scoring::AtomVDW
• setup_atom_map() : core::scoring::hbonds::HBondSet
• setup_atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_VDW_Energy
• setup_atom_ordering() : core::chemical::ResidueType
• setup_atom_tree() : core::conformation::Conformation
• setup_autoNOE() : protocols::abinitio::IterativeBase
• setup_base_pair_constraints() : protocols::rna::RNA_StructureParameters
• 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_catalytic_residue_minimization_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• setup_CDRsInfo() : protocols::antibody2::AntibodyInfo
• setup_centroid_screen() : protocols::swa::protein::StepWiseProteinScreener
• setup_chainbreak_variants() : protocols::rna::RNA_StructureParameters
• setup_charge_atoms() : protocols::qsar::scoring_grid::ChargeGrid
• setup_class_movemap_and_constraints() : protocols::relax::CentroidRelax
• setup_colors() : protocols::qsar::RenderGridsToKinemage
• setup_complete_ : protocols::pack_daemon::PackDaemon
• setup_complex_fold_tree() : protocols::ub_e2c::ubi_e2c_modeler
• setup_constraints() : core::scoring::dna::DNATorsionPotential , protocols::canonical_sampling::CanonicalSamplingMover , protocols::docking::DockingProtocol , protocols::ligand_docking::ResidueTorsionRestraints , protocols::moves::CanonicalSamplingMover , protocols::ddg::ddGMover , protocols::swa::StepWisePoseSetup
• setup_csts() : core::scoring::constraints::FabConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues
• setup_d2_bounds() : core::scoring::methods::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_min_move() : protocols::abinitio::FoldConstraints , protocols::abinitio::JumpingFoldConstraints
• setup_default_options() : protocols::pockets::PocketGrid
• setup_defaults() : protocols::docking::DockingPrepackProtocol , protocols::sparta::Sparta::SpartaLib , protocols::surface_docking::CentroidRelaxMover , protocols::docking::DockingEnsemblePrepackProtocol , protocols::surface_docking::FullatomRelaxMover
• setup_derived_free_and_fixed_data() : protocols::optimize_weights::IterativeOptEDriver
• setup_disulfides() : protocols::swa::StepWisePoseSetup
• setup_edge_counts() : core::kinematics::FoldTree
• setup_energycut_task() : protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::EnergyCutRotamerTrialsMinMover
• setup_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• setup_exchange_schedule() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering
• setup_fail_triangle_inequailty_list() : protocols::swa::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_fold() : protocols::abinitio::AbrelaxApplication
• setup_fold_tree() : protocols::jumping::MembraneJump , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• setup_fold_tree_and_jumps_and_variants() : protocols::rna::RNA_StructureParameters
• setup_foldtree() : protocols::abinitio::JumpingFoldConstraints , 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::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::dna::DNATorsionEnergy , 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::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::interface::DDPscore , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::CSD_TorsionEnergy , 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::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::VDW_Energy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MinimizationNode , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::saxs::FastSAXSEnergy , core::scoring::symmetry::SymmetricScoreFunction , protocols::constraints_additional::BindingSiteConstraint , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::ScoreFunction , core::scoring::MinimizationEdge , core::scoring::rna::RG_Energy_RNA , core::scoring::packing::HolesEnergyRes , core::scoring::methods::FACTSEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::methods::CenHBEnergy , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::constraints::Constraints , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy
• setup_for_derivatives_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• setup_for_derivatives_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• setup_for_lr2benmeth_minimization_for_respair() : core::scoring::ScoreFunction
• setup_for_minimizing() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackelec::HackElecEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::MinimizationNode , core::scoring::MinimizationEdge , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::ScoreFunction , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::etable::BaseEtableEnergy< Derived >
• setup_for_minimizing_for_node() : core::scoring::ScoreFunction
• setup_for_minimizing_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::OneBodyEnergy , protocols::comparative_modeling::IgnoreSubsetConstraintSet , core::scoring::methods::TwoBodyEnergy , core::scoring::constraints::ConstraintSet
• 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::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::methods::TwoBodyEnergy , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet , core::scoring::hbonds::HBondEnergy
• setup_for_minimizing_sr2b_enmeths_for_minedge() : core::scoring::ScoreFunction
• setup_for_packing() : core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::GenBornPotential , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface::DDPscore , core::scoring::methods::CSD_TorsionEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::nv::NVscore , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::methods::EnergyMethod , core::scoring::etable::BaseEtableEnergy< Derived >
• setup_for_residue_pair_energies() : core::scoring::hbonds::HBondSet
• setup_for_run() : protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• setup_for_scoring() : core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::Constraint , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::constraints::MultiConstraint , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::FACTSPotential , core::scoring::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::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface::DDPscore , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::BurialEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , 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::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::MinimizationNode , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::ScoreFunction , core::scoring::SecondaryStructurePotential , protocols::constraints_additional::BindingSiteConstraint , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::sparta::Sparta::SpartaLib , core::scoring::rna::RNA_VDW_Energy , protocols::scoring::methods::InterchainPairEnergy , core::scoring::sym_e::symEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::MinimizationEdge , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::CSD_TorsionEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::constraints::Constraints , core::scoring::dna::DNATorsionEnergy , core::scoring::constraints::NamedAtomPairConstraint
• setup_for_scoring_() : core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy
• setup_for_scoring_for_residue() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::OneBodyEnergy
• 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
• setup_FrameWorkInfo() : protocols::antibody2::AntibodyInfo
• setup_from_DelphiGrid() : protocols::pockets::DelphiElectrostatics
• setup_from_eggshell_pdb_file() : protocols::pockets::NonPlaidFingerprint
• setup_from_eggshell_triplet_file() : protocols::pockets::NonPlaidFingerprint
• setup_from_EggshellGrid() : 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_psipred() : core::scoring::SS_Killhairpins_Info
• setup_from_rotamer_dots() : core::pack::interaction_graph::InvRotamerDots
• setup_hash_maps() : protocols::loophash::LoopHashLibrary
• setup_heavy_atoms() : protocols::swa::RigidBodySampler
• 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_increased_vdw_radii() : protocols::relax::CentroidRelax
• setup_info_for_mg_calculation() : core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• setup_interpolation() : core::scoring::OmegaTether
• setup_invrot_tree_in_vlb() : protocols::fldsgn::BluePrintBDR
• setup_iterations() : core::pack::annealer::SimAnnealerBase
• setup_jump_numbers_and_partner() : protocols::rna::MultipleDomainMover
• setup_jumps() : protocols::abinitio::AbrelaxApplication , protocols::rna::RNA_StructureParameters
• setup_key_residues() : protocols::ub_e2c::ubi_e2c_modeler
• 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::SmallMover , protocols::simple_moves::ShearMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::BackboneMover
• setup_loop_definition() : protocols::loop_build::LoopBuildMover
• setup_loop_refinement_movers() : protocols::antibody2::SnugDockProtocol
• setup_loops_from_data() : protocols::loops::Loops
• setup_membrane_topology() : protocols::abinitio::AbrelaxApplication
• setup_min_map() : core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::kinematics::tree::Atom
• setup_monte_carlo_cycles() : protocols::rna::RNA_DeNovoProtocol
• setup_move_maps() : protocols::ub_e2c::ubi_e2c_modeler
• setup_movemap() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::rna::RNA_Minimizer
• setup_movemap_and_regions() : protocols::grafting::GraftMoverBase
• setup_movemaps() : protocols::anchored_design::AnchorMoversData
• setup_movers() : protocols::simple_moves::ShakeStructureMover
• setup_movers_ : protocols::forge::components::VarLengthBuild
• setup_native_pose() : protocols::swa::rna::StepWiseRNA_PoseSetup
• setup_objects() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::SnugDockProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::antibody2::SnugDock , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• setup_ok_for_centroid_calculation() : protocols::rna::MultipleDomainMover
• setup_one_color_scheme() : protocols::qsar::RenderGridsToKinemage
• setup_pack_operation_movers() : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• setup_packer_and_movemap() : protocols::simple_moves::DesignRepackMover
• setup_packer_task() : protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody::LoopRlxMover
• setup_packer_task_for_mutations() : protocols::ddg::ddGMover
• setup_packertask() : protocols::ddg::ddGMover
• setup_packing() : protocols::symmetric_docking::SymDockingHiRes , protocols::docking::DockingHighResLegacy
• setup_parallel_antiparallel_weights() : core::scoring::SecondaryStructureWeights
• setup_patterson_first_time() : core::scoring::electron_density::ElectronDensity
• setup_pdbnames_next_round() : protocols::optimize_weights::IterativeOptEDriver
• setup_pose_metric_calculators() : protocols::enzdes::EnzdesScorefileFilter
• setup_precise_zeta_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• setup_protocol() : protocols::docking::DockMCMCycle
• setup_reference_data() : protocols::simple_moves::GreenPacker
• 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::carbohydrates::RingConformationMover
• setup_residue_type_map() : protocols::loops::JSONFormattedLoopsFileReader
• setup_rigid_body_mover() : protocols::rna::RNA_DeNovoProtocol
• setup_rna_data() : protocols::rna::RNA_DataReader
• setup_rotamer_constraints() : protocols::ddg::ddGMover
• setup_rotamer_couplings() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• setup_rotamer_generator() : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• setup_rotamer_links() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• setup_rots_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• setup_sampling_probs() : protocols::medal::MedalExchangeMover
• setup_score_type_names() : core::scoring::ScoreTypeManager
• setup_scorefunctions() : protocols::hybridization::FoldTreeHybridize
• setup_secstruct() : protocols::swa::StepWisePoseSetup
• setup_sequence_recovery_cache() : protocols::enzdes::EnzdesBaseProtocol
• setup_silent_file_stream() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• setup_simple_fold_tree() : protocols::antibody::AntibodyModeler , protocols::antibody2::AntibodyInfo , protocols::ub_e2c::ubi_e2c_modeler
• setup_single_loop_double_arm_remodeling_foldtree() : protocols::grafting::GraftMoverBase
• setup_single_loop_single_arm_remodeling_foldtree() : protocols::grafting::GraftMoverBase
• setup_sub_communicators() : protocols::jd2::MPIMultiCommJobDistributor
• setup_sugar_ring_closure_constraints() : core::scoring::rna::RNA_SugarCloseEnergy
• setup_summary() : protocols::frag_picker::QuotaDebug
• setup_system_signal_handler() : protocols::jd2::JobDistributor
• setup_tag_to_source_map() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• setup_task() : protocols::analysis::InterfaceAnalyzerMover
• 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_sets() : protocols::swa::protein::StepWiseProteinScreener
• setup_torsions() : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger
• setup_two_color_scheme() : protocols::qsar::RenderGridsToKinemage
• setup_type_names() : core::scoring::hbonds::HBondTypeManager
• setup_using_user_input_VDW_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• setup_using_working_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• setup_variants_at_extra_cutpoints() : protocols::rna::RNA_LoopCloser
• setup_virtual_phosphate_variants() : protocols::rna::RNA_StructureParameters
• setup_virtual_phosphate_variants_OLD() : protocols::rna::RNA_StructureParameters
• setup_VL_VH_packing_angle() : protocols::antibody2::AntibodyInfo
• setup_weight_triple() : core::scoring::hackelec::HackElecEnergy
• setup_working_native_pose() : protocols::swa::StepWisePoseSetup
• setupFoldTree() : protocols::surface_docking::SurfaceDockingProtocol
• 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
• setupMovers() : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover
• 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 >
• setUseDensityInMinimizer() : core::scoring::electron_density::ElectronDensity
• setUseExactDerivatives() : core::scoring::electron_density::ElectronDensity
• setValue() : core::grid::CartGrid< T >
• setVAR() : protocols::sparta::GDB
• setWindow() : core::scoring::electron_density::ElectronDensity
• sf_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover
• SF_Replica() : protocols::toolbox::SF_Replica
• sfd_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream , protocols::inputter::SilentFileInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::SilentFileJobInputter , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWiseResidueSampler , protocols::viewer::SilentObserver , core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::swa::RigidBodySampler , protocols::outputter::SilentFileOutputter
• 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::MinimizationNode , core::scoring::MinimizationEdge
• sfd_req_2benmeths_begin() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• sfd_req_2benmeths_end() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• 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::MinimizationNode , core::scoring::MinimizationEdge
• sfs_req_2benmeths_begin() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• sfs_req_2benmeths_end() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• sfx_ : protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::forge::components::VarLengthBuild , protocols::fldsgn::BluePrintBDR , protocols::forge::remodel::RemodelLoopMover
• sfxn() : protocols::moves::RampingMover
• sfxn_ : core::pack::interaction_graph::SimpleInteractionGraph , core::pack::scmin::CartSCMinMultifunc , protocols::canonical_sampling::CanonicalSamplingMover , protocols::cluster::GatherPosesMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::MinimizeStoredRBConfs , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::forge::remodel::RemodelAccumulator , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::downstream::ScoringSecMatchRPE , protocols::pack_daemon::DynamicAggregateFunction , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::simple_moves::ConsensusDesignMover , protocols::moves::CanonicalSamplingMover , core::pack::scmin::SCMinMultifunc
• 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
• ShakeStructureMover() : protocols::simple_moves::ShakeStructureMover
• ShapeComplementarityCalculator : core::scoring::sc::Atom , core::scoring::sc::ShapeComplementarityCalculator
• ShapeComplementarityCalculatorException() : core::scoring::sc::ShapeComplementarityCalculatorException
• ShapeComplementarityFilter() : protocols::simple_filters::ShapeComplementarityFilter
• share_build_points_for_geomcsts_ : protocols::match::MatcherTask
• share_packer_data_from() : protocols::multistate_design::PackingState
• shared_silent_data_ : core::io::silent::SilentFileData
• SharedSilentData() : core::io::silent::SharedSilentData
• shear() : protocols::dna::DNABasepair
• shear_ : protocols::dna::DNABasepair
• shear_min_protocol() : protocols::ligand_docking::LigandDockProtocol
• shear_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• shear_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shearmin_type_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover
• ShearMinCCDTrial() : protocols::loops::loop_mover::refine::ShearMinCCDTrial
• ShearMinCCDTrialCreator() : protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator
• shearminmover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shearmonteCarlo_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shearmoveMapOP_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• ShearMover() : protocols::simple_moves::ShearMover
• shearmover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shearsequenceMover_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover
• sheet() : protocols::fldsgn::topology::SheetSet
• Sheet() : protocols::fldsgn::topology::Sheet
• sheet_ : protocols::nonlocal::SheetTranslate
• sheet_center_ : protocols::fldsgn::topology::Sheet
• sheet_fraction() : core::fragment::SecondaryStructure
• 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
• SheetConstraintsRCG() : protocols::fldsgn::SheetConstraintsRCG
• 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
• shell_cutoff_ : protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator
• shift() : core::scoring::SmoothScoreTermCoeffs , protocols::dna::DNABasestep , core::scoring::SmoothScoreTermCoeffs
• shift_ : core::scoring::SmoothScoreTermCoeffs , protocols::dna::DNABasestep
• SHIFT_DIR : protocols::sparta::Sparta::SpartaLib
• shift_span() : core::scoring::MembraneTopology
• shift_to() : core::fragment::Frame
• shifts() : protocols::frag_picker::CS2ndShift
• shmem_ : protocols::boinc::BoincCurrentPoseObserver
• 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
• short_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• short_range_energies_exist_ : core::pack::interaction_graph::SimpleEdge
• short_range_interactions_exist() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• short_range_interactions_exist_ : core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::OnTheFlyEdge
• shorten_long_terminal_loop() : protocols::LoopRebuild
• shorten_target_list() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• shortest_dis_pairs() : protocols::features::strand_assembly::StrandBundleFeatures
• 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
• Should_score_torsion() : core::scoring::rna::RNA_TorsionPotential
• shove_residues_ : protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::TryRotamers
• ShoveResidueMover() : protocols::protein_interface_design::movers::ShoveResidueMover
• show() : core::chemical::carbohydrates::CarbohydrateInfo , core::conformation::symmetry::SymmData , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::FragData , core::fragment::Frame , core::fragment::DownJumpSRFD , core::fragment::SecondaryStructure , core::fragment::SecstructSRFD , core::id::SequenceMapping , core::kinematics::EXCN_InvalidFoldTree , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pose::PDBInfo , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , core::scoring::CSA , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::Func , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MixtureFunc , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::DipolarCoupling , core::scoring::DC , core::scoring::Energies , protocols::topology_broker::ClaimerMessage , core::scoring::Energies , core::scoring::hbonds::FadeInterval , core::scoring::hbonds::HBondOptions , core::scoring::hbonds::HBond , core::scoring::hbonds::HBondSet , core::scoring::hbonds::Polynomial_1d , core::scoring::methods::EnergyMethodOptions , protocols::topology_broker::EXCN_FilterFailed , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::ResidualDipolarCoupling , core::scoring::RDC , core::scoring::ScoreFunction , protocols::abinitio::PairingStatEntry , protocols::topology_broker::SequenceClaim , protocols::abinitio::StrandConstraints , protocols::antibody2::Ab_TemplateInfo , protocols::antibody2::AntibodyInfo , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::topology_broker::EXCN_Input , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::rotamer_recovery::RRReporter , protocols::toolbox::ClusterBase , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::TemperedDocking , protocols::evaluation::PCA , protocols::simple_moves::LoggedFragmentMover , protocols::rotamer_recovery::RRReporterHuman , protocols::genetic_algorithm::Entity , protocols::jd2::archive::Batch , protocols::jd2::InnerJob , protocols::rotamer_recovery::RRReporterSQLite , protocols::jumping::SameStrand , protocols::rotamer_recovery::RRReporterSQLite , protocols::rotamer_recovery::RRReporterSimple , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::moves::TrialCounter , protocols::multistate_design::MultiStateEntity< T > , protocols::noesy_assign::CrossPeakInfo , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::loops::loop_mover::refine::RepackTrial , protocols::noesy_assign::FoldResonance , protocols::moves::TrialCounter , protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::PeakAssignmentParameters , protocols::rotamer_recovery::RotamerRecovery , protocols::noesy_assign::EXCN_UnknownResonance , protocols::toolbox::AllowInsert , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::rotamer_recovery::RRReporter , protocols::rotamer_recovery::RRReporterSimple , protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RotamerRecovery , protocols::scoring::Interface , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::noesy_assign::EXCN_NoesyAssign , protocols::topology_broker::DofClaim , protocols::topology_broker::EXCN_TopologyBroker , protocols::topology_broker::EXCN_FailedBroking , protocols::docking::DockingLowRes , protocols::jd2::Job , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::docking::DockSetupMover , protocols::abinitio::AlternativePairings , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::antibody2::SnugDock , protocols::antibody2::SnugDockProtocol , protocols::antibody2::AntibodyModelerProtocol , core::scoring::hbonds::HBondSet , core::scoring::ScoreFunction , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::hbonds::HBondSet , core::scoring::constraints::ResidueTypeConstraint , core::scoring::Energies , core::scoring::constraints::SiteConstraintResidues , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::CoordinateConstraint , core::kinematics::tree::Atom_ , core::scoring::ChemicalShiftAnisotropy , core::pack::task::PackerTask , core::fragment::NonContinuousFrame , core::kinematics::FoldTree , core::fragment::SingleResidueFragData
• show_all_atom_names() : core::chemical::ResidueType
• show_all_residue_tasks() : core::pack::task::PackerTask_ , core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_availability() : protocols::frag_picker::quota::TorsionBinPool , protocols::frag_picker::quota::QuotaPool
• show_available_silent_struct_types() : core::io::silent::SilentStructFactory
• show_classic() : core::fragment::Frame , core::fragment::FragData
• 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_def() : core::scoring::constraints::DihedralConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCouplingConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , protocols::pockets::PocketConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::LocalCoordinateConstraint , protocols::constraints_additional::BindingSiteConstraint , core::scoring::constraints::AngleConstraint
• show_def_nopose() : core::scoring::constraints::NamedAtomPairConstraint
• show_definition() : core::scoring::constraints::SoedingFunc , core::scoring::constraints::SOGFunc , core::scoring::constraints::USOGFunc , core::scoring::constraints::SplineFunc , core::scoring::constraints::SkipViolFunc , core::scoring::constraints::EtableFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::ConstraintSet , core::scoring::constraints::BoundFunc , core::scoring::constraints::MixtureFunc , core::scoring::constraints::SquareWell2Func , core::scoring::constraints::PeriodicFunc , core::scoring::constraints::CircularSigmoidalFunc , core::scoring::constraints::CountViolFunc , core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::constraints::CircularHarmonicFunc , core::scoring::constraints::Constraints , core::scoring::constraints::FadeFunc , core::scoring::constraints::Func , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::MinMultiHarmonicFunc , core::scoring::constraints::SigmoidFunc , core::scoring::constraints::SOGFunc_Impl , core::scoring::constraints::TopOutFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::ConstantFunc , core::scoring::constraints::KarplusFunc , core::scoring::constraints::LinearPenaltyFunction , core::scoring::constraints::GaussianFunc , core::scoring::constraints::ScalarWeightedFunc , core::scoring::constraints::SquareWellFunc
• 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::RotamerTrialsMover
• show_params() : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• show_pdb_ids() : protocols::frag_picker::PdbIdChunkFilter
• show_pos() : core::fragment::NonContinuousFrame
• show_pretty() : core::scoring::ScoreFunction
• show_rdc_values() : core::scoring::ResidualDipolarCoupling
• show_residue_connections() : core::conformation::Conformation
• show_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• show_scores() : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• show_scoring_methods() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::FragmentPicker
• show_state() : protocols::moves::MonteCarlo
• 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::hybridization::AllResiduesChanged , protocols::abinitio::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::ConstraintSet , core::scoring::constraints::ScalarWeightedFunc , core::scoring::constraints::TopOutFunc , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::Constraints , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::MultiConstraint , core::scoring::constraints::PeriodicFunc , core::scoring::constraints::SplineFunc , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::Constraint , core::scoring::constraints::CountViolFunc , core::scoring::constraints::FadeFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LinearPenaltyFunction , core::scoring::constraints::MinMultiHarmonicFunc , core::scoring::constraints::SigmoidFunc , core::scoring::constraints::SkipViolFunc , core::scoring::constraints::SquareWellFunc , protocols::constraints_additional::MaxSeqSepConstraintSet , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::Func , core::scoring::constraints::LocalCoordinateConstraint , protocols::constraints_additional::AmbiguousMultiConstraint , core::scoring::constraints::SquareWell2Func , protocols::constraints_additional::BindingSiteConstraint
• show_weighted() : core::scoring::EMapVector
• showCachedScores() : core::scoring::electron_density::ElectronDensity
• showGDB() : protocols::sparta::GDB
• ShowViolation() : protocols::abinitio::ShowViolation
• shrink() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , protocols::frags::RMSVallData , protocols::frags::VallData
• shrink_cluster() : protocols::forge::remodel::RemodelAccumulator
• shrink_factor_ : protocols::match::Bool3DGridKinemageWriter
• shuffle() : protocols::cluster::Cluster
• shuffle_order() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• shuffle_order_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• shuffle_sBR_rotamers() : core::pack::annealer::FASTERAnnealer
• shuffle_temperatures() : protocols::canonical_sampling::ParallelTempering
• ShuffleFileSystemJobDistributor() : protocols::jd2::ShuffleFileSystemJobDistributor
• shutdown() : protocols::jobdist::PlainSilentFileJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::AtomTreeDiffJobDistributor
• 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
• side1_nres_ : protocols::analysis::InterfaceAnalyzerMover
• side1_score_ : protocols::analysis::InterfaceAnalyzerMover
• side2_nres_ : protocols::analysis::InterfaceAnalyzerMover
• side2_score_ : protocols::analysis::InterfaceAnalyzerMover
• side_chains_only_ : protocols::pockets::PocketGrid
• side_inv_ : protocols::scoring::ImplicitFastClashCheck
• side_inv_ca_ : protocols::scoring::ImplicitFastClashCheck
• side_ONE_NUM_pose_list_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• side_ONE_pose_list_id_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• side_one_tag : protocols::swa::rna::Combine_Tags_Info
• side_TWO_NUM_pose_list_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• side_TWO_pose_list_id_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• side_two_tag : protocols::swa::rna::Combine_Tags_Info
• sidechain_ : protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::AtomicContactFilter
• 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::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• sidechainAtoms_begin() : core::conformation::Residue
• SidechainContactDistCutoff() : protocols::frag_picker::SidechainContactDistCutoff
• SidechainMCMover() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• SidechainMetropolisHastingsMover() : protocols::canonical_sampling::SidechainMetropolisHastingsMover
• SidechainMinMover() : protocols::docking::SidechainMinMover
• SidechainMover() : protocols::simple_moves::sidechain_moves::SidechainMover
• SidechainMoverBase() : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• SidechainRmsdFilter() : protocols::simple_filters::SidechainRmsdFilter
• SidechainStateAssignment() : core::pack::scmin::SidechainStateAssignment
• sigAxisR_ : protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::StrandTwistingMover
• sigAxisT_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::StrandTwistingMover , protocols::rbsegment_relax::RBSegment
• sigma() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::topology::DimerPairing , core::sequence::ChemicalShiftSequence
• 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_ : protocols::fldsgn::topology::DimerPairing , core::scoring::electron_density::OneGaussianScattering
• sigma_rot : protocols::rbsegment_relax::GaussianRBSegmentMover
• sigma_trans : protocols::rbsegment_relax::GaussianRBSegmentMover
• Sigmoid() : protocols::simple_filters::Sigmoid
• sigmoid() : core::scoring::SmoothScoreTermCoeffs
• sigmoid_coeffs_ : core::scoring::SmoothScoreTermCoeffs
• SIGMOID_WEIGHTED_CEN_LIST : core::pose::datacache::CacheableDataType
• SIGMOID_WEIGHTED_D_CEN_LIST : core::pose::datacache::CacheableDataType
• SigmoidFunc() : core::scoring::constraints::SigmoidFunc
• sigmoidish_neighbor() : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• SigmoidWeightedCenList() : core::scoring::SigmoidWeightedCenList< T >
• sign1() : protocols::fldsgn::topology::DimerPairing , core::scoring::DimerPairing
• sign1_ : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• sign2() : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• sign2_ : protocols::fldsgn::topology::DimerPairing , core::scoring::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::StrandTwistingMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment
• silent() : core::optimization::MinimizerOptions , core::optimization::LineMinimizationAlgorithm
• silent_ : protocols::forge::remodel::RemodelMover::instruction_flags , core::optimization::MinimizerOptions
• silent_comments_ : core::io::silent::SilentStruct
• silent_energies() : core::io::silent::SilentStruct
• silent_energies_ : core::io::silent::SilentStruct
• silent_Es() : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::EnzdesScorefileFilter
• silent_Es_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::EnzdesScorefileFilter
• silent_file_ : protocols::swa::StepWiseResidueSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::jd2::SilentFileJobOutputter , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::StepWiseScreener , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::rna::RNA_DeNovoProtocol , protocols::swa::protein::StepWiseProteinScreener
• silent_file_data() : protocols::swa::protein::StepWiseProteinResidueSampler , protocols::jd2::LazySilentFileJobInputter , protocols::swa::StepWiseClusterer , protocols::jd2::SilentFileJobInputter , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::RigidBodySampler , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::StepWiseResidueSampler
• silent_file_data_ : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• silent_file_name_ : protocols::viewer::SilentObserver
• silent_file_stream_ONE_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_stream_TWO_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_tags_ : protocols::jd2::SilentFileJobOutputter
• silent_files_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• silent_files_in_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::protein::StepWiseProteinPoseSetup , protocols::swa::rna::StepWiseRNA_PoseSetup
• silent_in() : protocols::jd2::archive::Batch
• silent_job_outputter_ : protocols::enzdes::EnzdesJobOutputter
• silent_out() : protocols::jd2::archive::Batch
• silent_output_ : protocols::enzdes::EnzdesJobOutputter
• silent_score_file_ : protocols::abinitio::AbrelaxApplication
• silent_struct_output_list() : protocols::swa::StepWiseClusterer
• silent_struct_output_list_ : protocols::swa::StepWiseClusterer , protocols::swa::rna::StepWiseRNA_Clusterer
• silent_struct_type_ : core::io::silent::SilentFileData , core::io::silent::SilentFileOptions
• SilentEnergy() : core::io::silent::SilentEnergy
• SilentFileData() : core::io::silent::SilentFileData
• SilentFileInputter() : protocols::inputter::SilentFileInputter
• 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
• SilentFileOutputter() : protocols::outputter::SilentFileOutputter
• SilentFilePoseInputStream() : core::import_pose::pose_stream::SilentFilePoseInputStream
• SilentInfoList : protocols::simple_filters::EvaluatedTrialMover
• 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::jd2::archive::VarianceStatisticsArchive , protocols::abinitio::IterativeBase
• SilentTrajectoryRecorder() : protocols::canonical_sampling::SilentTrajectoryRecorder
• SillyCountStruct() : protocols::swa::rna::SillyCountStruct
• sim_anneal_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• sim_type : core::scoring::APBSConfig::I_PARAM
• SimAnnealerBase() : core::pack::annealer::SimAnnealerBase
• simple_append_map_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• 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_rmsd_cutoff_relax() : protocols::rna::RNA_Relaxer , protocols::rna::RNA_DeNovoProtocol
• simple_rmsd_cutoff_relax_ : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Relaxer
• simple_tree() : core::kinematics::FoldTree
• SimpleDerivCheckResult() : core::optimization::SimpleDerivCheckResult
• SimpleEdge() : core::pack::interaction_graph::SimpleEdge
• SimpleInteractionGraph() : core::pack::interaction_graph::SimpleInteractionGraph
• SimpleNode() : core::pack::interaction_graph::SimpleNode
• SimplePDB() : core::scoring::packstat::SimplePDB
• SimplePDB_Atom() : core::scoring::packstat::SimplePDB_Atom
• SimpleScoringScheme() : core::sequence::SimpleScoringScheme
• SimpleSequenceCreator() : core::sequence::SimpleSequenceCreator
• SimpleSequenceData() : core::io::silent::SimpleSequenceData
• SimulatedTempering() : protocols::canonical_sampling::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_chain_ : protocols::frag_picker::nonlocal::NonlocalFrags
• single_loop_double_arm_ : protocols::grafting::AnchoredGraftMover
• 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
• 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::dunbrack::SingleLigandRotamerLibrary
• SingleMotif() : protocols::motifs::SingleMotif
• SingleResidueDunbrackLibrary : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• SingleResidueFragData() : core::fragment::SingleResidueFragData
• SingleResidueInvrotTarget() : protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget
• SingleResidueMultifunc() : core::optimization::SingleResidueMultifunc
• 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
• six_membered_ring_conformers_ : protocols::simple_moves::carbohydrates::RingConformationMover
• Size : protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::match::output::ResidueKinemageWriter
• size() : protocols::fldsgn::topology::StrandPairingSet , protocols::topology_broker::SequenceClaim
• Size : protocols::topology_broker::DofClaim , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• size() : protocols::wum2::WUQueue
• Size : protocols::toolbox::SelectResiduesByLayer , core::fragment::IndependentBBTorsionSRFD , protocols::sic_dock::RigidScore , core::conformation::signals::LengthEvent , core::fragment::picking_old::concepts::Library< Books > , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::UserDefinedGroupDiscriminator , core::pose::PDBInfo , protocols::simple_moves::BBGaussianMover , core::id::DOF_ID_Map< T > , protocols::simple_moves::DME_FilterMover , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::protein_interface_design::ReportPSSMDifferences , protocols::optimize_weights::PNatRotOptERotamerData , core::pose::datacache::ObserverCache , core::scoring::ResidualDipolarCoupling , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityCorrespondence , protocols::optimize_weights::OptEPositionData , protocols::fldsgn::filters::HSSTripletFilter , protocols::optimize_weights::OptEMultifunc , protocols::fldsgn::MatchResiduesMover , protocols::optimize_weights::IterativeOptEDriver , protocols::match::upstream::SampleStrategyData , protocols::fldsgn::MatchResidues , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::nonlocal::Region , protocols::fldsgn::topology::DimerPairing , protocols::match::VoxelSetIterator , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::fldsgn::topology::DimerPairings , protocols::match::upstream::FullChiSampleSet , protocols::fldsgn::topology::BB_Pos , protocols::match::upstream::UpstreamBuilder , protocols::forge::remodel::RemodelLoopMover , protocols::match::HitHasher , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::HSSTripletSet , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchConsolidator , protocols::match::output::BestMatchesCollection , protocols::match::MatchCounter , protocols::flexpack::interaction_graph::FlexbbNode , protocols::match::OccupiedSpaceHash , protocols::flxbb::DesignTask , protocols::forge::remodel::RemodelMover , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesign , protocols::match::downstream::TargetRotamerCoords , protocols::match::Bool3DGridKinemageWriter , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::forge::build::SegmentSwap , protocols::genetic_algorithm::EntityElement , protocols::forge::build::Interval , protocols::jd2::parser::FragmentReader , protocols::fldsgn::topology::SS_Base , protocols::forge::remodel::RemodelDesignMover , protocols::forge::build::BuildManager , protocols::forge::build::SegmentRebuild , protocols::forge::constraints::RemoveCsts , protocols::forge::build::SegmentInsert , protocols::forge::build::GrowLeft , protocols::forge::build::Bridge , protocols::fldsgn::topology::SS_Info2 , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::fldsgn::topology::StrandPairingSet , protocols::enzdes::ModifyStoredRBConfs , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential
• size() : protocols::topology_broker::JumpClaim
• Size : protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::HelixKinkFilter
• size() : protocols::topology_broker::CutClaim
• Size : core::util::ABEGOManager , core::fragment::picking_old::vall::VallLibrarian , core::pose::datacache::SpecialSegmentsObserver , core::fragment::picking_old::vall::VallResidue , core::fragment::picking_old::vall::gen::SecStructGen
• size() : protocols::topology_broker::RootClaim
• Size : core::conformation::signals::IdentityEvent
• size() : protocols::wum::SilentStructStore , protocols::optimize_weights::PNatAAOptEPositionData , protocols::simple_filters::BatchEvaluator , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::swa::StepWiseIdentitySampleGenerator , protocols::swa::protein::StepWiseProteinJumpSampleGenerator , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pack_daemon::IterativeVectorExpression , protocols::optimize_weights::DDGMutationOptEData , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::optimize_weights::OptEPositionData , protocols::jumping::JumpSetup , protocols::loops::Loops , protocols::jumping::PairingLibrary , protocols::jumping::DisulfPairingLibrary , protocols::frag_picker::quota::ABEGO_SS_Config , protocols::frags::TorsionFragment , protocols::frag_picker::scores::FragmentScoreMap , core::sequence::SequenceAlignment , protocols::dna::DnaChains , core::kinematics::AtomTree , protocols::filters::FilterCollection , protocols::evaluation::PoseEvaluator , core::sequence::SequenceProfile , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::abinitio::ShowViolation , core::kinematics::FoldTree , core::scoring::Hairpins , core::scoring::GenBornResidueInfo , core::scoring::PeptideBondedEnergyContainer , core::scoring::GenBornRotamerSetInfo , core::scoring::FACTSPoseInfo , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::scoring::constraints::MultiConstraint , core::pose::MiniPose , core::conformation::Conformation , core::fragment::picking_old::concepts::Library< Books > , core::conformation::symmetry::VirtualCoordinates
• Size : protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::optimize_weights::PNatAAOptERotamerData , protocols::pack_daemon::PackDaemon , protocols::match::MatcherTask , protocols::match::output::SameChiBinComboGrouper , protocols::match::MatcherMover , protocols::forge::build::BuildInstruction , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::filters::HelixPairingFilter , core::fragment::picking_old::vall::gen::VallFragmentGen
• size() : protocols::topology_broker::DofClaim , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::scoring::ImplicitFastClashCheck , protocols::rosetta_scripts::ParsedProtocol , protocols::jumping::JumpSample , protocols::constraints_additional::ConstraintEvaluator , protocols::abinitio::ComputeTotalDistCst , protocols::constraints_additional::CombinedConstraintEvaluator , core::scoring::rna::RNA_ScoringInfo , core::chemical::sdf::MolData , protocols::viewer::triangleIterator , core::scoring::FACTSRotamerSetInfo , core::conformation::PseudoBondCollection , core::fragment::FragData , core::fragment::picking_old::concepts::Book< Pages > , core::graph::EdgeList , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::io::silent::SilentFileData , core::pack::task::TaskFactory , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::Energies , core::scoring::etable::etrie::GenericResidueConnectionData , core::scoring::GenBornPoseInfo , core::scoring::MembraneEmbed , core::scoring::OneToAllEnergyContainer , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::SigmoidWeightedCenList< T > , protocols::abinitio::PcaEvaluator , protocols::backrub::BackrubSegment , protocols::noesy_assign::ResonanceList , protocols::checkpoint::FileBuffer , protocols::cluster::Cluster , protocols::coarse_rna::SourcePositions , protocols::comparative_modeling::AlignmentSet , protocols::docking::DockingEnsemble , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::features::helixAssembly::HelicalFragment , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::forge::build::BuildManager , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::VallChunk , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::hotspot_hashing::HotspotStubSet , protocols::inputter::InputterStream , protocols::jumping::JumpSelector , protocols::jumping::ResiduePairJumpSetup , protocols::loops::Loop , protocols::moves::MoverContainer , protocols::noesy_assign::CrossPeakList , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::pack_daemon::VariableVectorExpression , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::ResidueBBDofs , protocols::qsar::qsarMap , protocols::rna::RNA_SecStructInfo , protocols::swa::protein::StepWiseProteinFragmentSampleGenerator , protocols::swa::protein::StepWiseProteinMainChainSampleGenerator , protocols::swa::StepWiseDoNothingSampleGenerator
• Size : core::scoring::DipolarCoupling , protocols::fldsgn::SheetConstraintsRCG
• size() : protocols::toolbox::ClusterBase , protocols::topology_broker::BBClaim , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• Size : core::conformation::ResidueKinWriter , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::VallLibrary , core::id::AtomID_Map< T > , core::pack::task::operation::OptH , core::pose::PDBPoseMap , core::scoring::ChemicalShiftAnisotropy , core::scoring::ResidualDipolarCoupling_Rohl , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::MyAtom , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::sspot::HSPairPotential , 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::Sheet , protocols::fldsgn::topology::StrandPairing , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::InterlockAroma , protocols::forge::build::ConnectRight , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::constraints::NtoC_RCG , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::VallResidue , protocols::jd2::parser::BluePrint , protocols::loophash::FastGapMover , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::match::Matcher , protocols::match::HitNeighborFinder , protocols::match::match_lite_hasher , protocols::match::output::DownstreamRMSEvaluator , protocols::protein_interface_design::ReportSequenceDifferences , protocols::match::output::PoseInserter , protocols::match::output::ProcessorFactory , protocols::match::output::SameSequenceGrouper , protocols::match::upstream::BuildSet , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamResTypeGeometry , protocols::moves::FilterMover , protocols::moves::ReplicaExchangeMC , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::OptEData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::MultistateFitnessFunction , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::sic_dock::Rose , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::LayerOperations
• size() : core::fragment::TorsionInfoSet , core::fragment::FragSet , core::graph::Array0< T > , core::io::raw_data::RawFileData , core::scoring::dna::BasePartner , core::scoring::constraints::Constraints , core::scoring::DenseEnergyContainer , core::scoring::CenListInfo , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_DataInfo , core::scoring::methods::LKB_ResiduesInfo , core::scoring::saxs::DistanceHistogram , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::abinitio::PairingStatEntry , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::comparative_modeling::AlignmentCluster , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::evaluation::MetaPoseEvaluator , protocols::frags::TorsionFragmentLibrary , protocols::frag_picker::VallProvider , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::hybridization::TemplateHistory , protocols::loops::LoopsFileData , protocols::moves::DataMap , protocols::loophash::BackboneDB , protocols::optimize_weights::DDGBindOptEData , protocols::pack_daemon::VectorExpression , protocols::pockets::PClusterSet , protocols::pockets::PCluster , protocols::qsar::scoring_grid::GridManager , protocols::swa::StepWisePoseCombineSampleGenerator , protocols::swa::StepWisePoseSampleGenerator , protocols::swa::StepWiseCombineSampleGenerator
• size1() : core::id::SequenceMapping , protocols::fldsgn::topology::StrandPairing
• size2() : core::id::SequenceMapping , protocols::fldsgn::topology::StrandPairing
• Size2 : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , core::scoring::methods::ResidueCartBondedParameters
• size2_ : core::id::SequenceMapping
• Size2Tuple : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size3 : protocols::match::OccupiedSpaceHash , core::scoring::methods::ResidueCartBondedParameters
• Size4 : core::scoring::methods::ResidueCartBondedParameters
• Size6 : protocols::match::VoxelSetIterator
• size_ : protocols::rna::TorsionSet , core::io::serialization::BUFFER , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer , protocols::backrub::BackrubSegment , protocols::loophash::EXCN_Invalid_Hashmap , core::scoring::Energies , protocols::moves::ReplicaExchangeMC , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , core::optimization::ParticleSwarmMinimizer , core::scoring::DenseEnergyContainer , core::graph::Array0< T >
• size_front() : protocols::wum2::WUQueue
• size_left() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::QuotaPool
• size_of_query() : protocols::frag_picker::FragmentPicker
• size_per_coords_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• size_type : core::id::DOF_ID_Map< T > , boost::unordered_object_pool< T, UserAllocator > , core::id::AtomID_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::pack_daemon::DaemonSet , protocols::enzdes::EnzdesFlexibleRegion
• SizeRealPairs : protocols::pack_daemon::DaemonSet
• Sizes : core::scoring::methods::LK_BallEnergy , protocols::motifs::MotifSearch , protocols::sic_dock::RigidScore , protocols::motifs::LigandMotifSearch
• SizeSet : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• skip_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• skip_ala_scan_ : protocols::simple_filters::RotamerBoltzmannWeight
• skip_best_check() : protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::GreedyOptMutationMover
• skip_best_check_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• skip_ccd_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• skip_chainbreak_torsions_ : core::scoring::rna::RNA_TorsionPotential
• skip_clustering_ : protocols::swa::rna::StepWiseRNA_Clusterer
• skip_completely_buried_positions_ : protocols::match::Bool3DGridKinemageWriter
• skip_complicated_stuff_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• skip_low_temp_phase : protocols::simple_moves::ShakeStructureMover
• skip_o2star_trials() : protocols::rna::RNA_Minimizer
• skip_o2star_trials_ : protocols::rna::RNA_Minimizer
• skip_rate : protocols::loops::SerializedLoop , protocols::loops::Loop , protocols::loops::LoopFromFileData
• skip_rate_ : protocols::loops::Loop , protocols::loops::LoopFromFileData
• skip_redundant_ : protocols::topology_broker::ConstraintClaimer
• skip_redundant_width_ : protocols::topology_broker::ConstraintClaimer
• skip_relax() : protocols::vip::VIP_Mover
• skip_reporting_ : protocols::analysis::InterfaceAnalyzerMover
• 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
• SkipViolFunc() : core::scoring::constraints::SkipViolFunc
• slash_char : protocols::sparta::Sparta::SpartaLib , protocols::sparta::ANN
• 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::MPIWorkPoolJobDistributor , protocols::jd2::MPIFileBufJobDistributor
• slave_mark_current_job_id_for_repetition() : protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MPIFileBufJobDistributor
• 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
• Slice() : core::scoring::packstat::Slice
• slice_coords_ : core::scoring::packstat::LeeRichards
• slice_res() : protocols::swa::InputStreamWithResidueInfo
• slice_res_ : protocols::swa::InputStreamWithResidueInfo
• sliced_pose_best_alignment : protocols::swa::rna::SlicedPoseJobParameters
• sliced_pose_full_to_sub : protocols::swa::rna::SlicedPoseJobParameters
• sliced_pose_Is_prepend_map : protocols::swa::rna::SlicedPoseJobParameters
• sliced_pose_job_params_ : protocols::swa::rna::StepWiseRNA_Clusterer
• sliced_pose_rmsd_res_list : protocols::swa::rna::SlicedPoseJobParameters
• sliced_to_working_res_map_ : protocols::swa::rna::SlicedPoseJobParameters
• SlicedPoseJobParameters() : protocols::swa::rna::SlicedPoseJobParameters
• slices_ : core::scoring::packstat::LeeRichards
• slide() : protocols::simple_moves::symmetry::SymmetrySlider , protocols::dna::DNABasestep
• slide_ : protocols::dna::DNABasestep , protocols::docking::DockingInitialPerturbation , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::simple_moves::symmetry::SetupForSymmetryMover
• slide_away() : protocols::simple_moves::symmetry::SymmetrySlider
• slide_back_to_origin() : protocols::rna::MultipleDomainMover
• slide_cutpoint() : core::kinematics::FoldTree
• slide_info_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• slide_into_contact() : protocols::sic_dock::SICFast , protocols::simple_moves::symmetry::SetupForSymmetryMover
• slide_jump() : core::kinematics::FoldTree
• slide_order_ : protocols::simple_moves::symmetry::SequentialSymmetrySlider , protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider , core::conformation::symmetry::SymSlideInfo
• 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
• slideaxis : protocols::surface_docking::SurfaceParameters
• SlideCriteriaType_ : protocols::simple_moves::symmetry::SymmetrySlider
• SlideCriteriaVal_ : core::conformation::symmetry::SymSlideInfo
• SlideIntoSurface() : protocols::surface_docking::SlideIntoSurface
• SlideThreshold_ : protocols::simple_moves::symmetry::SymmetrySlider
• SlideTogether() : protocols::ligand_docking::SlideTogether
• SlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• slope : core::util::Line , core::scoring::constraints::SigmoidFunc , core::scoring::etable::ExtraQuadraticRepulsion
• slope_ : core::scoring::constraints::SigmoidFunc , core::scoring::constraints::LinearPenaltyFunction
• 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::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator
• small_frag_insertion_weight_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::FoldTreeHybridize
• small_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• small_moves() : protocols::flexpep_docking::FlexPepDockingProtocol
• small_scores_ : protocols::frag_picker::scores::FragmentScoreMap
• small_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• SmallAtNb() : core::scoring::SmallAtNb
• SMALLER : protocols::enzdes::ValueEvaluator
• smallest_native_violation() : protocols::noesy_assign::CrossPeak
• SmallFragWeight() : protocols::topology_broker::weights::SmallFragWeight
• smallmin_type_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• SmallMinCCDTrial() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• SmallMinCCDTrialCreator() : protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator
• smallminmover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• smallmonteCarlo_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover
• smallmoveMapOP_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• SmallMover() : protocols::simple_moves::SmallMover
• smallmover_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::CentroidRelaxMover
• smallsequenceMover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• smax_ : protocols::noesy_assign::PeakAssignmentParameters
• smooth() : protocols::hybridization::TMalign
• smooth_ : core::scoring::constraints::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_hack_elec() : core::scoring::methods::EnergyMethodOptions
• smooth_hack_elec_ : core::scoring::hackelec::HackElecEnergy , core::scoring::methods::EnergyMethodOptions
• smooth_hb_env_dep() : core::scoring::hbonds::HBondOptions
• smooth_hb_env_dep_ : core::scoring::hbonds::HBondOptions
• smooth_move_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover
• 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::constraints::SOGFunc_Impl
• smooth_trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• 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
• 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
• snug_fit_ : protocols::antibody2::RefineOneCDRLoopCentroid , protocols::antibody::CDRH3Modeler
• SnugDock() : protocols::antibody2::SnugDock
• SnugDockProtocol() : protocols::antibody2::SnugDockProtocol
• snugfit_ : protocols::antibody::AntibodyModeler , protocols::antibody2::AntibodyModelerProtocol
• snugfit_MC_min() : protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody::AntibodyModeler
• snugfit_mcm_protocol() : protocols::antibody::AntibodyModeler , protocols::antibody2::LHSnugFitLegacy
• socket_addr_ : protocols::moves::UDPSocketClient
• socket_h_ : protocols::moves::UDPSocketClient
• SoedingFunc() : core::scoring::constraints::SoedingFunc
• soft_scorefxn_ : protocols::ligand_docking::LigandBaseProtocol
• sog_cst_param() : core::scoring::constraints::SOGFunc_Impl
• sog_cst_param_ : core::scoring::constraints::SOGFunc_Impl
• SOGFunc() : core::scoring::constraints::SOGFunc
• SOGFunc_Impl() : core::scoring::constraints::SOGFunc_Impl
• sol_weight() : core::scoring::etable::EtableEvaluator
• sol_weight_ : core::scoring::etable::EtableEvaluator
• SOLID_STATE_NMR : core::io::pdb::HeaderInformation
• SOLUTION_NMR : core::io::pdb::HeaderInformation
• SOLUTION_SCATTERING : core::io::pdb::HeaderInformation
• SOLUTION_SCATTERING_THEORETICAL_MODEL : core::io::pdb::HeaderInformation
• solv1() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solv1_ : core::scoring::etable::TableLookupEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::etable::MembEtable , core::scoring::etable::Etable
• solv2() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• solv2_ : core::scoring::etable::MembEtable , core::scoring::etable::Etable , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::etable::TableLookupEvaluator , core::scoring::etable::BaseEtableEnergy< Derived >
• solvation : core::scoring::etable::AtomPairEnergy
• solvation_ : protocols::MakeRotLib::RotData
• SolvationGrid() : protocols::qsar::scoring_grid::SolvationGrid
• SolvationMetaGrid() : protocols::qsar::scoring_grid::SolvationMetaGrid
• solve_pb() : core::scoring::PoissonBoltzmannPotential
• SolventAccessibility() : protocols::frag_picker::scores::SolventAccessibility
• 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
• 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_weighted_energy() : core::scoring::hbonds::HBondSet
• sort_Combine_Tags_Info() : protocols::swa::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_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
• sorted : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• sorted_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• sorted_capacity_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• SortPredicate() : protocols::jd2::archive::SortPredicate
• source_ : protocols::comparative_modeling::StealSideChainsMover , protocols::comparative_modeling::StealLigandMover
• SOURCE_FILE : protocols::jd2::archive::ArchiveBase
• 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::SearchPatternTransform , protocols::hotspot_hashing::SICPatternAtTransform , protocols::hotspot_hashing::SearchPatternExpansion
• source_pattern_a : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pattern_b : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pdb() : protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::ResidueBBDofs , protocols::protein_interface_design::movers::Splice
• source_pdb_ : protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::ResidueBBDofs
• 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::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• source_positions_ : protocols::coarse_rna::SourcePositions
• source_positions_map_ : protocols::coarse_rna::CoarseRNA_Fragments
• sourceName : protocols::sparta::Sparta::SpartaLib
• SourcePositions() : protocols::coarse_rna::SourcePositions
• sp2_BAH180_rise() : core::scoring::hbonds::HBondOptions
• sp2_BAH180_rise_ : core::scoring::hbonds::HBondOptions
• space : core::scoring::APBSConfig
• space_ : protocols::match::downstream::DownstreamBuilder
• spacing_ : protocols::pockets::PocketGrid
• spairs2foldtype_ : protocols::fldsgn::topology::SheetFoldTypeManager
• 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::scoring::MembraneTopology
• 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
• spanning() : core::scoring::MembraneEmbed
• spanning_ : core::scoring::MembraneEmbed
• sparse_aa_neighbors_ : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::DoubleLazyEdge
• sparse_mat_info_for_state_ : core::pack::interaction_graph::PDNode , core::pack::interaction_graph::OnTheFlyNode
• 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_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::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator
• 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
• specificity_repacks_ : protocols::dna::DnaInterfacePacker
• SpecificResiduesNearInterfaceFilter() : protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter
• Sphere() : core::scoring::packstat::Sphere
• sphere() : core::scoring::packstat::CavityBall
• Sphere : protocols::match::BumpGrid , core::scoring::packstat::Sphere
• 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::scoring::SecondaryStructurePotential , core::kinematics::Stub
• SphericalRotationSearchPattern() : protocols::hotspot_hashing::SphericalRotationSearchPattern
• spin() : protocols::noesy_assign::CrossPeak
• Spin() : protocols::noesy_assign::CrossPeak::Spin
• spin() : protocols::noesy_assign::CrossPeak
• spin_ : protocols::docking::DockingInitialPerturbation
• spin_assign_index1_ : protocols::noesy_assign::PeakAssignment
• spin_assign_index2_ : protocols::noesy_assign::PeakAssignment
• spin_axis() : protocols::rigid::RigidBodySpinMover
• spin_axis_ : protocols::rigid::RigidBodySpinMover
• spin_id() : protocols::noesy_assign::PeakAssignment
• SpinAssignments : protocols::noesy_assign::CrossPeak::Spin
• SpinMover() : protocols::protein_interface_design::movers::SpinMover
• Splice() : protocols::protein_interface_design::movers::Splice
• splice_filter() : protocols::protein_interface_design::movers::Splice
• splice_filter_ : protocols::protein_interface_design::movers::Splice
• splice_segments_ : protocols::protein_interface_design::movers::Splice
• SpliceSegment() : protocols::protein_interface_design::movers::SpliceSegment
• spline_coeffs() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• spline_deriv() : core::scoring::etable::Etable
• spline_interpolation() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• spline_interpolator_ : core::scoring::saxs::FormFactor
• SplineFunc() : core::scoring::constraints::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_pose_into_groups() : protocols::simple_moves::GreenPacker
• SplitSDF() : core::chemical::sdf::SDFParser
• splitString() : protocols::forge::remodel::RemodelData
• SplitSurfaceVectorString() : protocols::surface_docking::SurfaceParameters
• spread_ : protocols::dna::DesignProteinBackboneAroundDNA
• spring_constant_ : protocols::optimize_weights::WeightRangeConstraint
• sqr() : protocols::frag_picker::scores::RDCScore
• 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
• SquareWell2Func() : core::scoring::constraints::SquareWell2Func
• SquareWellFunc() : core::scoring::constraints::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_ : protocols::flxbb::LayerDesignOperation
• src_ : protocols::simple_moves::symmetry::SetupNCSMover
• src_begin : protocols::forge::remodel::WorkingRemodelSet
• src_end : protocols::forge::remodel::WorkingRemodelSet
• 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() : protocols::frag_picker::VallResidue , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentInsert , core::fragment::picking_old::vall::VallResidue , protocols::forge::build::GrowRight , protocols::frag_picker::VallResidue , protocols::forge::build::SegmentRebuild , protocols::forge::remodel::WorkingRemodelSet , protocols::forge::components::BDRSegmentInfo , protocols::forge::remodel::RemodelData
• ss_ : core::fragment::picking_old::vall::VallResidue , core::fragment::picking_old::vall::eval::IdentityEval , protocols::seeded_abinitio::PlaceFragments , protocols::forge::build::SegmentInsert , protocols::forge::build::GrowLeft , protocols::frag_picker::VallResidue , protocols::forge::build::Bridge , protocols::jd2::parser::FragmentReader , protocols::forge::build::SegmentRebuild , protocols::forge::build::GrowRight , core::fragment::picking_old::vall::gen::SecStructGen
• ss_abego_types_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::ABEGO_SS_Map
• SS_Base() : protocols::fldsgn::topology::SS_Base
• ss_chunks_pose_ : protocols::hybridization::FoldTreeHybridize
• ss_cutoff_ : core::scoring::SecondaryStructureWeights
• ss_def_ : protocols::abinitio::AbrelaxApplication , protocols::topology_broker::TemplateJumpClaimer , protocols::abinitio::LoopJumpFoldCst
• 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_from_blueprint() : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::BluePrintBDR
• ss_from_blueprint_ : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::BluePrintBDR
• SS_INFO : core::pose::datacache::CacheableDataType
• SS_Info2 : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairingSet , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::potentials::sspot::HSPairPotential
• SS_Info2_COP : protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::topology::StrandPairingSet , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::HSSTriplet
• SS_Info2_OP : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::topology::StrandPairing
• ss_info_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• SS_Killhairpins_Info() : core::scoring::SS_Killhairpins_Info
• SS_KILLHAIRPINS_INFO : core::pose::datacache::CacheableDataType
• ss_lowstrand_ : core::scoring::SecondaryStructureWeights
• ss_motifs_ : protocols::match::SecondaryStructureMPM
• 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_resnum : core::scoring::Strands
• ss_str() : protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::eval::IdentityEval
• 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_type : protocols::jumping::DisulfPairing , protocols::comparative_modeling::features::SSFeature
• ss_type_ : protocols::comparative_modeling::features::SSFeature , protocols::frag_picker::quota::SecondaryStructurePool
• ss_type_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• ss_types_ : core::io::silent::SilentStructFactory
• ss_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• ss_weights_ : core::scoring::methods::EnergyMethodOptions
• ssdist_ : core::scoring::SecondaryStructurePotential
• ssdist_initializer() : core::scoring::SecondaryStructurePotential
• SSFeature() : protocols::comparative_modeling::features::SSFeature
• ssinfo_ : protocols::fldsgn::filters::SheetTopologyFilter
• sspair() : core::scoring::SecondaryStructurePotential
• SSPairPotential() : protocols::fldsgn::potentials::sspot::SSPairPotential
• sspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• sstype : protocols::forge::remodel::LineObject
• sstype_ : protocols::simple_filters::AbinitioBaseFilter , protocols::jd2::parser::BluePrint
• st_atr() : core::scoring::etable::EtableEvaluator
• st_atr_ : core::scoring::etable::EtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , protocols::relax::ClassicRelax
• st_rep() : core::scoring::etable::EtableEvaluator
• st_rep_ : core::scoring::etable::BaseEtableEnergy< Derived > , protocols::relax::ClassicRelax , core::scoring::etable::EtableEvaluator
• st_sol() : core::scoring::etable::EtableEvaluator
• st_sol_ : protocols::relax::ClassicRelax , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::EtableEvaluator
• stacked_on_terminal_res_in_original_pose_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• stage() : protocols::abinitio::IterativeBase
• stage1_1_cycles_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::FoldTreeHybridize
• stage1_2_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_3_cycles_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::FoldTreeHybridize
• 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
• stage2_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::relax::ClassicRelax , protocols::abinitio::MembraneAbinitio
• stage2_cycles_ : protocols::abinitio::MembraneAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio
• stage2_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage2_mover() : protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• stage2_repack_period : protocols::relax::ClassicRelax
• STAGE2_RESAMPLING : protocols::abinitio::IterativeBase
• stage2_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage3_cycles() : protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::relax::ClassicRelax
• stage3_cycles_ : protocols::abinitio::MembraneAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio
• stage3_mover() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::MembraneAbinitio
• stage4_cycles() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler
• stage4_cycles_ : protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• stage4_mover() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio
• stage5_cycles() : protocols::abinitio::ClassicAbinitio
• stage5_cycles_ : protocols::abinitio::ClassicAbinitio
• stage5_mover() : protocols::abinitio::ClassicAbinitio
• stage_ : protocols::abinitio::IterativeBase
• STAGE_1 : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• STAGE_2 : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• STAGE_3a : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_3b : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• STAGE_4 : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• STAGE_5 : protocols::abinitio::ClassicAbinitio
• staged_constraints_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• staged_manual_design_ : protocols::forge::remodel::RemodelMover::instruction_flags
• StageID : protocols::abinitio::ClassicAbinitio , protocols::topology_broker::TopologyBroker , protocols::abinitio::MembraneAbinitio
• 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
• standard_sampling() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• standard_sampling_WRAPPER() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• StandardDisulfPairingLibrary() : protocols::jumping::StandardDisulfPairingLibrary
• StandardPairingLibrary() : protocols::jumping::StandardPairingLibrary
• staple_gap_ : protocols::simple_moves::PeptideStapleMover
• stapler_ : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• StarAbinitio() : protocols::star::StarAbinitio
• start() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo , core::fragment::Frame , core::kinematics::Edge , protocols::rbsegment_relax::RBResidueRange , core::sequence::Sequence , protocols::noesy_assign::FoldResonance , protocols::loops::Loop , protocols::features::helixAssembly::HelicalFragment , protocols::antibody2::FrameWork , core::io::pdb::Field , protocols::jumping::Interval , core::kinematics::Edge , protocols::anchored_design::Anchor , protocols::nonlocal::Chunk , protocols::loops::SerializedLoop , core::sequence::Sequence , protocols::nonlocal::Region
• start_ : protocols::noesy_assign::FoldResonance , core::io::serialization::BUFFER , protocols::loops::Loop , protocols::simple_filters::RmsdEvaluator , protocols::nonlocal::Region , core::scoring::ResRangePredicate , protocols::jumping::Interval , protocols::anchored_design::Anchor , protocols::features::helixAssembly::HelicalFragment , protocols::floppy_tail::FloppyTailMover , core::kinematics::Edge , core::fragment::Frame , protocols::grafting::GraftMoverBase , protocols::rbsegment_relax::CCDMoveWrapper , protocols::features::strand_assembly::StrandFragment , core::scoring::packstat::trace , core::sequence::Sequence
• start_added_residue_in_aform_ : protocols::swa::monte_carlo::RNA_AddMover
• start_atom() : core::kinematics::Edge
• start_atom_ : core::kinematics::Edge
• 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_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_key() : protocols::noesy_assign::ResonanceList
• start_loop() : protocols::protein_interface_design::movers::ResidueBBDofs
• start_loop_ : protocols::protein_interface_design::movers::ResidueBBDofs
• start_new_batch() : protocols::jd2::archive::ArchiveManager
• 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_pose() : protocols::abinitio::ResolutionSwitcher
• start_pose_ : protocols::antibody::CDRH3Modeler , protocols::protein_interface_design::movers::Splice , protocols::topology_broker::StartStructClaimer , protocols::antibody::AntibodyModeler , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::H3RefineCCD
• start_pose_cuts_ : protocols::topology_broker::TopologyBroker
• start_ramp_cstweight_ : protocols::abinitio::FoldConstraints
• start_rep_weight : protocols::relax::ClassicRelax
• start_res() : protocols::toolbox::task_operations::ThreadSequenceOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::loops::LoopFromFileData , protocols::docking::DockingEnsemble , protocols::loops::LoopFromFileData , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• start_res_ : protocols::toolbox::task_operations::ThreadSequenceOperation , protocols::loophash::LoopHashMoverWrapper , protocols::simple_moves::ReturnSidechainMover , protocols::rigid::RollMover , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::loophash::LoopHashSampler , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::loophash::LoopHashDiversifier , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::loops::LoopFromFileData , protocols::docking::DockingEnsemble , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• start_residue() : protocols::features::LoopAnchorFeatures
• start_seq2() : core::sequence::DerivedSequenceMapping
• start_seq2_ : core::sequence::DerivedSequenceMapping
• start_struct : protocols::relax::SRelaxPose
• start_tags_ : protocols::swa::protein::StepWiseProteinPoseSetup
• start_time() : protocols::simple_filters::ExpiryFilter
• start_time_ : protocols::canonical_sampling::ParallelTempering , protocols::simple_filters::ExpiryFilter , protocols::jobdist::BaseJobDistributor , protocols::evaluation::TimeEvaluator
• start_time_wall_clock_ : protocols::wum::MPI_WorkUnitManager
• start_timer() : protocols::wum::MPI_WorkUnitManager
• 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
• StartFrom() : protocols::ligand_docking::StartFrom
• starting_cst_set_OP : protocols::swa::rna::FB_Pose_Data
• starting_displacement_ : protocols::hotspot_hashing::SICPatternAtTransform
• starting_dofs() : core::pack::scmin::SCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap
• starting_fold_tree : protocols::swa::rna::FB_Pose_Data
• starting_points_ : protocols::ligand_docking::StartFrom
• starting_pose() : protocols::dna::PDBOutput , protocols::jd2::JobOutputter
• starting_pose_ : protocols::abinitio::JumpingFoldConstraints , protocols::motifs::MotifDnaPacker
• starting_reference_energies_ : protocols::optimize_weights::OptEMultifunc
• starting_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• starting_templates_ : protocols::hybridization::HybridizeProtocol
• startpos_ : core::fragment::AnnotatedFragData
• StarTreeBuilder() : protocols::nonlocal::StarTreeBuilder
• StartStructClaimer() : protocols::topology_broker::StartStructClaimer
• startup() : protocols::jobdist::PlainSilentFileJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::BaseJobDistributor
• state() : protocols::forge::build::BuildInstruction , protocols::wum2::WorkUnit_ElScripts
• state_ : protocols::wum2::WorkUnit_ElScripts , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::forge::remodel::RemodelDesignMover , protocols::forge::build::BuildInstruction
• state_assignments_ : core::pack::scmin::SidechainStateAssignment
• 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::LinearMemNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::SymmLinearMemNode , 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
• StateEnergiesAndNPDs : protocols::pack_daemon::MultistateFitnessFunction
• StateEsAndNPDs : protocols::pack_daemon::DaemonSet
• StateIndices : protocols::pack_daemon::MultistateAggregateFunction
• states() : protocols::multistate_design::MultiStateFitnessFunction
• states_ : protocols::multistate_design::MultiStateFitnessFunction
• 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::moves::TrialMover
• 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_prefix() : protocols::jd2::Job
• status_prefix_ : protocols::jd2::Job
• stb_ : protocols::kinmatch::FunGroupTK
• std_dev_ : protocols::MakeRotLib::RotData
• std_devs_ : core::scoring::constraints::USOGFunc
• stddev() : core::scoring::dna::DNA_BasePotential
• stddev_ : protocols::seeded_abinitio::CAcstGenerator , core::scoring::dna::DNA_BasePotential , protocols::seeded_abinitio::CoordinateCst
• stddev_degrees_ : protocols::ligand_docking::ResidueTorsionRestraints
• steal() : core::fragment::FragData , core::fragment::SingleResidueFragData , core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::Frame , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::BBTorsionAndAnglesSRFD
• steal_def() : core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::Constraint
• steal_def_clone() : core::scoring::constraints::ConstraintSet
• steal_frags() : protocols::abinitio::Template
• 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
• StealLigandMover() : protocols::comparative_modeling::StealLigandMover
• StealSideChainsMover() : protocols::comparative_modeling::StealSideChainsMover
• steepness() : core::scoring::Membrane_FAEmbed , protocols::simple_filters::Sigmoid , core::scoring::Membrane_FAEmbed
• steepness_ : core::scoring::hbonds::HBondEnergy , protocols::simple_filters::Sigmoid , core::scoring::Membrane_FAEmbed
• stem_copy_size_ : protocols::antibody2::GraftOneCDRLoop
• step : protocols::pockets::PCluster , core::optimization::GA_Minimizer
• step_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator
• step_count() : protocols::canonical_sampling::TrajectoryRecorder
• step_count_ : protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::MetricRecorder
• step_data() : core::optimization::SimpleDerivCheckResult
• step_data_ : core::optimization::SimpleDerivCheckResult
• step_size() : protocols::match::upstream::SampleStrategyData , protocols::rigid::RigidBodyDofRandomTransMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyTransMover , protocols::simple_moves::symmetry::SymmetrySlider , protocols::rigid::RigidBodyDofSeqTransMover
• step_size_ : protocols::rigid::RigidBodyTransMover , protocols::match::upstream::SampleStrategyData , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::UniformSphereTransMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::rigid::RigidBodyDofSeqTransMover
• step_x_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator
• step_y_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator
• step_z_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcs2::GridSearchIterator
• stepSize_ : protocols::pockets::PocketGrid
• stepsize_ : core::scoring::constraints::EtableFunc
• stepwise_pose_setup_ : protocols::swa::StepWisePoseCombineSampleGenerator , protocols::swa::StepWiseIdentitySampleGenerator
• StepWiseBetaAntiParallelJumpSampleGenerator() : protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator
• StepWiseClusterer() : protocols::swa::StepWiseClusterer
• StepWiseCombineSampleGenerator() : protocols::swa::StepWiseCombineSampleGenerator
• StepWiseDoNothingSampleGenerator() : protocols::swa::StepWiseDoNothingSampleGenerator
• StepWiseFilterer() : protocols::swa::StepWiseFilterer
• StepWiseIdentitySampleGenerator() : protocols::swa::StepWiseIdentitySampleGenerator
• StepWiseJobParameters() : protocols::swa::StepWiseJobParameters
• StepWisePoseCombineSampleGenerator() : protocols::swa::StepWisePoseCombineSampleGenerator
• StepWisePoseSampleGenerator() : protocols::swa::StepWisePoseSampleGenerator
• StepWisePoseSetup() : protocols::swa::StepWisePoseSetup
• StepWiseProteinCCD_Closer() : protocols::swa::protein::StepWiseProteinCCD_Closer
• StepWiseProteinFilterer() : protocols::swa::protein::StepWiseProteinFilterer
• StepWiseProteinFragmentSampleGenerator() : protocols::swa::protein::StepWiseProteinFragmentSampleGenerator
• StepWiseProteinJumpSampleGenerator() : protocols::swa::protein::StepWiseProteinJumpSampleGenerator
• StepWiseProteinLoopBridger() : protocols::swa::protein::StepWiseProteinLoopBridger
• StepWiseProteinMainChainSampleGenerator() : protocols::swa::protein::StepWiseProteinMainChainSampleGenerator
• StepWiseProteinPacker() : protocols::swa::protein::StepWiseProteinPacker
• StepWiseProteinPoseMinimizer() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• StepWiseProteinPoseSetup() : protocols::swa::protein::StepWiseProteinPoseSetup
• StepWiseProteinResidueSampler() : protocols::swa::protein::StepWiseProteinResidueSampler
• StepWiseProteinScreener() : protocols::swa::protein::StepWiseProteinScreener
• StepWiseResidueSampler() : protocols::swa::StepWiseResidueSampler
• StepWiseRNA_AnalyticalLoopCloseSampler() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• StepWiseRNA_Base_Sugar_Rotamer() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• StepWiseRNA_BaseCentroidScreener() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• StepWiseRNA_Clusterer() : protocols::swa::rna::StepWiseRNA_Clusterer
• StepWiseRNA_CombineLongLoopFilterer() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• StepWiseRNA_JobParameters() : protocols::swa::rna::StepWiseRNA_JobParameters
• StepWiseRNA_JobParameters_Setup() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• StepWiseRNA_Minimizer() : protocols::swa::rna::StepWiseRNA_Minimizer
• StepWiseRNA_PoseSetup() : protocols::swa::rna::StepWiseRNA_PoseSetup
• StepWiseRNA_ResidueSampler() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• StepWiseRNA_RotamerGenerator() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• StepWiseRNA_RotamerGenerator_Wrapper() : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• StepWiseRNA_VDW_Bin_Screener() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• StepWiseScreener() : protocols::swa::StepWiseScreener
• stereochem() : core::chemical::carbohydrates::CarbohydrateInfo
• stereochem_ : core::chemical::carbohydrates::CarbohydrateInfo
• steric_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• STERIC_DIST_CUTOFF_squared_ : protocols::swa::RigidBodySampler
• stf() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• stf_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• stiffness() : core::scoring::dna::DNA_BasePotential
• stiffness_ : core::scoring::dna::DNA_BasePotential
• still_interested() : protocols::jd2::archive::AbstractArchiveBase , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase
• STM_STORED_TASKS : core::pose::datacache::CacheableDataType
• stochastic_pack() : protocols::simple_moves::MinPackMover
• stochastic_pack_ : protocols::simple_moves::MinPackMover
• StochasticFilter() : protocols::filters::StochasticFilter
• stop() : core::fragment::Frame , protocols::jumping::Interval , protocols::loops::Loop , protocols::nonlocal::Region , protocols::nonlocal::Chunk , protocols::antibody2::FrameWork , protocols::jd2::MpiFileBuffer , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo , core::kinematics::Edge , protocols::loops::SerializedLoop
• stop_ : protocols::nonlocal::Region , protocols::rbsegment_relax::CCDMoveWrapper , core::kinematics::Edge , protocols::loops::Loop , protocols::floppy_tail::FloppyTailMover
• stop_atom() : core::kinematics::Edge
• stop_atom_ : core::kinematics::Edge
• stop_before_condition() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• stop_before_condition_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• stop_loop() : protocols::protein_interface_design::movers::ResidueBBDofs
• stop_loop_ : protocols::protein_interface_design::movers::ResidueBBDofs
• 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 , protocols::protein_interface_design::filters::RelativeSegmentFilter
• stop_res_ : protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::loophash::LoopHashDiversifier , protocols::rigid::RollMover , protocols::loophash::LoopHashSampler , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::loophash::LoopHashMoverWrapper
• stop_running_worker() : protocols::boinc::Boinc
• stopping_condition() : protocols::design_opt::GreedyOptMutationMover , protocols::simple_moves::GenericMonteCarloMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• stopping_condition_ : protocols::design_opt::ParetoOptMutationMover , protocols::simple_moves::GenericMonteCarloMover , protocols::design_opt::GreedyOptMutationMover
• Storage : protocols::simple_moves::LoggedFragmentMover
• storage_ : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::QuotaCollector
• store() : core::fragment::CacheWrapper< T, XCacheUnit > , boost::unordered_object_pool< T, UserAllocator > , protocols::wum::SilentStructStore , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T > , boost::unordered_object_pool< T, UserAllocator > , core::fragment::CacheWrapper< T, XCacheUnit >
• store_ : 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::pdb::HeaderInformation
• store_compound() : core::io::pdb::HeaderInformation
• store_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• store_curr_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge
• store_current_derivatives() : core::optimization::LineMinimizationAlgorithm
• store_deposition_date() : core::io::pdb::HeaderInformation
• store_energies() : protocols::ddg::ddGMover
• store_energies_ : protocols::toolbox::DecoySetEvaluation
• store_experimental_technique() : core::io::pdb::HeaderInformation
• store_experimental_techniques() : core::io::pdb::HeaderInformation
• store_H3_cter_fragment() : protocols::antibody::CDRH3Modeler
• store_header_record() : core::io::pdb::FileData
• store_heterogen_names() : core::io::pdb::FileData
• store_idCode() : core::io::pdb::HeaderInformation
• store_interaction_energy_first_node() : core::pack::interaction_graph::LazyEdge
• store_interaction_energy_second_node() : core::pack::interaction_graph::LazyEdge
• store_keywords() : core::io::pdb::HeaderInformation
• store_line() : protocols::jd2::SingleFileBuffer
• store_link_record() : core::io::pdb::FileData
• store_path() : protocols::motifs::Motif
• store_record() : core::io::pdb::HeaderInformation
• store_reference_pose_geometry() : protocols::simple_moves::GreenPacker
• store_remark() : protocols::motifs::Motif
• store_rotamer_coords() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• store_rpes_ : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::LinearMemEdge
• store_title() : core::io::pdb::HeaderInformation
• store_to_channel() : protocols::jd2::MpiFileBuffer
• store_top_energy() : core::pack::annealer::MultiCoolAnnealer
• store_trie() : core::pack::rotamer_set::RotamerSet_ , core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSubset
• stored_rpes_ : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::LinearMemEdge
• storeJobStatistics() : protocols::flexpep_docking::FlexPepDockingProtocol
• str() : core::scoring::packstat::CavityBall , core::kinematics::Node
• str_type() : protocols::topology_broker::CutClaim , protocols::topology_broker::BBClaim , protocols::topology_broker::JumpClaim , protocols::topology_broker::RootClaim , protocols::topology_broker::SequenceClaim , protocols::topology_broker::DofClaim
• Strand() : protocols::fldsgn::topology::Strand
• strand() : protocols::fldsgn::topology::SS_Info2
• Strand() : protocols::fldsgn::topology::Strand
• strand1() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand1_ : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::BetaAlphaBetaMotif
• strand2() : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::BetaAlphaBetaMotif
• strand2_ : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::BetaAlphaBetaMotif
• strand_dist_cutoff_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , core::scoring::SecondaryStructureWeights , 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::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::fldsgn::topology::StrandPairingSet , protocols::abinitio::Template , protocols::jd2::parser::BluePrint
• strand_pairings_ : protocols::fldsgn::topology::StrandPairingSet , protocols::abinitio::Template , 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() : protocols::fldsgn::topology::StrandPairing , core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• StrandPairings : core::scoring::dssp::StrandPairingSet
• StrandPairingSet : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::topology::StrandPairingSet , core::scoring::dssp::StrandPairingSet , protocols::fldsgn::topology::StrandPairingSet , core::scoring::dssp::StrandPairingSet , protocols::fldsgn::topology::StrandPairingSet , protocols::fldsgn::topology::SheetSet , core::scoring::dssp::StrandPairingSet
• StrandPairingSetCOP : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::topology::SheetSet
• StrandPairingSetOP : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• Strands() : core::scoring::Strands
• strands() : core::scoring::SS_Info
• Strands() : core::scoring::Strands
• 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
• stretch() : protocols::dna::DNABasepair
• stretch_ : protocols::dna::DNABasepair
• stretch_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• strict_base_pairing_count : protocols::swa::rna::SillyCountStruct
• strict_column_mode() : core::io::silent::SilentFileData
• strict_column_mode_ : core::io::silent::SilentStruct , core::io::silent::SilentFileData
• 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::TrajectoryRecorder , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• stride_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::TrajectoryRecorder , protocols::qsar::RenderGridsToKinemage
• String : protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::HelixKinkFilter , protocols::flxbb::DesignTask , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::topology::HelixPairingSet , core::fragment::picking_old::vall::VallResidue , protocols::toolbox::task_operations::LayerOperations , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::topology::HelixPairing , core::fragment::picking_old::vall::gen::SecStructGen , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::Loop , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::flxbb::InterlockAroma , protocols::fldsgn::topology::StrandPairing , protocols::forge::build::Bridge , protocols::flxbb::FlxbbDesign , protocols::forge::build::ConnectRight
• string : protocols::simple_moves::ExtendedPoseMover
• String : protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::forge::build::SegmentInsert
• string : core::sequence::CompositeSequence , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::sequence::SequenceCoupling
• String : protocols::forge::build::GrowRight
• string : core::sequence::ChemicalShiftSequence
• String : protocols::fldsgn::potentials::SetSecStructEnergies
• string : core::scoring::dna::DirectReadoutPotential
• String : protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::flxbb::FilterStructs , protocols::forge::constraints::ConstraintFileRCG , core::fragment::picking_old::vall::eval::IdentityEval , protocols::forge::build::SegmentRebuild , protocols::jd2::parser::FragmentReader , protocols::frag_picker::VallResidue , protocols::simple_filters::HolesFilter , protocols::toolbox::task_operations::JointSequenceOperation , protocols::forge::build::GrowLeft
• string : core::io::silent::SilentStruct
• String : protocols::forge::components::VarLengthBuild
• string : core::import_pose::pose_stream::SilentFilePoseInputStream
• String : protocols::simple_filters::RangeFilter , protocols::jd2::parser::BluePrint
• string : core::sequence::SequenceProfile
• String : protocols::simple_moves::GenericMonteCarloMover , protocols::forge::build::BuildManager , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::forge::build::SegmentSwap , protocols::forge::remodel::RemodelMover , protocols::forge::components::BDRSegmentInfo , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::forge::build::BuildInstruction , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::forge::remodel::RemodelLoopMover , protocols::fldsgn::topology::SheetFoldTypeManager , core::fragment::picking_old::vall::eval::EnergyEval , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::filters::CoreDunbrackFilter , core::pose::PDBInfo , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , core::util::ABEGOManager , core::util::ABEGO , protocols::forge::build::RelativeConnectRight , protocols::forge::components::BDR , protocols::toolbox::pose_metric_calculators::FragQualCalculator , core::fragment::picking_old::vall::eval::ABEGOEval
• string_list() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• STRING_MAP : core::pose::datacache::CacheableDataType
• 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::simple_filters::ResidueSetChainEnergyFilter , protocols::toolbox::task_operations::DesignAroundOperation , protocols::simple_filters::NMerPSSMEnergyFilter
• string_string_pairs_ : protocols::jd2::Job
• string_to_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• string_to_compound_token() : core::io::pdb::HeaderInformation
• string_to_experimental_technique() : core::io::pdb::HeaderInformation
• string_to_farray() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• string_value() : core::io::silent::SilentEnergy
• string_value_ : core::io::silent::SilentEnergy
• StringRealPairs : protocols::jd2::Job
• Strings : protocols::dna::PDBOutput , protocols::jd2::Job , protocols::moves::Mover , core::io::pdb::FileData
• StringsMap : protocols::dna::PDBOutput
• StringStringPairs : protocols::jd2::Job
• StrongWolfe() : core::optimization::StrongWolfeLineMinimization
• StrongWolfeLineMinimization() : core::optimization::StrongWolfeLineMinimization
• strSURFA0 : protocols::surface_docking::SurfaceParameters
• strSURFA1 : protocols::surface_docking::SurfaceParameters
• strSURFA2 : protocols::surface_docking::SurfaceParameters
• struct_from_job() : protocols::jd2::SilentFileJobInputter , protocols::jd2::LazySilentFileJobInputter
• struct_id1_ : protocols::rotamer_recovery::RRReporterSQLite
• struct_id2_ : protocols::rotamer_recovery::RRReporterSQLite
• struct_id_selection_ : protocols::qsar::qsarOptFunc
• STRUCTURAL_CONSERVATION : core::pose::datacache::CacheableDataType
• StructuralSimilarityEvaluator() : protocols::simple_filters::StructuralSimilarityEvaluator
• structure_features_ : protocols::features::ReportToDB , protocols::features::ProteinSilentReport
• structure_has_moved() : core::scoring::Energies
• structure_is_outdated_ : core::pose::metrics::PoseMetricContainer , core::pose::metrics::StructureDependentCalculator
• structure_map_ : core::io::raw_data::RawFileData , protocols::features::ProteinSilentReport , core::io::silent::SilentFileData
• structure_moved() : core::conformation::Conformation
• structure_moved_ : core::conformation::Conformation
• structure_score : core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy
• structure_scores_features_ : protocols::features::ProteinSilentReport
• 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_ : protocols::noesy_assign::StructureDependentPeakCalibrator
• StructureScoresFeatures() : protocols::features::StructureScoresFeatures
• StructureScoresFeaturesCreator() : protocols::features::StructureScoresFeaturesCreator
• StructureSimilarityEvaluatorCreator() : protocols::simple_filters::StructureSimilarityEvaluatorCreator
• Stub() : core::kinematics::Stub , protocols::sic_dock::RigidScore , core::kinematics::Stub
• stub1() : core::chemical::orbitals::ICoorOrbitalData
• stub1_ : core::chemical::SetICoor , core::chemical::orbitals::ICoorOrbitalData
• stub2() : core::chemical::orbitals::ICoorOrbitalData
• stub2_ : core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor
• stub3() : core::chemical::orbitals::ICoorOrbitalData
• stub3_ : core::chemical::SetICoor , core::chemical::orbitals::ICoorOrbitalData
• stub_atom() : core::chemical::Adduct , core::chemical::AtomICoor
• stub_atom1() : core::kinematics::tree::BondedAtom , core::chemical::Adduct , core::kinematics::tree::Atom , core::chemical::AtomICoor , core::kinematics::tree::JumpAtom
• stub_atom1_ : core::chemical::AtomICoor , core::chemical::Adduct
• stub_atom1_id() : core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• stub_atom2() : core::kinematics::tree::JumpAtom , core::chemical::Adduct , core::kinematics::tree::Atom , core::chemical::AtomICoor , core::kinematics::tree::BondedAtom
• stub_atom2_ : core::chemical::AtomICoor , core::chemical::Adduct
• stub_atom2_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• stub_atom3() : core::chemical::Adduct , core::kinematics::tree::Atom , core::kinematics::tree::JumpAtom , core::chemical::AtomICoor , core::kinematics::tree::BondedAtom
• stub_atom3_ : core::chemical::AtomICoor , core::chemical::Adduct
• 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_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_minimize_movers() : protocols::protein_interface_design::movers::PlaceStubMover
• stub_minimize_movers_ : protocols::protein_interface_design::movers::PlaceStubMover
• stub_offset() : protocols::hotspot_hashing::HotspotStubSet
• stub_score_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_set_ : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::PlaceStubMover , protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::PlaceOnLoop
• 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 , protocols::protein_interface_design::movers::PlacementAuctionMover
• stub_sets_ : protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• StubGenerator() : protocols::hotspot_hashing::StubGenerator
• StubID() : core::id::StubID , core::kinematics::AtomTree , core::id::StubID
• StubMinimize() : protocols::protein_interface_design::movers::PlaceStubMover
• Stubs : protocols::sic_dock::RigidScore
• StubScoreFilter() : protocols::protein_interface_design::filters::StubScoreFilter
• StubScoreLoopsFilter() : protocols::protein_interface_design::filters::StubScoreLoopsFilter
• StubsetStubPair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlacementAuctionMover
• StubSetStubPos : protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::filters::StubScoreLoopsFilter
• stuck_in_network_state_loop() : core::pack::annealer::FASTERAnnealer
• stwist_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• 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() : protocols::swa::StepWiseJobParameters , protocols::swa::monte_carlo::SubToFullInfo , protocols::swa::rna::StepWiseRNA_JobParameters
• sub_to_full_ : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters , protocols::swa::monte_carlo::SubToFullInfo
• SUB_TO_FULL_INFO : core::pose::datacache::CacheableDataType
• SubArc() : core::scoring::sc::MolecularSurfaceCalculator
• SubCir() : core::scoring::sc::MolecularSurfaceCalculator
• subclusters_ : protocols::toolbox::KClusterElement
• 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::ReplicateFilter , protocols::filters::MoveBeforeFilter
• subgroup_rotamer() : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• subgroup_rotamer_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• submatrix_size() : core::pack::interaction_graph::DoubleLazyEdge
• subMatrixFile_ : protocols::frag_picker::scores::ProfileScoreSubMatrix
• submover() : protocols::moves::IteratedConvergenceMover
• submover_ : protocols::filters::MoveBeforeFilter , protocols::moves::IteratedConvergenceMover
• subpools_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• SubroutineMover() : protocols::protein_interface_design::movers::SubroutineMover
• subsample_hits() : protocols::match::Matcher
• subset() : protocols::hotspot_hashing::HotspotStubSet
• Subsitution : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• substitute_variables_in_stream() : protocols::jd2::DockDesignParser
• SubToFullInfo() : protocols::swa::monte_carlo::SubToFullInfo
• 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 >
• 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::SymmetryInfo , core::conformation::symmetry::SymmData
• success() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover , protocols::LoopRebuild , protocols::hybridization::InsertChunkMover
• success_ : protocols::hybridization::InsertChunkMover
• successful_loop_closure() : protocols::motifs::IRCollection
• successfully_initialized_ : protocols::canonical_sampling::HamiltonianExchange
• SuckerEnergy() : core::scoring::methods::SuckerEnergy
• suggest_residue_number() : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• suggest_topology() : protocols::abinitio::PairingStatistics
• suggestRadius() : core::scoring::electron_density::ElectronDensity
• SuggestValueMessage() : protocols::topology_broker::SuggestValueMessage
• suite_cluster_radius_ : protocols::swa::rna::StepWiseRNA_Clusterer
• suite_info() : protocols::rna::suite_info
• sulfur_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• sum() : core::grid::CartGrid< T > , protocols::ddg::ddGMover , protocols::cluster::DataPoint , core::scoring::EMapVector , protocols::frag_picker::scores::AdaptiveScoreHistogram
• sum_all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• sum_contributions_for_atom_pair() : core::scoring::methods::LK_BallEnergy
• sum_contributions_for_atom_pair_one_way() : core::scoring::methods::LK_BallEnergy
• sum_ddG() : protocols::simple_moves::ddG
• sum_energies() : core::scoring::etable::EtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived >
• sum_Hbond_terms() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• sum_of_neighbors_masses() : core::scoring::TenANeighborNode
• sum_of_neighbors_masses_ : core::scoring::TenANeighborNode
• SumFunc() : core::scoring::constraints::SumFunc
• sumName : protocols::sparta::Sparta::SpartaLib
• Super : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::forge::build::Bridge , protocols::forge::build::ConnectRight , core::pack::task::operation::OptH , core::conformation::signals::IdentityEvent , core::kinematics::tree::Atom_ , protocols::forge::build::BuildManager , core::conformation::signals::LengthEvent , core::fragment::picking_old::vall::VallSection , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , core::fragment::picking_old::vall::gen::VallFragmentGen , protocols::fldsgn::filters::CoreDunbrackFilter , core::kinematics::tree::BondedAtom , core::pack::task::operation::NoRepackDisulfides , protocols::forge::build::BuildInstruction , protocols::fldsgn::NcontactsCalculator , protocols::simple_filters::PackStatFilter , protocols::forge::build::RelativeConnectRight , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::potentials::SetAACompositionPotential , core::pose::signals::EnergyEvent , core::fragment::picking_old::vall::eval::IdentityEval , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::simple_filters::ShapeComplementarityFilter , core::fragment::picking_old::vall::gen::SecStructGen , protocols::forge::remodel::RemodelDesignMover , core::fragment::picking_old::vall::eval::EnergyEval , core::pose::signals::ConformationEvent , protocols::viewer::ConformationViewer , protocols::forge::remodel::RemodelAccumulator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::fldsgn::CircularPermutation , protocols::enzdes::EnzdesFlexibleRegion , protocols::fldsgn::BluePrintBDR , protocols::simple_filters::RangeFilter , protocols::forge::components::VarLengthBuild , protocols::flxbb::FilterStructs_Packstat , protocols::forge::components::BDR , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::VallLibrarian , protocols::forge::build::GrowRight , core::pose::PDBPoseMap , core::pose::datacache::ObserverCache , protocols::flxbb::FilterStructs_TotalCharge , core::pose::datacache::CacheableObserver , core::fragment::IndependentBBTorsionSRFD , protocols::forge::build::SegmentSwap , core::fragment::picking_old::vall::VallLibrary , core::conformation::signals::XYZEvent , core::fragment::picking_old::vall::eval::ABEGOEval , protocols::fldsgn::filters::NcontactsFilter , protocols::forge::build::SegmentRebuild , protocols::simple_filters::HolesFilter , core::kinematics::tree::JumpAtom , protocols::viewer::SilentObserver , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , core::pack::task::operation::OptCysHG , protocols::simple_moves::GenericMonteCarloMover , protocols::flxbb::InterlockAroma , core::fragment::picking_old::vall::gen::LengthGen , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::flxbb::FlxbbDesign , core::pose::PDBInfo , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::forge::build::SegmentInsert , protocols::forge::build::GrowLeft
• 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
• superimpose() : protocols::toolbox::DecoySetEvaluation , protocols::simple_moves::SuperimposeMover , protocols::topology_broker::CoordConstraintClaimer , protocols::toolbox::DecoySetEvaluation
• superimpose_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::fldsgn::MatchResiduesMover , protocols::simple_filters::LoopRmsdEvaluator
• superimpose_comb() : protocols::fldsgn::MatchResidues
• superimpose_on_all() : protocols::protein_interface_design::filters::RmsdFilter
• superimpose_on_all_ : protocols::protein_interface_design::filters::RmsdFilter
• superimpose_overhangs_heavy() : protocols::grafting::GraftMoverBase
• superimpose_regions_ : protocols::topology_broker::CoordConstraintClaimer
• superimpose_res_ : protocols::swa::StepWisePoseSetup
• superimpose_strand_pairings_to_templates() : protocols::hybridization::FoldTreeHybridize
• superimpose_to_first_chunk() : protocols::rna::RNA_ChunkLibrary
• SuperimposeMover() : protocols::simple_moves::SuperimposeMover
• superposition_bonus_ : core::scoring::constraints::BackboneStubConstraint
• supervoxel_dimprods_ : protocols::match::Bool3DGrid
• supervoxel_dimsizes_ : protocols::match::Bool3DGrid
• supplied_movemap_ : protocols::simple_moves::ConstrainToIdealMover
• suppress_bp_constraint_ : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_StructureParameters
• surf : core::scoring::packing::SurfVol , core::scoring::packing::PoseBalls , core::scoring::packing::SurfVolDeriv
• surf_ : core::scoring::packing::PoseBalls
• surf_dist_ : protocols::pockets::PocketGrid
• 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::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• 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_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::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• surface_exposed_ : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• SURFACE_EXPOSED_CUTOFF : core::pack::interaction_graph::SurfacePotential , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• 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_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
• surfaceAntiNormalVec : protocols::surface_docking::SurfaceParameters
• 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
• SurfaceCG : protocols::surface_docking::SurfaceParameters
• 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
• SurfaceInteractionGraph() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• SurfaceNode() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• surfaceNormalVec : protocols::surface_docking::SurfaceParameters
• SurfaceOrientMover() : protocols::surface_docking::SurfaceOrientMover
• SurfaceParameters() : protocols::surface_docking::SurfaceParameters
• surfaceParameters_ : protocols::surface_docking::SurfaceDockingProtocol
• surfaceParams_ : protocols::surface_docking::FaSlideIntoSurface
• surfacePlane : protocols::surface_docking::SurfaceParameters
• SurfacePotential() : core::pack::interaction_graph::SurfacePotential
• SurfaceSearchPattern() : protocols::hotspot_hashing::SurfaceSearchPattern
• 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
• svbksb() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• svd_s_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• svdcmp() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• swap() : core::id::DOF_ID_Map< T > , core::id::AtomID_Map< T >
• swap_atoms() : protocols::noesy_assign::FragsToAtomDist
• swap_buffer_ : protocols::wum::WorkUnitQueue_Swapped
• swap_chain() : protocols::seeded_abinitio::SwapSegment
• swap_chain_ : protocols::seeded_abinitio::SwapSegment
• swap_coordinates_in_pose() : protocols::enzdes::ModifyStoredRBConfs
• swap_edge_energies() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::DensePDEdge
• 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_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::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• 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_movemap() : protocols::loops::Loop , protocols::loops::Loops
• switch_residue_type_set() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• switch_to_fullatom() : protocols::topology_broker::TopologyClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::RigidChunkClaimer
• SwitchChainOrderMover() : protocols::simple_moves::SwitchChainOrderMover
• SwitchResidueTypeSetMover() : protocols::simple_moves::SwitchResidueTypeSetMover
• sym_docking_mover_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• sym_dof_name() : protocols::simple_filters::ShapeComplementarityFilter
• sym_dof_name_ : protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::simple_filters::ShapeComplementarityFilter
• sym_dof_names() : protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::RotamerBoltzmannWeight
• sym_dof_names_ : protocols::simple_filters::InterfaceSasaFilter , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::simple_filters::RotamerBoltzmannWeight
• sym_rotamer_sets_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• SymAtomTreeMinimizer() : core::optimization::symmetry::SymAtomTreeMinimizer
• SymAtomTreeMultifunc() : core::optimization::symmetry::SymAtomTreeMultifunc
• symbol() : core::chemical::Element
• symbol2index() : core::util::ABEGOManager
• symbol_ : core::chemical::Element
• 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
• 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_ddG() : protocols::simple_moves::ddG
• symm_definition_file_ : protocols::symmetric_docking::SymDockBaseProtocol
• 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_ptrs : core::scoring::electron_density::ElectronDensity
• 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_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 , core::pack::task::operation::RestrictToInterface
• symmetric_task_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symmetric_transform() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetric_transforms_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• symmetrical_allow_hbonds() : core::scoring::symmetry::SymmetricScoreFunction
• SymmetricConformation : core::scoring::symmetry::SymmetricScoreFunction , core::conformation::symmetry::SymmetricConformation , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::simple_moves::symmetry::SymRotamerTrialsMover , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::conformation::symmetry::SymmetricConformation , core::scoring::symmetry::SymmetricEnergies , protocols::symmetric_docking::SymFoldandDockRbTrialMover , core::optimization::symmetry::SymAtomTreeMinimizer , protocols::symmetric_docking::SymDockingHiRes , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::symmetric_docking::SymDockProtocol , core::scoring::SecondaryStructurePotential , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymmetricRMSMover
• 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::symmetry::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_
• symmetry_ : protocols::simple_filters::AlaScan , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::simple_moves::ddG , protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_moves::DesignRepackMover , protocols::simple_filters::DdgFilter
• symmetry_compliance() : protocols::noesy_assign::PeakAssignment
• symmetry_compliance_ : protocols::noesy_assign::PeakAssignment
• symmetry_compliance_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• symmetry_definition() : protocols::simple_filters::RelativePoseFilter
• symmetry_definition_ : protocols::simple_filters::RelativePoseFilter
• Symmetry_Info() : core::conformation::symmetry::SymmetricConformation
• symmetry_info() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• Symmetry_Info() : core::conformation::symmetry::SymmetricConformation
• symmetry_name_ : core::conformation::symmetry::SymmData
• symmetry_status_ : core::pack::task::PackerTask_
• symmetry_type_ : core::conformation::symmetry::SymmData
• SymmetryInfo : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::symmetric_docking::SymDockProtocol , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , core::conformation::symmetry::SymmetryInfo , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , core::conformation::symmetry::SymmetryInfo , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• SymmetryInfoCOP : core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::optimization::symmetry::SymMinimizerMap , core::scoring::SecondaryStructurePotential , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• SymmetryInfoOP : core::optimization::symmetry::SymAtomTreeMinimizer , protocols::simple_moves::symmetry::SymmetricRMSMover , protocols::fldsgn::potentials::SetSecStructEnergies
• SymmetrySlider() : protocols::simple_moves::symmetry::SymmetrySlider
• symminfo_ : core::io::silent::ProteinSilentStruct_Template< T > , protocols::topology_broker::FibrilModelingClaimer , core::io::silent::BinaryProteinSilentStruct
• 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
• symmOps : core::scoring::electron_density_atomwise::ElectronDensityAtomwise , core::scoring::electron_density::ElectronDensity
• 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
• sync_batches() : protocols::jd2::archive::MPIArchiveJobDistributor
• sync_objects_with_flags() : protocols::docking::TemperedDocking , protocols::antibody2::AntibodyModelerProtocol , protocols::docking::DockingProtocol , protocols::docking::DockingLowRes
• SYNONYM : core::io::pdb::HeaderInformation