- k -

• Kabsch() : protocols::hybridization::TMalign
• KCluster() : protocols::toolbox::KCluster
• KClusterData() : protocols::toolbox::KClusterData
• KClusterElement() : protocols::toolbox::KClusterElement
• keep_aas() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• keep_all_protocol() : protocols::frag_picker::FragmentPicker
• keep_fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• keep_history() : protocols::moves::PyMolMover
• keep_known_bb_torsions_at_junctions() : protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild
• keep_motif() : protocols::motifs::BuildPosition
• keep_motifhit() : protocols::motifs::BuildPosition
• keep_native() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• keep_rotamer() : protocols::motifs::BuildPosition
• keep_stats_type() : protocols::moves::TrialMover
• keep_task_allowed_aas() : protocols::antibody::design::ResidueProbDesignOperation
• keep_top_pose() : protocols::forge::remodel::RemodelAccumulator
• keep_trying() : protocols::matdes::MatDesGreedyOptMutationMover
• KeepRegionMover() : protocols::grafting::simple_movers::KeepRegionMover
• kept_match() : protocols::match::output::BestMatchesCollection
• kept_match_dspos1() : protocols::match::output::BestMatchesCollection
• key() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::VallChunk , protocols::frag_picker::VallResidue , protocols::toolbox::pose_metric_calculators::MetricValueGetter
• keyname() : protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::JumpSampleDataCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::comparative_modeling::GenericJobInputterCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::comparative_modeling::ThreadingJobInputterCreator , protocols::constraints_additional::BindingSiteConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator , protocols::constraints_additional::SequenceCoupling1BDConstraintCreator , protocols::constraints_additional::SequenceCouplingConstraintCreator , protocols::contact_map::ContactMapCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::DensityMorphingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::environment::AutoCutDataCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::AddRigidBodyLigandConfsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::DetectProteinLigandInterfaceOperationCreator , protocols::enzdes::DiffAtomSasaFilterCreator , protocols::enzdes::EnzdesJobInputterCreator , protocols::enzdes::EnzdesJobOutputterCreator , protocols::enzdes::EnzdesScorefileFilterCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::EnzScoreFilterCreator , protocols::enzdes::LigBurialFilterCreator , protocols::enzdes::LigDSasaFilterCreator , protocols::enzdes::LigInterfaceEnergyFilterCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , protocols::enzdes::RemoveLigandFilterCreator , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::enzdes::ResidueConformerFilterCreator , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::features::DatabaseJobInputterCreator , protocols::features::DatabaseJobOutputterCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::filters::CalculatorFilterCreator , protocols::filters::CombinedFilterCreator , protocols::filters::CompoundFilterCreator , protocols::filters::ContingentFilterCreator , protocols::filters::FalseFilterCreator , protocols::filters::FilterCreator , protocols::filters::IfThenFilterCreator , protocols::filters::MoveBeforeFilterCreator , protocols::filters::ReplicateFilterCreator , protocols::filters::StochasticFilterCreator , protocols::filters::TimeFilterCreator , protocols::filters::TrueFilterCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::filters::CoreDunbrackFilterCreator , protocols::fldsgn::filters::FragQualFilterCreator , protocols::fldsgn::filters::HelixKinkFilterCreator , protocols::fldsgn::filters::HelixPairingFilterCreator , protocols::fldsgn::filters::HSSTripletFilterCreator , protocols::fldsgn::filters::InterlockingAromaFilterCreator , protocols::fldsgn::filters::NcontactsFilterCreator , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator , protocols::fldsgn::filters::SecondaryStructureCountFilterCreator , protocols::fldsgn::filters::SecondaryStructureFilterCreator , protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator , protocols::fldsgn::filters::SheetTopologyFilterCreator , protocols::fldsgn::MatchResiduesMoverCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::flxbb::LayerDesignOperationCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::forge::remodel::RemodelLoopMoverCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianHybridizeCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::FoldTreeHybridizeCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::hybridization::HybridizeSetupMoverCreator , protocols::idealize::IdealizeMoverCreator , protocols::indexed_structure_store::filters::FragmentLookupFilterCreator , protocols::jd2::AtomTreeDiffJobInputterCreator , protocols::jd2::AtomTreeDiffJobOutputterCreator , protocols::jd2::JD2ResourceManagerJobInputterCreator , protocols::jd2::JobInputterCreator , protocols::jd2::JobOutputterCreator , protocols::jd2::LazySilentFileJobInputterCreator , protocols::jd2::NoOutputJobOutputterCreator , protocols::jd2::parser::DataLoaderCreator , protocols::jd2::parser::FragSetLoaderCreator , protocols::jd2::parser::MonteCarloLoaderCreator , protocols::jd2::parser::ResidueSelectorLoaderCreator , protocols::jd2::parser::ScoreFunctionLoaderCreator , protocols::jd2::parser::TaskOperationLoaderCreator , protocols::jd2::PDBJobInputterCreator , protocols::jd2::PDBJobOutputterCreator , protocols::jd2::PoseInputStreamJobInputterCreator , protocols::jd2::ScoreOnlyJobOutputterCreator , protocols::jd2::ScreeningJobInputterCreator , protocols::jd2::SilentFileJobInputterCreator , protocols::jd2::SilentFileJobOutputterCreator , protocols::kinematic_closure::KicMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::AtomCountFilterCreator , protocols::ligand_docking::ChainExistsFilterCreator , protocols::ligand_docking::CompleteConnectionsFilterCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::ligand_docking::HBondDonorFilterCreator , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::InterfaceBuilderLoaderCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandAreaLoaderCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::MolarMassFilterCreator , protocols::ligand_docking::MolecularMassFilterCreator , protocols::ligand_docking::MoveMapBuilderLoaderCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loop_build::LoopmodelWrapperCreator , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::loop_modeling::LoopBuilderCreator , protocols::loop_modeling::LoopModelerCreator , protocols::loop_modeling::LoopProtocolCreator , protocols::loop_modeling::refiners::MinimizationRefinerCreator , protocols::loop_modeling::refiners::RepackingRefinerCreator , protocols::loop_modeling::refiners::RotamerTrialsRefinerCreator , protocols::loop_modeling::samplers::LegacyKicSamplerCreator , protocols::loop_modeling::utilities::PrepareForCentroidCreator , protocols::loop_modeling::utilities::PrepareForFullatomCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator , protocols::loops::loop_mover::refine::RepackTrialCreator , protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator , protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator , protocols::loops::loops_definers::LoopsDefinerLoaderCreator , protocols::make_rot_lib::MakeRotLibJobInputterCreator , protocols::match::MatcherMoverCreator , protocols::matdes::BuildingBlockInterfaceOperationCreator , protocols::matdes::ClashCheckFilterCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::GetRBDOFValuesCreator , protocols::matdes::InterfacePackingFilterCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::OligomericAverageDegreeFilterCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::matdes::SymUnsatHbondFilterCreator , protocols::md::CartesianMDCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::symmetry::SetupForMembraneSymmetryCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::moves::PyMolMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::pockets::PocketConstraintCreator , protocols::pose_reporters::EnergyReporterCreator , protocols::pose_reporters::FilterReporterCreator , protocols::pose_reporters::RMSDReporterCreator , protocols::pose_selectors::AndSelectorCreator , protocols::pose_selectors::ClusterPoseSelectorCreator , protocols::pose_selectors::FilterCreator , protocols::pose_selectors::OrSelectorCreator , protocols::pose_selectors::TopNByPropertyCreator , protocols::protein_interface_design::filters::AtomicContactCountFilterCreator , protocols::protein_interface_design::filters::AverageDegreeFilterCreator , protocols::protein_interface_design::filters::BindingStrainFilterCreator , protocols::protein_interface_design::filters::BoltzmannFilterCreator , protocols::protein_interface_design::filters::ClashWithTargetFilterCreator , protocols::protein_interface_design::filters::DesignableResiduesFilterCreator , protocols::protein_interface_design::filters::DisulfideFilterCreator , protocols::protein_interface_design::filters::FilterScanFilterCreator , protocols::protein_interface_design::filters::FNatFilterCreator , protocols::protein_interface_design::filters::HbondsToAtomFilterCreator , protocols::protein_interface_design::filters::HbondsToResidueFilterCreator , protocols::protein_interface_design::filters::InterfaceHolesFilterCreator , protocols::protein_interface_design::filters::IRmsdFilterCreator , protocols::protein_interface_design::filters::LRmsdFilterCreator , protocols::protein_interface_design::filters::RelativeSegmentFilterCreator , protocols::protein_interface_design::filters::RmsdFilterCreator , protocols::protein_interface_design::filters::RmsdSimpleFilterCreator , protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCreator , protocols::protein_interface_design::filters::SSamountFilterCreator , protocols::protein_interface_design::filters::StubScoreFilterCreator , protocols::protein_interface_design::filters::StubScoreLoopsFilterCreator , protocols::protein_interface_design::filters::TorsionCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::protein_interface_design::ParserJobInputterCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ScoringGridLoaderCreator , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGridCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::PosePropertyReporterCreator , protocols::rosetta_scripts::PoseSelectorCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::simple_filters::AlaScanFilterCreator , protocols::simple_filters::AngleToVectorFilterCreator , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::AveragePathLengthFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::ConservedPosMutationFilterCreator , protocols::simple_filters::ConstraintScoreCutoffFilterCreator , protocols::simple_filters::DdgFilterCreator , protocols::simple_filters::DeltaFilterCreator , protocols::simple_filters::DisulfideEntropyFilterCreator , protocols::simple_filters::EnergyPerResidueFilterCreator , protocols::simple_filters::ExpiryFilterCreator , protocols::simple_filters::FileExistFilterCreator , protocols::simple_filters::FileRemoveFilterCreator , protocols::simple_filters::GeometryFilterCreator , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::InterfaceBindingEnergyDensityFilterCreator , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterRepeatContactFilterCreator , protocols::simple_filters::IntraRepeatContactFilterCreator , protocols::simple_filters::MotifScoreFilterCreator , protocols::simple_filters::MultipleSigmoidsFilterCreator , protocols::simple_filters::MutationsFilterCreator , protocols::simple_filters::NeighborTypeFilterCreator , protocols::simple_filters::NetChargeFilterCreator , protocols::simple_filters::NMerPSSMEnergyFilterCreator , protocols::simple_filters::NMerSVMEnergyFilterCreator , protocols::simple_filters::NonSequentialNeighborsFilterCreator , protocols::simple_filters::OperatorFilterCreator , protocols::simple_filters::PackStatFilterCreator , protocols::simple_filters::PoseCommentFilterCreator , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::RelativePoseFilterCreator , protocols::simple_filters::RepeatParameterFilterCreator , protocols::simple_filters::ReportFilterCreator , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ResidueCountFilterCreator , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::simple_filters::ResidueIEFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::simple_filters::RotamerBoltzmannWeightFilterCreator , protocols::simple_filters::SavePoseConstraintToFileFilterCreator , protocols::simple_filters::SaveResfileToDiskFilterCreator , protocols::simple_filters::ScoreCutoffFilterCreator , protocols::simple_filters::ScoreTypeFilterCreator , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::simple_filters::SigmoidFilterCreator , protocols::simple_filters::SSMotifFinderFilterCreator , protocols::simple_filters::StemFinderFilterCreator , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::TaskAwareAlaScanCreator , protocols::simple_filters::TaskAwareSASAFilterCreator , protocols::simple_filters::TaskAwareScoreTypeFilterCreator , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::TotalSasaFilterCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::BoltzmannRotamerMoverCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FindConsensusSequenceCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::MonteCarloResetCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::simple_moves::MSDMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ResetBaselineMoverCreator , protocols::simple_moves::ResidueTypeConstraintMoverCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::symmetry::TaskAwareSymMinMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::toolbox::task_operations::AlignedThreadOperationCreator , protocols::toolbox::task_operations::CrystalContactsOperationCreator , protocols::toolbox::task_operations::DatabaseThreadCreator , protocols::toolbox::task_operations::DesignAroundOperationCreator , protocols::toolbox::task_operations::DsspDesignOperationCreator , protocols::toolbox::task_operations::ImportUnboundRotamersOperationCreator , protocols::toolbox::task_operations::InteractingRotamerExplosionCreator , protocols::toolbox::task_operations::JointSequenceOperationCreator , protocols::toolbox::task_operations::LimitAromaChi2OperationCreator , protocols::toolbox::task_operations::LinkResiduesCreator , protocols::toolbox::task_operations::ModifyAnnealerCreator , protocols::toolbox::task_operations::PreventChainFromRepackingOperationCreator , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::toolbox::task_operations::ProteinCoreFilterCreator , protocols::toolbox::task_operations::ProteinInterfaceDesignOperationCreator , protocols::toolbox::task_operations::ReadResfileFromDBCreator , protocols::toolbox::task_operations::RestrictByCalculatorsOperationCreator , protocols::toolbox::task_operations::RestrictChainToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictConservedLowDdgOperationCreator , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , protocols::toolbox::task_operations::RestrictIdentitiesOperationCreator , protocols::toolbox::task_operations::RestrictInterGroupVectorOperationCreator , protocols::toolbox::task_operations::RestrictNativeResiduesOperationCreator , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::toolbox::task_operations::RestrictToCDRH3LoopCreator , protocols::toolbox::task_operations::RestrictToInterfaceCreator , protocols::toolbox::task_operations::RestrictToInterfaceOperationCreator , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsCreator , protocols::toolbox::task_operations::RestrictToLoopsCreator , protocols::toolbox::task_operations::RestrictToNeighborhoodOperationCreator , protocols::toolbox::task_operations::RestrictToTerminiOperationCreator , protocols::toolbox::task_operations::RetrieveStoredTaskOperationCreator , protocols::toolbox::task_operations::SelectByDeltaScoreOperationCreator , protocols::toolbox::task_operations::SelectByDensityFitOperationCreator , protocols::toolbox::task_operations::SelectBySASAOperationCreator , protocols::toolbox::task_operations::SelectResiduesWithinChainOperationCreator , protocols::toolbox::task_operations::SeqprofConsensusOperationCreator , protocols::toolbox::task_operations::SetIGTypeOperationCreator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::toolbox::task_operations::StoreCompoundTaskMoverCreator , protocols::toolbox::task_operations::StoreTaskMoverCreator , protocols::toolbox::task_operations::ThreadSequenceOperationCreator
• KIC_loop_close() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• KIC_loop_close_with_perturbations() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• kic_modeler_if_relevant() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• kick_out_pose_at_idx() : protocols::stepwise::modeler::align::StepWiseClusterer
• KicMover() : protocols::kinematic_closure::KicMover
• KinematicAbinitio() : protocols::abinitio::KinematicAbinitio
• KinematicControl() : protocols::abinitio::KinematicControl
• KinematicMover() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• KinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• kinematics() : protocols::abinitio::Protocol
• KinematicTaskControl() : protocols::abinitio::KinematicTaskControl
• KinematicWrapper() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• KinFunGroupTK() : protocols::kinmatch::KinFunGroupTK
• kink_anion_atoms() : protocols::antibody::AntibodyInfo
• kink_anion_residue() : protocols::antibody::AntibodyInfo
• kink_begin() : protocols::antibody::AntibodyInfo
• kink_cation_atoms() : protocols::antibody::AntibodyInfo
• kink_cation_residue() : protocols::antibody::AntibodyInfo
• kink_end() : protocols::antibody::AntibodyInfo
• kink_trp() : protocols::antibody::AntibodyInfo
• kinmover() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• KMedoid() : protocols::toolbox::KMedoid
• KRSQuery() : protocols::kinmatch::KRSQuery
• kurtosis() : protocols::toolbox::InteratomicVarianceMatrix