- s -

• s : protocols::pockets::SmallMol
• s1_ : protocols::fldsgn::topology::StrandPairing
• s2_ : protocols::fldsgn::topology::StrandPairing
• s_ : protocols::normalmode::NormalMode
• s_ik : protocols::cluster::Exemplar
• s_kk : protocols::cluster::DataPoint
• sa_ : protocols::frag_picker::VallResidue
• sa_norm_ : protocols::frag_picker::VallResidue
• sa_scale_ : protocols::pack_daemon::FASTER_IG_Repacker
• safe_root_ : protocols::forge::remodel::RemodelWorkingSet
• salt_bridge_total_ : protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• same_build_resids_for_all_csts_ : protocols::match::Matcher
• same_strand_ : protocols::jumping::SameStrand , protocols::jumping::SheetBuilder
• sample_all_o2prime_ : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_bb_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_beta_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• sample_both_sugar_base_rotamer_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• sample_level_ : protocols::match::upstream::SampleStrategyData
• sample_lower_nucleoside_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_near_a_form_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_nonpivot_torsions_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sample_nucleoside_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• sample_nucleoside_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• sample_nucleoside_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• sample_omega_for_pre_prolines_ : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• sample_ONLY_multiple_virtual_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sample_pc : protocols::flexpep_docking::FlexPepDockingFlags
• sample_range_large_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_range_small_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• sample_rotwells_unif_ : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• sample_scorefxn_ : protocols::stepwise::modeler::StepWiseModeler
• sample_strategy_for_chi_ : protocols::match::upstream::BuildSet
• sample_sugar : protocols::stepwise::modeler::rna::sugar::SugarModeling
• sample_suite_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• sample_type_ : protocols::enzdes::DiffAtomSasaFilter , protocols::simple_moves::GenericMonteCarloMover
• sample_types_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_moves::GenericMonteCarloMover
• sample_upper_nucleoside_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sample_virtual_sugar_string_list_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• sample_weight_const_ : protocols::loophash::LoopHashMoverWrapper
• sample_weight_str_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• sampled_space_file_ : protocols::ligand_docking::Transform
• sampled_structures_ : protocols::simple_moves::CombinePoseMover
• sampler_ : protocols::docking::TemperedDocking , protocols::match::upstream::ProteinUpstreamBuilder , protocols::nonlocal::Chunk , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::StepWiseSampleAndScreen
• sampler_assert_no_virt_sugar_sampling_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_beta_rotamer_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_extra_epsilon_rotamer_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• sampler_include_torsion_value_in_tag_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::screener::TagDefinition
• sampler_max_centroid_distance_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_num_pose_kept_ : protocols::stepwise::options::StepWiseBasicOptions
• sampler_perform_phosphate_pack_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sampler_silent_file_ : protocols::stepwise::options::StepWiseBasicOptions
• sampler_try_sugar_instantiation_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• samples_ : protocols::helical_bundle::PerturbBundleOptions
• sampling_chunk_ : protocols::hybridization::ChunkTrialMover
• sampling_fold_tree_ : protocols::abinitio::KinematicControl
• sampling_mode_ : protocols::matdes::SymDofMover
• sampling_protocol_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicTaskControl
• sampling_temperature_ : protocols::simple_moves::sidechain_moves::SidechainMover
• SASA : protocols::analysis::PerResidueInterfaceData
• Sasa_ : protocols::analysis::InterfaceAnalyzerMover
• sasa_ : protocols::features::helixAssembly::HelicalFragment
• sasa_cutoff_ : protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::simple_moves::ConsensusDesignMover
• sasa_filter_ : protocols::features::helixAssembly::HelixBundleFeatures , protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• sasa_threshold_ : protocols::simple_filters::ChiWellRmsdEvaluator
• save_all_solutions_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• save_archive_time_interval_ : protocols::jd2::archive::ArchiveManager
• save_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover
• save_state_interval_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• save_times_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• saved_accept_file_name_ : protocols::simple_moves::GenericMonteCarloMover
• saved_bb_constraints_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• saved_coord_constraints_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_ft_ : protocols::hybridization::HybridizeFoldtreeDynamic
• saved_input_pose_ : protocols::protein_interface_design::PatchdockReader
• saved_input_tag_ : protocols::protein_interface_design::PatchdockReader
• saved_n_residue_ : protocols::hybridization::HybridizeFoldtreeDynamic
• saved_native_pose_ : protocols::protein_interface_design::PatchdockReader
• saved_native_tag_ : protocols::protein_interface_design::PatchdockReader
• saved_placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• saved_pose_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_prevent_repacking_ : protocols::protein_interface_design::movers::PlaceStubMover
• saved_state_poses_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• saved_structs_ : protocols::jd2::SilentFileJobOutputter
• saved_stub_sets_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• saved_transformations_ : protocols::protein_interface_design::PatchdockReader
• saved_trial_number_file_ : protocols::simple_moves::GenericMonteCarloMover
• sc_ : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid
• 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::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::RefineBetaBarrel , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• sc_min_only : protocols::simple_moves::ShakeStructureMover
• sc_only_ : protocols::hotspot_hashing::HotspotStubSet , protocols::simple_filters::TaskAwareSASAFilter
• sc_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• sc_scale_ : protocols::cryst::LoadDensityMapMover
• sc_value : protocols::analysis::InterfaceData
• scaf_name_ : protocols::match::output::PDBWriter
• scaffold_fragment_data : protocols::motif_grafting::movers::MotifMatch
• scaffold_movemap_ : protocols::grafting::AnchoredGraftMover
• scaffold_status_ : protocols::hotspot_hashing::HotspotStub
• scaffoldHigh : protocols::motif_grafting::movers::motif2scaffold_indexes
• scaffoldLow : protocols::motif_grafting::movers::motif2scaffold_indexes
• 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
• scale_dynamic_ : protocols::normalmode::NormalModeRelaxMover
• scale_factor_ : protocols::frag_picker::SidechainContactDistCutoff , protocols::optimize_weights::ScaleAnnealerTemperatureOperation
• scale_temp_cycles_ : protocols::loop_modeling::LoopProtocol
• scaling_ : protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_moves::FavorSequenceProfile
• scanner_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• scc_ : protocols::simple_filters::ShapeComplementarityFilter
• 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
• sch_stage_ : protocols::mpi_refinement::MPI_Refine_Master
• scheduled_ : protocols::md::MDBase
• scheduler_ : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• scheme_file_ : protocols::antibody::AntibodyNumberingParser
• schemes_defined_ : protocols::antibody::AntibodyNumberingParser
• scmin_ : protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scmin_mover_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• score : protocols::hybridization::TMalign , protocols::sic_dock::CBScoreVisitor , protocols::simple_filters::SAXSScoreFilter , protocols::stepwise::legacy::modeler::rna::Cluster_Member
• score_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::Template , protocols::fldsgn::topology::DimerPairing , protocols::moves::MoverStatistics , protocols::nonlocal::SmoothPolicy::Candidate , protocols::simple_filters::PDDFScoreFilter
• score_cut_count : protocols::stepwise::modeler::rna::Filterer_Count
• score_cut_per_batch_ : protocols::abinitio::HedgeArchive
• score_cutoff_ : protocols::docking::DockingProtocol , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::task_operations::InteractingRotamerExplosion
• score_d8 : protocols::hybridization::TMalign
• score_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_expression_ : protocols::pack_daemon::EntityFunc
• score_file_tags_ : protocols::jd2::ScoreOnlyJobOutputter
• score_filt_ : protocols::loophash::LoopHashSampler
• score_filter : protocols::flexpep_docking::FlexPepDockingFlags
• score_function_ : protocols::cryst::SetCrystWeightMover , protocols::dna::PDBOutput , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::RotamerDump::RotamerDumpMover , protocols::simple_moves::ScoreMover
• score_function_ref_ : protocols::cryst::SetCrystWeightMover
• score_fxn_ : protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol , protocols::simple_moves::CoupledMover , protocols::simple_moves::CyclizationMover
• score_high_res_ : protocols::surface_docking::FullatomRelaxMover
• score_list_ : protocols::optimize_weights::OptEMultifunc
• score_log_file_ : protocols::protein_interface_design::filters::FilterScanFilter
• score_low_res_ : protocols::surface_docking::CentroidRelaxMover
• score_map : protocols::qsar::qsarOptData
• score_map_ : protocols::antibody_legacy::AntibodyModeler , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::qsar::scoring_grid::GridManager , protocols::simple_moves::ScoreMover , protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• score_margin_ : protocols::docking::DockingHighResFilter
• score_min_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_min_defined_ : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• score_offset_ : protocols::canonical_sampling::SimulatedTempering
• score_only : protocols::flexpep_docking::FlexPepDockingFlags
• score_only_ : protocols::enzdes::DetectProteinLigandInterface , protocols::outputter::SilentFileOutputter
• score_output_file_name_ : protocols::match::MatcherTask
• score_output_filename_ : protocols::match::output::MatchScoreWriter
• score_pairmatrix_ : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• 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_sidechain_pack_ : protocols::surface_docking::SurfaceDockingProtocol
• score_stage1_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage2_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage2_beginning : protocols::relax::ClassicRelax
• score_stage2_end : protocols::relax::ClassicRelax
• score_stage2_half : protocols::relax::ClassicRelax
• score_stage2_quarter : protocols::relax::ClassicRelax
• score_stage3a_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage3b_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage4_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• score_stage4rot_ : protocols::abinitio::ClassicAbinitio
• score_stage4rot_sc_ : protocols::abinitio::ClassicAbinitio
• score_stage5_ : protocols::abinitio::ClassicAbinitio
• score_stride_ : protocols::canonical_sampling::SilentTrajectoryRecorder
• score_term_ : protocols::features::TopCountOfAllInputs , protocols::features::TopCountOfEachInput
• score_threshold_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_filters::MotifScoreFilter
• score_type : protocols::mpi_refinement::MethodParams
• score_type_ : 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 , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ConstrainToIdealMover , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type_features_ : protocols::features::ProteinSilentReport
• score_type_name_ : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• score_type_threshold_ : protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ScoreTypeFilter
• score_types_ : protocols::simple_filters::ScoreCutoffFilter
• score_value_ : protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter
• score_variations_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• score_variations_are_clean_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• score_weights_ : protocols::frag_picker::scores::FragmentScoreManager
• scored_context_pose_ : protocols::flexpack::OtherContextScoreFunction
• scored_core_ : protocols::abinitio::IterativeBase
• scored_frag_cycle_ratio_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• scorefile_ : protocols::jobdist::PlainPdbJobDistributor , protocols::simple_moves::ScoreMover
• scorefile_name_ : protocols::jd2::FileJobOutputter , protocols::jobdist::PlainPdbJobDistributor
• scorefile_writer_ : protocols::enzdes::EnzdesJobOutputter
• scorefilter_ : protocols::docking::DockingHighResFilter
• scorefunction_ : protocols::docking::DockingHighResFilter
• scorefunction_initialized : protocols::simple_moves::ShakeStructureMover
• SCOREFXN : protocols::loop_modeling::ToolboxKeys
• scorefxn : protocols::simple_moves::ShakeStructureMover
• scorefxn_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::analysis::PeptideDeriverPoseOutputter , protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::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::DockingLowRes , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::FaDockingSlideIntoContact , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::farna::RNA_Minimizer , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::InterfaceFeatures , protocols::features::TotalScoreFeatures , protocols::flexpack::FlexPacker , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::DesignTask , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::hybridization::DomainAssembly , protocols::hybridization::FoldTreeHybridize , protocols::jd2::archive::EvaluatedArchive , protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::RigidSearchMover , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::md::MDBase , protocols::motifs::MotifDnaPacker , protocols::moves::JumpOutMover , protocols::moves::RampingMover , protocols::moves::SimulatedTempering , protocols::multistate_design::MultiStateFitnessFunction , protocols::normalmode::NormalModeMinimizer , protocols::pmut_scan::PointMutScanDriver , protocols::pose_reporters::EnergyReporter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::Revert , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , protocols::relax::WorkUnit_BatchRelax , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::JScoreEvaluator , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ScoreEvaluator , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ddG , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::Scorer , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::symmetric_docking::SymSidechainMinMover , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• scorefxn_cen_cst : protocols::loophash::LoopHashLibrary
• scorefxn_cen_cst_ : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashDiversifier
• scorefxn_centroid_ : protocols::abinitio::Protocol
• scorefxn_deriver_ : protocols::analysis::PeptideDeriverFilter
• scorefxn_design_ : protocols::flxbb::FlxbbDesign
• scorefxn_fa_ : protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher
• scorefxn_high_ : protocols::docking::DockingEnsemble
• scorefxn_hires_ : protocols::symmetric_docking::SymDockBaseProtocol
• scorefxn_input_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• scorefxn_low_ : protocols::docking::DockingEnsemble
• scorefxn_lowres_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::symmetric_docking::SymDockBaseProtocol
• scorefxn_minimize_ : protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::DesignRepackMover
• scorefxn_minimizer_ : protocols::analysis::PeptideDeriverFilter
• scorefxn_name_ : protocols::simple_moves::symmetry::TaskAwareSymMinMover
• scorefxn_obj_ : protocols::md::MDBase
• scorefxn_pack_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes
• scorefxn_rama_cst : protocols::loophash::LoopHashLibrary
• scorefxn_rama_cst_ : protocols::loophash::LocalInserter_SimpleMin , protocols::loophash::LoopHashDiversifier
• scorefxn_rb_ : protocols::RBSegmentRelaxImpl
• scorefxn_relax_ : protocols::flxbb::FlxbbDesign
• scorefxn_repack_ : protocols::enzdes::BackboneSampler , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::DesignRepackMover
• scorefxn_repack_greedy_ : protocols::enzdes::PackRotamersMoverPartGreedy
• scorefxn_sampling_ : protocols::rbsegment_relax::OptimizeThreadingMover
• scorename : protocols::md::MDscheduleData
• scorename_ : protocols::filters::Filter
• scorer_ : protocols::nonlocal::SmoothPolicy
• scores_ : 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
• scorescale_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• scoretype : protocols::md::MDscheduleData
• scoretype_ : protocols::pose_reporters::EnergyReporter
• scoring_ : protocols::frag_picker::CompareTotalScore
• scoring_scheme_ : protocols::frag_picker::CustomScoreSelector
• scoringEval_counter : protocols::match::downstream::ScoringSecMatchRPE
• scrambled_job_order_ : protocols::jd2::ShuffleFileSystemJobDistributor
• scratch_ : protocols::simple_moves::sidechain_moves::SidechainMover
• scratch_dir_ : protocols::simple_filters::ExternalEvaluator
• scratch_poses_ : protocols::farna::BasePairStepLibrary
• scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• screen_all_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• screen_for_donor_contact_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• screener_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• screener_whose_counts_to_check_ : protocols::stepwise::screener::IntegrationTestBreaker
• screeners_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::StepWiseSampleAndScreen
• screening_moving_rsd_at_origin_ : protocols::stepwise::screener::VDW_BinScreener
• screening_pose_ : protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::NativeRMSD_Screener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::VDW_BinScreener
• screening_pose_list_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• scrfxn_ : protocols::make_rot_lib::MakeRotLibMover
• 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
• sd_ : protocols::simple_moves::symmetry::SetupNCSMover
• sd_range_ : protocols::match::upstream::SampleStrategyData
• search13_ : protocols::pockets::PocketGrid
• search_density_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• search_points_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• search_radius_ : protocols::electron_density::DensityMorphingMover
• search_stubs_ : protocols::hotspot_hashing::SearchPatternRotSetOp
• searchpoints_ : protocols::hotspot_hashing::CartesianSearchPattern , protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SphericalRotationSearchPattern
• sec_matcher_ : protocols::match::downstream::SecondaryMatchUpstreamResProcessor
• sec_shift_data_ : protocols::frag_picker::VallResidue
• sec_struct_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• secmatch_prot_ : protocols::enzdes::PoseFoundResiduesCombination
• secmatch_scotypes_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• secmatch_value_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• second : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• second_ : protocols::match::downstream_hit , protocols::match::Hit
• second_atom_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• second_mover_ : protocols::moves::JumpOutMover
• second_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• secondary_shifts_ : protocols::frag_picker::CS2ndShift
• secondary_structure_ : protocols::jumping::SameStrand , protocols::jumping::SheetBuilder
• seconds_ : protocols::simple_filters::ExpiryFilter
• seconds_to_keep_files_alive_ : protocols::jd2::MpiFileBuffer
• secstruct : protocols::farna::TorsionSet , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• secstruct_ : 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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::viewer::ConformationViewer
• secstruct_defined_ : protocols::farna::RNA_StructureParameters
• secstruct_input_ : protocols::fldsgn::filters::SheetTopologyFilter
• secstructure_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• section_index_ : protocols::frag_picker::VallResidue
• 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
• seeds_only_ : protocols::seeded_abinitio::SeedFoldTree
• seeds_pdb_ : protocols::seeded_abinitio::SwapSegment
• seeds_presence_ : protocols::seeded_abinitio::SwapSegment
• seg_len_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• seg_size : protocols::forge::remodel::RemodelGlobalFrame
• seg_type : protocols::rbsegment_relax::RBResidueRange
• seg_vector_ : protocols::seeded_abinitio::SegmentHybridizer
• segment_ : protocols::rbsegment_relax::RBSegmentMover
• segment_definitions_ : protocols::scoring::ResidualDipolarCouplingRigidSegments
• segment_id : protocols::features::SecondaryStructureSegment
• segments_ : protocols::backrub::BackrubMover , protocols::rbsegment_relax::RBSegment
• select_around_resnums_ : protocols::simple_filters::EnergyPerResidueFilter
• select_low_ : protocols::helical_bundle::BundleGridSampler
• select_range_ : protocols::fldsgn::filters::HelixKinkFilter
• select_resnums_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::simple_filters::EnergyPerResidueFilter
• select_weights_ : protocols::jd2::archive::EvaluatedArchive
• selected_boundary_residues_ : protocols::toolbox::SelectResiduesByLayer
• selected_core_residues_ : protocols::toolbox::SelectResiduesByLayer
• selected_pairings_ : protocols::jumping::MembraneJump
• selected_resis_ : protocols::simple_filters::SaveResfileToDiskFilter
• selected_resis_property_ : protocols::simple_filters::SaveResfileToDiskFilter
• selected_surface_residues_ : protocols::toolbox::SelectResiduesByLayer
• selection_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::TruncatedScoreEvaluator
• selection_bias_ : protocols::hybridization::CartesianSampler
• selection_from_segment_cache_ : protocols::protein_interface_design::filters::RmsdFilter
• selectmode_ : protocols::md::MDBase
• selector_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim , protocols::frag_picker::FragmentPicker , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::loops::loop_mover::LoopCM
• selector_filters_ : protocols::rosetta_scripts::MultiplePoseMover
• selector_list_ : protocols::environment::claims::EnvClaim
• selector_sfxn_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• selector_tag_ : protocols::rosetta_scripts::MultiplePoseMover
• selectors_ : protocols::frag_picker::CompositeFragmentSelector , protocols::pose_selectors::LogicalSelector , protocols::rosetta_scripts::MultiplePoseMover
• selectortype_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• self_transition_ : protocols::canonical_sampling::SimulatedTempering
• semi_energy_dist_ : protocols::make_rot_lib::RotData
• semi_prob_dist_ : protocols::make_rot_lib::RotData
• semiexpl_water_cutoff_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• semirotameric_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::make_rot_lib::RotData
• send_level_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• send_wu_time_ : protocols::wum::MPI_WorkUnitManager
• send_wu_time_n_ : protocols::wum::MPI_WorkUnitManager
• sent_termination_ : protocols::mpi_refinement::MPI_Refine_Master
• sentCount_ : protocols::moves::UDPSocketClient
• separate_moving_residue_to_estimate_baseline_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• separate_prt_ligand_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• separated_energy : protocols::analysis::PerResidueInterfaceData
• separated_interface_score : protocols::analysis::InterfaceData
• separated_SASA : protocols::analysis::InterfaceData
• separated_sasa : protocols::analysis::PerResidueInterfaceData
• separated_total_energy : protocols::analysis::InterfaceData
• seq_ : protocols::seeded_abinitio::GrowPeptides
• seq_design_creator_ : protocols::antibody::design::AntibodyGraftDesignMover
• seq_designer_ : protocols::antibody::design::AntibodyDesignMover
• seq_num : protocols::stepwise::modeler::rna::Residue_info
• seq_recovery_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• seq_sep : protocols::jumping::DisulfPairing
• 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_separation_ : protocols::seeded_abinitio::CAcstGenerator
• seqfrags_only_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• seqmap_ : protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelConstraintGenerator
• seqmapping_ : protocols::frag_picker::scores::FragmentChunkCrms
• seqpos : protocols::simple_filters::nmer_svm_res_data
• seqpos1_ : protocols::constraints_additional::SequenceCouplingConstraint
• seqpos2_ : protocols::constraints_additional::SequenceCouplingConstraint
• seqpos_ : protocols::contact_map::ContactPartner , protocols::enzdes::ResidueConformerFilter , protocols::metal_interface::MetalSiteResidue , protocols::motifs::BuildPosition , protocols::pockets::PocketConstraint , protocols::simple_moves::PeptideStapleMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• seqpos_aa_vals_vec_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• seqpos_aligned_start_ : protocols::hybridization::InsertChunkMover
• seqpos_aligned_stop_ : protocols::hybridization::InsertChunkMover
• seqpos_for_geomcst_ : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• seqpos_map_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• seqpos_moved_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• seqpos_start_ : protocols::hybridization::InsertChunkMover
• seqpos_stop_ : protocols::hybridization::InsertChunkMover
• seqprof_ : protocols::simple_moves::ConsensusDesignMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqprof_filename_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• seqsep_intcpt_ : protocols::abinitio::abscript::AbscriptStageMover
• seqsep_slope_ : protocols::abinitio::abscript::AbscriptStageMover
• sequence : protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet , protocols::loophash::BBExtraData , protocols::sparta::Sparta::SpartaLib
• sequence_ : protocols::abinitio::AbrelaxApplication , protocols::frag_picker::CSTalosIO , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::TorsionBinIO , protocols::frag_picker::VallChunk , protocols::frags::RMSVallData , protocols::frags::TorsionFragment , protocols::frags::VallData , protocols::jd2::parser::BluePrint , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::NoesyModule , protocols::noesy_assign::ResonanceList , protocols::simple_moves::ExtendedPoseMover , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• sequence_alignment_ : protocols::hybridization::InsertChunkMover
• sequence_alignment_local_ : protocols::hybridization::InsertChunkMover
• sequence_alignments_ : protocols::hybridization::ChunkTrialMover
• sequence_chunks_ : protocols::seeded_abinitio::GrowPeptides
• sequence_claim_ : protocols::topology_broker::SequenceClaimer
• sequence_claims_ : protocols::topology_broker::TopologyBroker
• sequence_coupling_ : protocols::constraints_additional::SequenceCouplingConstraint
• sequence_indexer_ : protocols::match::output::SameSequenceGrouper
• sequence_length_ : protocols::frag_picker::JCouplingIO
• sequence_map_ : protocols::antibody::AntibodyInfo
• sequence_match_position_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_match_sequence_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_matched_fragments_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• sequence_number_resolver_ : protocols::topology_broker::TopologyBroker
• sequence_pos_map_ : protocols::match::output::SameSequenceAndDSPositionGrouper
• sequence_rama_tables_ : protocols::frag_picker::scores::RamaScore
• sequence_shift_ : protocols::topology_broker::FibrilModelingClaimer
• sequences_ : protocols::toolbox::task_operations::JointSequenceOperation
• sequenceSep_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• seqx : protocols::hybridization::TMalign
• seqy : protocols::hybridization::TMalign
• serial_data_ : protocols::wum::WorkUnitBase
• set_as_mover_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• set_fold_tree_from_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• set_jumps_manually : protocols::seeded_abinitio::SeedFoldTree
• set_names_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
• set_sampler_ : protocols::matdes::SymDofMover
• set_task_for_filters_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• set_tf_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• setmap_type_ : protocols::cryst::SetRefinementOptionsMover
• setup_align_pose_ : protocols::forge::constraints::InvrotTreeRCG
• setup_complete_ : protocols::pack_daemon::PackDaemon
• setup_movers_ : protocols::forge::components::VarLengthBuild
• sf_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover
• sfd_ : protocols::inputter::SilentFileInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::SilentFileJobInputter , protocols::outputter::SilentFileOutputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::setup::StepWiseCSA_JobDistributor , protocols::viewer::SilentObserver
• sfx_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover
• sfxn0_ : protocols::simple_moves::CombinePoseMover
• sfxn_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::cluster::GatherPosesMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::forge::remodel::RemodelAccumulator , protocols::helical_bundle::BundleGridSampler , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::downstream::ScoringSecMatchRPE , protocols::mpi_refinement::StructAvrgMover , protocols::normalmode::NormalModeRelaxMover , protocols::pack_daemon::DynamicAggregateFunction , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::sidechain_moves::SidechainMCMover
• sfxn_cen_ : protocols::normalmode::NormalModeRelaxMover
• sfxn_cycles_ : protocols::loop_modeling::LoopProtocol
• sfxn_set_ : protocols::helical_bundle::BundleGridSampler
• share_build_points_for_geomcsts_ : protocols::match::MatcherTask
• shave_frac_ : protocols::mpi_refinement::StructAvrgMover
• shear_ : protocols::dna::DNABasepair
• shear_min_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_min_type_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• shear_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_sequence_mover_ : protocols::surface_docking::FullatomRelaxMover
• shear_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• sheet_ : protocols::nonlocal::SheetTranslate
• sheet_center_ : protocols::fldsgn::topology::Sheet
• sheet_id_ : protocols::features::strand_assembly::SandwichFragment
• 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
• sheets_ : protocols::fldsgn::topology::SheetSet , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::topology_broker::TemplateJumpClaimer
• shift_ : protocols::dna::DNABasestep
• SHIFT_DIR : protocols::sparta::Sparta::SpartaLib
• shmem_ : protocols::boinc::BoincCurrentPoseObserver
• short_backrub_mover_ : protocols::simple_moves::CoupledMover
• short_frag_cycle_ratio_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• short_insert_region_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• shortest_path_ : protocols::constraints_additional::MaxSeqSepConstraintSet
• shortRange_ : protocols::match::downstream::ScoringSecMatchRPE
• shorts_ : protocols::moves::UDPSocketClient::UUID
• shove_residues_ : protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::TryRotamers
• show_extended_ : protocols::anchored_design::AnchoredDesignMover
• show_H_state : protocols::viewer::GraphicsState
• show_packer_task_ : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::RotamerTrialsMover
• show_viol_level_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• shrink_factor_ : protocols::match::Bool3DGridKinemageWriter
• shrink_frag_ends_ : protocols::simple_moves::BBGaussianMover
• shuffle_order_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• sic_fast_ : protocols::hotspot_hashing::SICPatternAtTransform
• side_chain_only_ : protocols::simple_moves::CopyDofMover
• side_chains_only_ : protocols::pockets::PocketGrid
• side_inv_ : protocols::scoring::ImplicitFastClashCheck
• side_ONE_NUM_pose_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_ONE_pose_list_id_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_one_tag : protocols::stepwise::modeler::rna::Combine_Tags_Info
• side_TWO_NUM_pose_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_TWO_pose_list_id_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• side_two_tag : protocols::stepwise::modeler::rna::Combine_Tags_Info
• sidechain_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , 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
• sig_ : protocols::simple_filters::MultipleSigmoids
• sigAxisR_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigAxisT_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigma_ : protocols::fldsgn::topology::DimerPairing
• sigma_rot : protocols::rbsegment_relax::GaussianRBSegmentMover
• sigma_trans : protocols::rbsegment_relax::GaussianRBSegmentMover
• sign1_ : protocols::fldsgn::topology::DimerPairing
• sign2_ : protocols::fldsgn::topology::DimerPairing
• signature_map_ : protocols::match::output::PDBWriter
• sigOffAxisR_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• sigOffAxisT_ : protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegment , protocols::rbsegment_relax::StrandTwistingMover
• silent_ : protocols::forge::remodel::RemodelMover::instruction_flags
• silent_Es_ : protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• silent_file_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::jd2::SilentFileJobOutputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::setup::StepWiseJobDistributor
• silent_file_data_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• silent_file_name_ : protocols::viewer::SilentObserver
• silent_file_out_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList
• silent_file_stream_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_stream_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_file_tags_ : protocols::jd2::SilentFileJobOutputter
• silent_files_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silent_files_in_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• silent_job_outputter_ : protocols::enzdes::EnzdesJobOutputter
• silent_output_ : protocols::enzdes::EnzdesJobOutputter
• silent_score_file_ : protocols::abinitio::AbrelaxApplication
• silent_struct_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• silentname_ : protocols::md::MDBase
• silentout_file_name_ : protocols::abinitio::Protocol
• sim_anneal_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• sim_origin_ : protocols::abinitio::abscript::RigidChunkCM
• sim_replace_obj_ : protocols::mpi_refinement::Clusterer , protocols::mpi_refinement::MPI_Refinement
• sim_selector_ : protocols::abinitio::abscript::RigidChunkCM
• similarity_measure_ : protocols::mpi_refinement::Clusterer
• similarity_method_ : protocols::mpi_refinement::Clusterer
• simple_append_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• simple_ft_ : protocols::protein_interface_design::movers::SetAtomTree
• simple_inserter_ : protocols::loophash::FastGapMover
• simple_rmsd_cutoff_relax_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Relaxer
• simtol_ : protocols::mpi_refinement::Clusterer
• simultaneous_cycles_ : protocols::forge::remodel::RemodelLoopMover
• single_chain_ : protocols::frag_picker::nonlocal::NonlocalFrags
• single_state_entity_data_ : protocols::multistate_design::MultiStateEntity< T >
• size : protocols::viewer::triangleIterator
• size_ : protocols::backrub::BackrubSegment , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::farna::TorsionSet , protocols::moves::ReplicaExchangeMC , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• size_list_ : protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• size_per_coords_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• size_x_ : protocols::pockets::PocketGrid
• size_y_ : protocols::pockets::PocketGrid
• size_z_ : protocols::pockets::PocketGrid
• skip_ala_scan_ : protocols::simple_filters::RotamerBoltzmannWeight
• skip_antigen_reports_ : protocols::antibody::AntibodyFeatures
• skip_best_check_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• skip_ccd_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• skip_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• skip_completely_buried_positions_ : protocols::match::Bool3DGridKinemageWriter
• skip_complicated_stuff_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• skip_coord_constraints_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_deletions_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• skip_long_min_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• skip_low_temp_phase : protocols::simple_moves::ShakeStructureMover
• skip_minimize_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• skip_o2prime_trials_ : protocols::farna::RNA_Minimizer
• skip_rate : protocols::loops::SerializedLoop
• skip_rate_ : protocols::loops::Loop , protocols::loops::LoopFromFileData
• skip_redundant_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• skip_redundant_width_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• skip_reporting_ : protocols::analysis::InterfaceAnalyzerMover
• skip_same_pucker_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• skip_sampling_ : protocols::grafting::AnchoredGraftMover
• skip_stages_ : protocols::abinitio::FragmentSampler
• slash_char : protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib
• slave_current_batch_id_ : protocols::jd2::MPIFileBufJobDistributor
• slave_current_job_id_ : protocols::jd2::MPIFileBufJobDistributor
• slave_current_runtime_ : protocols::jd2::MPIFileBufJobDistributor
• slaves_finished_ : protocols::mpi_refinement::MPI_Refine_Master
• slice_res_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• sliced_pose_best_alignment : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_calc_rms_res : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_full_to_sub : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_is_prepend_map : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• sliced_pose_job_params_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• sliced_to_working_res_map_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• slide_ : protocols::dna::DNABasestep , protocols::docking::DockingInitialPerturbation , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SymDockingInitialPerturbation
• slide_away_from_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• slide_axis_ : protocols::docking::DockingInitialPerturbation , protocols::docking::DockingSlideIntoContact , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::surface_docking::SurfaceParameters
• slide_docking_jumps_ : protocols::stepwise::monte_carlo::mover::ResampleMover
• slide_into_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• slide_order_ : protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider , protocols::simple_moves::symmetry::SequentialSymmetrySlider
• slide_pattern_ : protocols::hotspot_hashing::SICPatternAtTransform
• SlideCriteriaType_ : protocols::simple_moves::symmetry::SymmetrySlider
• slideintocontact : protocols::flexpep_docking::FlexPepDockingFlags
• SlideThreshold_ : protocols::simple_moves::symmetry::SymmetrySlider
• small_ : protocols::seeded_abinitio::SegmentHybridizer
• small_angle_ : protocols::simple_moves::BackboneMover
• small_cutoff_square_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• small_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• small_min_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_min_type_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• small_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• small_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_scores_ : protocols::frag_picker::scores::FragmentScoreMap
• small_sequence_mover_ : protocols::surface_docking::FullatomRelaxMover
• small_trial_min_mover_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• smax_ : protocols::noesy_assign::PeakAssignmentParameters
• smooth_move_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• smooth_move_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• smooth_trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• smooth_trial_small_pack_ : protocols::abinitio::ClassicAbinitio
• smoothing_factor_ : protocols::ligand_docking::ComputeLigandRDF
• smove_angle_range : protocols::flexpep_docking::FlexPepDockingFlags
• smUR_pose_build_resids_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• snapshot_counter_ : protocols::hybridization::BackboneTorsionPerturbation
• snapshot_interval_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• snapshot_prefix_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• snug_fit_ : protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody_legacy::CDRH3Modeler
• snugfit_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody_legacy::AntibodyModeler
• socket_addr_ : protocols::moves::UDPSocketClient
• socket_h_ : protocols::moves::UDPSocketClient
• soft_scorefxn_ : protocols::ligand_docking::LigandBaseProtocol
• sol_sec_struct_ : protocols::surface_docking::FullatomRelaxMover
• solo_res_ : protocols::protein_interface_design::movers::TryRotamers
• solution_picker_ : protocols::kinematic_closure::KicMover
• solvation_ : protocols::make_rot_lib::RotData
• solventExposed_ : protocols::pockets::CCluster , protocols::pockets::PCluster
• some_claim_ : protocols::topology_broker::SuggestValueMessage
• some_private_int_ : protocols::toolbox::SF_Replica
• sor_ : protocols::md::Rattle
• sorted_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• sorted_capacity_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• source_ : protocols::comparative_modeling::StealLigandMover , protocols::comparative_modeling::StealSideChainsMover
• source_chain_ : protocols::simple_moves::AlignChainMover
• SOURCE_FILE : protocols::jd2::archive::ArchiveBase
• source_file_name_ : protocols::frag_picker::quota::ABEGO_SS_Config
• source_pattern_ : protocols::hotspot_hashing::PartitionedSearchPattern , protocols::hotspot_hashing::SearchPatternExpansion , protocols::hotspot_hashing::SearchPatternTransform , protocols::hotspot_hashing::SICPatternAtTransform
• source_pattern_a : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pattern_b : protocols::hotspot_hashing::ComposeSearchPatterns
• source_pose_ : protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• source_positions_ : protocols::coarse_rna::SourcePositions
• source_positions_map_ : protocols::coarse_rna::CoarseRNA_Fragments
• sourceName : protocols::sparta::Sparta::SpartaLib
• south_pucker_dof_key_values_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• south_pucker_dofs_have_not_been_initialized_ : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• space_ : protocols::match::downstream::DownstreamBuilder
• spacing_ : protocols::membrane::visualize::VisualizeMembraneMover , protocols::pockets::PocketGrid
• spairs2foldtype_ : protocols::fldsgn::topology::SheetFoldTypeManager
• spairset_ : protocols::fldsgn::topology::SheetSet
• spairset_name_ : protocols::fldsgn::topology::StrandPairingSet
• span_ : protocols::grafting::simple_movers::ReplaceRegionMover
• span_file_ : protocols::simple_moves::MembraneTopology
• span_vector_ : protocols::seeded_abinitio::CoordinateCst
• spanfile_ : protocols::membrane::AddMembraneMover , protocols::membrane::TransformIntoMembraneMover
• spanfiles_ : protocols::docking::membrane::MPDockingSetupMover
• sparta_ : protocols::sparta::ChemicalShiftEvaluator
• SPARTA_ANN : protocols::sparta::Sparta::SpartaLib
• SPARTA_DIR : protocols::sparta::Sparta::SpartaLib
• SPARTA_ERR_SURF : 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::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• special_region_bur_unsat_polars_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• special_region_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• special_region_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• special_region_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• special_rotweight_ : protocols::motifs::MotifDnaPacker
• specificity_repacks_ : protocols::dna::DnaInterfacePacker
• specify_both_spans_ : protocols::protein_interface_design::filters::RmsdFilter
• SpherePointNo : protocols::sparta::PDB
• SpherePoints : protocols::sparta::PDB
• spin_ : protocols::docking::DockingInitialPerturbation
• spin_assign_index1_ : protocols::noesy_assign::PeakAssignment
• spin_assign_index2_ : protocols::noesy_assign::PeakAssignment
• spin_axis_ : protocols::rigid::RigidBodySpinMover
• spin_center_ : protocols::docking::DockingInitialPerturbation
• split_ : protocols::fldsgn::CircularPermutation
• spread_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::kinematic_closure::perturbers::VicinityPerturber
• spring_constant_ : protocols::optimize_weights::WeightRangeConstraint
• sr_aa_neighbors_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• 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
• srbl_ : protocols::flxbb::LayerDesignOperation
• src_ : protocols::simple_moves::symmetry::SetupNCSMover
• src_begin : protocols::forge::remodel::RemodelWorkingSet
• src_end : protocols::forge::remodel::RemodelWorkingSet
• src_pose_ : protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::ReplaceRegionMover
• src_pose_start_ : protocols::grafting::simple_movers::ReplaceRegionMover
• srcD_ : protocols::simple_moves::symmetry::SetupNCSMover
• srcE_ : protocols::simple_moves::symmetry::SetupNCSMover
• ss : protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet
• ss1_ : protocols::sic_dock::scores::MotifHashRigidScore
• ss2_ : protocols::sic_dock::scores::MotifHashRigidScore
• ss_ : protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , protocols::jd2::parser::FragmentReader
• ss_abego_types_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• ss_chunks_pose_ : protocols::hybridization::FoldTreeHybridize
• ss_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::LoopJumpFoldCst , protocols::topology_broker::TemplateJumpClaimer
• ss_dist_ : protocols::fldsgn::topology::HSSTriplet
• ss_element_id_ : protocols::fldsgn::topology::SS_Info2
• ss_entrpy_ : protocols::fldsgn::NcontactsCalculator
• ss_from_blueprint_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies
• ss_helix_nres : protocols::analysis::InterfaceData
• ss_info_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• ss_loop_nres : protocols::analysis::InterfaceData
• ss_motifs_ : protocols::match::SecondaryStructureMPM
• ss_only_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• ss_orient_ : protocols::fldsgn::topology::HSSTriplet
• ss_pair_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• ss_select_task_factory_ : protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• ss_sheet_nres : protocols::analysis::InterfaceData
• ss_str_ : protocols::frag_picker::VallResidue
• ss_strings_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• ss_type : protocols::jumping::DisulfPairing , protocols::ss_prediction::SS_predictor
• ss_type_ : protocols::comparative_modeling::features::SSFeature , protocols::frag_picker::quota::SecondaryStructurePool
• ss_type_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• ss_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• sse_residues_ : protocols::toolbox::task_operations::DsspDesignOperation
• ssids_by_name_ : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• ssinfo1_ : protocols::sic_dock::scores::MotifHashRigidScore
• ssinfo2_ : protocols::sic_dock::scores::MotifHashRigidScore
• ssinfo_ : protocols::fldsgn::filters::SheetTopologyFilter
• sspot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• sstype : protocols::forge::remodel::LineObject
• sstype_ : protocols::jd2::parser::BluePrint , protocols::simple_filters::AbinitioBaseFilter
• st_atr_ : protocols::relax::ClassicRelax
• st_rep_ : protocols::relax::ClassicRelax
• st_sol_ : protocols::relax::ClassicRelax
• stacked_on_terminal_res_in_original_pose_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• stage1_1_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_2_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_3_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_4_cycles_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• stage1_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage1_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage1_probability_ : protocols::hybridization::HybridizeProtocol
• stage1_sampler_ : protocols::abinitio::DoubleLayerKinematicAbinitio
• stage1_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage25_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage2_cycles : protocols::relax::ClassicRelax
• stage2_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage2_decoys_ : protocols::abinitio::IterativeCentroid
• stage2_increase_cycles_ : protocols::hybridization::HybridizeProtocol
• stage2_repack_period : protocols::relax::ClassicRelax
• stage2_scorefxn_ : protocols::hybridization::HybridizeProtocol
• stage3_cycles : protocols::relax::ClassicRelax
• stage3_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage4_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• stage4_cycles_pack_rate_ : protocols::abinitio::ClassicAbinitio
• stage5_cycles_ : protocols::abinitio::ClassicAbinitio
• stage_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::IterativeBase
• stage_movers_ : protocols::abinitio::abscript::AbscriptMover
• staged_constraints_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• staged_manual_design_ : protocols::forge::remodel::RemodelMover::instruction_flags
• stagename_ : protocols::abinitio::abscript::AbscriptMover::StageTracker
• stagger_ : protocols::dna::DNABasepair
• staple_gap_ : protocols::simple_moves::PeptideStapleMover
• stapler_ : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• start : protocols::antibody::FrameWork , protocols::loops::SerializedLoop
• start_ : protocols::anchored_design::Anchor , protocols::antibody::clusters::CDRCluster , protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::floppy_tail::FloppyTailMover , protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::jumping::Interval , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::noesy_assign::FoldResonance , protocols::nonlocal::Region , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::simple_filters::GeometryFilter , protocols::simple_filters::RmsdEvaluator
• start_added_residue_in_aform_ : protocols::stepwise::monte_carlo::mover::AddMover
• start_atom_ : protocols::topology_broker::BasicJumpClaimer
• start_atomid1_ : protocols::backrub::BackrubSegment
• start_atomid2_ : protocols::backrub::BackrubSegment
• start_atomid_ : protocols::backrub::BackrubSegment
• start_centroid_ : protocols::abinitio::ResolutionSwitcher
• start_coord_csts_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• start_coords_ : protocols::sic_dock::ConstraintSetScore , protocols::sic_dock::NoPoseXYX_Func
• start_eval_time_ : protocols::jd2::archive::EvaluatedArchive
• start_from_pts_ : protocols::ligand_docking::LigandDockProtocol
• start_from_random_rb_conf_ : protocols::enzdes::EnzdesFixBBProtocol
• start_index_ : protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixMultiFunc
• start_label_ : protocols::topology_broker::BasicJumpClaimer
• start_pose_ : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::helix_capper::HelixNCapperMover , protocols::stepwise::setup::StepWiseJobDistributor , protocols::topology_broker::StartStructClaimer
• start_pose_cuts_ : protocols::topology_broker::TopologyBroker
• start_position_ : protocols::topology_broker::BasicJumpClaimer
• start_ramp_cstweight_ : protocols::abinitio::FoldConstraints
• start_rep_weight : protocols::relax::ClassicRelax
• start_res_ : protocols::docking::DockingEnsemble , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::LoopFromFileData , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::rigid::RollMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ReturnSidechainMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• start_struct : protocols::relax::SRelaxPose
• start_time_ : protocols::canonical_sampling::ParallelTempering , protocols::evaluation::TimeEvaluator , protocols::jd2::Job , protocols::jobdist::BaseJobDistributor , protocols::simple_filters::ExpiryFilter , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• start_time_wall_clock_ : protocols::wum::MPI_WorkUnitManager
• start_tree_at_chain_ : protocols::protein_interface_design::movers::SetAtomTree
• start_weight_ : protocols::moves::TrialMover
• start_weights_ : protocols::moves::RampingMover
• starting_displacement_ : protocols::hotspot_hashing::SICPatternAtTransform
• starting_points_ : protocols::ligand_docking::StartFrom
• starting_pose_ : protocols::motifs::MotifDnaPacker
• starting_rama_scores_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase
• starting_reference_energies_ : protocols::optimize_weights::OptEMultifunc
• starting_templates_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• starttime_ : protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::mpi_refinement::MPI_Refinement , protocols::rpc::JSON_RPC
• state_ : protocols::forge::build::BuildInstruction , protocols::forge::remodel::RemodelDesignMover , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::wum2::WorkUnit_ElScripts
• state_energies_ : protocols::pack_daemon::MultistateFitnessFunction
• state_indices_for_state_vector_ : protocols::pack_daemon::DynamicAggregateFunction
• state_info_ : 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_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_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
• states_ : protocols::multistate_design::MultiStateFitnessFunction
• static_grid_ : protocols::pockets::PocketGrid
• stationary_label_ : protocols::environment::CoMTrackerCM , protocols::rigid::UniformRigidBodyCM
• statistics_ : protocols::frag_picker::scores::PValuedFragmentScoreManager
• statistics_filename_ : protocols::backrub::BackrubSidechainMover
• stats_ : protocols::moves::TrialMover
• stats_file_ : protocols::canonical_sampling::TemperingBase
• stats_line_output_ : protocols::canonical_sampling::TemperingBase
• stats_silent_output_ : protocols::canonical_sampling::TemperingBase
• stats_type_ : protocols::moves::TrialMover
• status_prefix_ : protocols::jd2::Job
• stb_ : protocols::kinmatch::FunGroupTK
• std_dev_ : protocols::make_rot_lib::RotData
• stddev_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst
• stddev_degrees_ : protocols::ligand_docking::ResidueTorsionRestraints
• stdev_ : protocols::stepwise::sampler::MC_OneTorsion
• stdv_ : protocols::constraints_additional::COMCoordinateConstraint
• steal_times_ : protocols::jd2::parser::FragmentReader
• steepness_ : protocols::simple_filters::Sigmoid
• stem_copy_size_ : protocols::antibody::GraftOneCDRLoop
• stem_not_graft_ : protocols::antibody::GraftOneCDRLoop
• stem_optimize_ : protocols::antibody::GraftCDRLoopsProtocol
• stem_pairing_sets_ : protocols::farna::RNA_StructureParameters
• stem_size_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::GraftedStemOptimizer
• stems_are_neighbors_ : protocols::simple_filters::StemFinder
• stems_on_sse_ : protocols::simple_filters::StemFinder
• step : protocols::make_rot_lib::TorsionRange , protocols::pockets::CCluster , protocols::pockets::PCluster
• step_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_count_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• step_counter_ : protocols::canonical_sampling::BiasEnergy
• step_penalty_ : protocols::rbsegment_relax::OptimizeThreadingMover
• STEP_SIZE : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• step_size_ : protocols::match::upstream::SampleStrategyData , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• step_x_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_y_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• step_z_ : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• stepSize_ : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• stepwise_clusterer_ : protocols::stepwise::screener::PoseSelectionScreener
• stepwise_modeler_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• stepwise_monte_carlo_ : protocols::stepwise::setup::StepWiseJobDistributor
• stepwise_packer_ : protocols::stepwise::screener::PackScreener
• stepwise_pose_setup_ : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• steric_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• stf_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• stop : protocols::antibody::FrameWork , protocols::loops::SerializedLoop
• stop_ : protocols::floppy_tail::FloppyTailMover , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::nonlocal::Region , protocols::rbsegment_relax::CCDMoveWrapper
• stop_at_closure_ : protocols::grafting::AnchoredGraftMover
• stop_before_condition_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• stop_res_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::rigid::RollMover , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• stopping_condition_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_moves::GenericMonteCarloMover
• storage_ : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool
• store_ : protocols::wum::SilentStructStore
• store_energies_ : protocols::toolbox::DecoySetEvaluation
• store_silents_ : protocols::simple_moves::CombinePoseMover
• store_trj_ : protocols::md::MDBase
• stored_angle_ : protocols::stepwise::sampler::MC_OneTorsion
• stored_pucker_state_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• stored_task_names_ : protocols::matdes::MatDesPointMutationCalculator
• str_access_ : protocols::environment::Comparator
• strand1_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand2_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• strand_dist_cutoff_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• strand_id_ : protocols::features::strand_assembly::SandwichFragment , protocols::fldsgn::topology::SS_Info2
• strand_order_ : protocols::fldsgn::topology::Sheet
• strand_pair_library_positions_ : protocols::hybridization::HybridizeFoldtreeDynamic
• strand_pairing_ : protocols::abinitio::PairingStatEntry
• strand_pairings_ : protocols::abinitio::Template , protocols::fldsgn::topology::StrandPairingSet , protocols::jd2::parser::BluePrint
• strand_pairings_template_indices_ : protocols::hybridization::FoldTreeHybridize
• strand_pairs_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• 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
• StrandMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• strands_ : protocols::fldsgn::topology::SS_Info2
• strategy_ : protocols::match::upstream::SampleStrategyData
• stretch_ : protocols::dna::DNABasepair
• strict_base_pairing_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• 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::BiasEnergy , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::TrajectoryRecorder , protocols::features::TrajectoryReportToDB , protocols::qsar::RenderGridsToKinemage
• string_around_resnums_ : protocols::simple_filters::EnergyPerResidueFilter
• string_exclude_resnums_ : protocols::simple_moves::FavorSequenceProfile
• string_key_ : protocols::simple_moves::AddJobPairData
• string_real_pairs_ : protocols::jd2::Job
• string_refine_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• string_resnums_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::toolbox::task_operations::DesignAroundOperation
• string_string_pairs_ : protocols::jd2::Job
• string_target_seqpos_ : protocols::toolbox::task_operations::InteractingRotamerExplosion
• string_to_enum_ : protocols::antibody::clusters::CDRClusterEnumManager
• string_value_ : protocols::simple_moves::AddJobPairData
• struct_id1_ : protocols::rotamer_recovery::RRReporterSQLite
• struct_id_selection_ : protocols::qsar::qsarOptFunc
• structure_based_ : protocols::membrane::MembranePositionFromTopologyMover
• structure_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• structure_input_tag_ : protocols::features::ReportToDB
• structure_map_ : protocols::features::ProteinSilentReport
• structure_scores_features_ : protocols::features::ProteinSilentReport
• structure_tag_ : protocols::features::ReportToDB
• structures_ : protocols::noesy_assign::StructureDependentPeakCalibrator
• structures_per_cluster_ : protocols::pose_selectors::ClusterPoseSelector
• stub_ : protocols::stepwise::screener::StubApplier
• stub_anchor_rsd_ : protocols::cyclic_peptide::PeptideStubMover
• stub_anchor_rsd_connecting_atom_ : protocols::cyclic_peptide::PeptideStubMover
• stub_energy_fxn_ : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• stub_energy_threshold_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• stub_insert_pos_ : protocols::cyclic_peptide::PeptideStubMover
• stub_minimize_movers_ : protocols::protein_interface_design::movers::PlaceStubMover
• stub_mode_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_connecting_atom_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_jumping_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_names_ : protocols::cyclic_peptide::PeptideStubMover
• stub_rsd_repeat_ : protocols::cyclic_peptide::PeptideStubMover
• stub_score_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_set_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceStubMover
• stub_set_filters_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stub_set_vec_ : protocols::hotspot_hashing::HotspotStubSet
• stub_sets_ : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• stubs_intra_residue_ : protocols::environment::claims::JumpClaim
• stwist_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• style_ : protocols::loops::loop_mover::LoopCM
• sub_matrix_ : protocols::frag_picker::scores::ProfileScoreSubMatrix
• sub_ndx_deque_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• sub_rank_ : protocols::jd2::MPIMultiCommJobDistributor
• sub_to_full_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• subclusters_ : protocols::toolbox::KClusterElement
• subexpression_name_dec_line_ : protocols::pack_daemon::EntityFunc
• subexpression_name_map_ : protocols::pack_daemon::EntityFunc
• subfilter_ : protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter
• subMatrixFile_ : protocols::frag_picker::scores::ProfileScoreSubMatrix
• submover_ : protocols::filters::MoveBeforeFilter , protocols::moves::IteratedConvergenceMover
• subpools_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• subprio_ : protocols::environment::claims::ClaimStrength
• subtarget_ : protocols::pockets::CCluster , protocols::pockets::PCluster
• subtype_ : protocols::environment::claims::ClaimStrength
• subunit_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• success : protocols::LoopRebuild
• success_ : protocols::hybridization::InsertChunkMover , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• successfully_initialized_ : protocols::canonical_sampling::HamiltonianExchange
• suffix_ : protocols::jd2::JobOutputter , protocols::matdes::ExtractSubposeMover
• sugar_modeling_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• sugar_modeling_sets_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• sugar_rotamer_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• sugar_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• sugar_screening_pose_ : protocols::stepwise::screener::AnchorSugarScreener
• sugar_setup_success_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• suite_cluster_radius_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• suite_num_ : protocols::stepwise::monte_carlo::mover::AddMover
• suite_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_MultiSuite
• suitename_ : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• sum : protocols::cluster::DataPoint
• sumName : protocols::sparta::Sparta::SpartaLib
• super_quick_relax_of_centroids_ : protocols::abinitio::IterativeBase
• super_secret_fixed_interface_mode_ : protocols::anchored_design::AnchorMoversData
• superimpose_ : protocols::fldsgn::MatchResiduesMover , protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::LoopRmsdEvaluator
• superimpose_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_on_all_ : protocols::protein_interface_design::filters::RmsdFilter
• superimpose_over_all_ : protocols::stepwise::setup::StepWiseJobDistributor
• superimpose_over_all_instantiated_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_regions_ : protocols::topology_broker::CoordConstraintClaimer
• superimpose_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• superimpose_res_in_pose_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• superimpose_rmsd_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• supervoxel_dimprods_ : protocols::match::Bool3DGrid
• supervoxel_dimsizes_ : protocols::match::Bool3DGrid
• suppress_bp_constraint_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_StructureParameters
• 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_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::SelectBySASAOperation
• surface_accessibility_ : protocols::analysis::PackStatMover
• surface_asa_ : protocols::toolbox::task_operations::SelectBySASAOperation
• surface_contact_mover_ : protocols::surface_docking::FullatomRelaxMover
• surface_density_ : protocols::hotspot_hashing::SurfaceSearchPattern
• surface_exposed_nb_cutoff_ : protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
• SURFACE_EXPOSURE : protocols::sparta::Sparta::SpartaLib
• surface_exposure_ : protocols::toolbox::pose_metric_calculators::SequenceComparison
• surface_orient_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• surface_parameters_ : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover
• surface_selection_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• surface_vectors_ : protocols::hotspot_hashing::SurfaceSearchPattern
• SurfPrec : protocols::sparta::PDB
• surrogate_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• svd_s_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• svm_energies : protocols::simple_filters::nmer_svm_res_data
• sw_can_by_sh_id_ : protocols::features::strand_assembly::SandwichFragment
• swa_move_ : protocols::stepwise::monte_carlo::mover::AddMover
• swa_move_selector_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::ResampleMover
• swap_buffer_ : protocols::wum::WorkUnitQueue_Swapped
• swap_chain_ : protocols::seeded_abinitio::SwapSegment
• swap_chain_number_ : protocols::simple_moves::AddChainMover
• swap_file_ : protocols::wum::WorkUnitQueue_Swapped
• swap_in_ : protocols::forge::build::SegmentSwap
• swap_in_movemap_ : protocols::forge::build::SegmentSwap
• swap_invite_recv_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• swap_invite_send_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• swap_segment_ : protocols::seeded_abinitio::SwapSegment
• sweep_iterator_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_nonpivot_torsion_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• sweep_nonpivot_torsion_starts_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_step_sizes_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• sweep_torsion_ids_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• switch_focus_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• sym_docking_mover_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• sym_dof_name_ : protocols::matdes::GetRBDOFValues , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::simple_filters::ShapeComplementarityFilter
• sym_dof_names_ : protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::matdes::SymUnsatHbondFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectBySASAOperation
• sym_rotamer_sets_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symm_axes : protocols::simple_filters::SymmetricMotifFilter
• symm_data_ : protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::SymmetryClaimer
• symm_def_file_ : protocols::hybridization::MRMover
• symm_definition_file_ : protocols::symmetric_docking::SymDockBaseProtocol
• symm_file_ : protocols::matdes::SymDofMover
• symm_orders : protocols::simple_filters::SymmetricMotifFilter
• symm_type_ : protocols::simple_filters::SymmetricMotifFilter
• symmdata_ : protocols::simple_filters::RelativePoseFilter
• symmdef_ : protocols::simple_moves::symmetry::SetupForSymmetryMover
• symmdef_files_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• symmetric_ig_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symmetric_rmsd_ : protocols::relax::FastRelax
• symmetric_sequence_ : protocols::simple_moves::symmetry::SetupNCSMover
• symmetric_task_ : protocols::simple_moves::symmetry::SymPackRotamersMover
• symmetric_units_ : protocols::simple_moves::FavorSymmetricSequence
• symmetry_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::simple_filters::AlaScan , protocols::simple_moves::DesignRepackMover
• symmetry_compliance_ : protocols::noesy_assign::PeakAssignment
• symmetry_compliance_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• symmetry_definition_ : protocols::simple_filters::RelativePoseFilter
• symminfo_ : protocols::topology_broker::FibrilModelingClaimer