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

- k -

• k() : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering , core::scoring::GenTorsionParams
• K() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• k() : core::scoring::SpringParams , core::scoring::TorsionParams , protocols::cluster::Exemplar , protocols::md::Constraint , protocols::normalmode::ContactStruct
• K0_ : core::scoring::methods::BBIndepCartBondedParameters
• k1 : core::scoring::fiber_diffraction::Hankel
• k1_ : core::scoring::GenTorsionParams
• k2 : core::scoring::fiber_diffraction::Hankel
• k2_ : core::scoring::GenTorsionParams
• k3_ : core::scoring::GenTorsionParams
• k48r_48_lys_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_48k_mtsl_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_end_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_swap_ : protocols::ub_e2c::ubi_e2c_modeler
• k48r_trim_end_ : protocols::ub_e2c::ubi_e2c_modeler
• k4_ : core::scoring::GenTorsionParams
• k6() : core::scoring::GenTorsionParams
• k6_ : core::scoring::GenTorsionParams
• k_ : core::scoring::carbohydrates::OmegaPreferencesFunction
• K_ : core::scoring::constraints::KofNConstraint
• k_ : core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::PeriodicFunc , core::scoring::SpringParams , protocols::normalmode::NormalMode
• K_ : protocols::relax::LocalRelax
• k_angle() : core::scoring::methods::IdealParametersDatabase
• k_angle_ : core::scoring::methods::IdealParametersDatabase
• k_dampen_ : protocols::normalmode::NormalModeMultifunc
• k_fit() : core::scoring::epr_deer::DEERDecayData
• k_length() : core::scoring::methods::IdealParametersDatabase
• k_length_ : core::scoring::methods::IdealParametersDatabase
• k_long_ : protocols::normalmode::NormalMode
• k_short_ : protocols::normalmode::NormalMode
• k_SS_ : protocols::normalmode::NormalMode
• k_torsion() : core::scoring::methods::IdealParametersDatabase
• k_torsion_ : core::scoring::methods::IdealParametersDatabase
• k_torsion_improper() : core::scoring::methods::IdealParametersDatabase
• k_torsion_improper_ : core::scoring::methods::IdealParametersDatabase
• k_torsion_proton() : core::scoring::methods::IdealParametersDatabase
• k_torsion_proton_ : core::scoring::methods::IdealParametersDatabase
• k_uniform_ : protocols::normalmode::NormalMode
• Kabsch() : protocols::hybridization::TMalign
• Kappa() : core::scoring::FACTSPotential , protocols::md::MDBase
• Kappa_ : core::scoring::FACTSPotential , protocols::md::MDBase
• KarplusFunc() : core::scoring::func::KarplusFunc
• KB_description_ : core::scoring::func::SplineFunc
• kB_T_ : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc
• kbp_data_ : protocols::qsar::scoring_grid::ShapeGrid
• KBPGridCOP : protocols::qsar::scoring_grid::ShapeGrid
• KBPGridOP : protocols::qsar::scoring_grid::ShapeGrid
• kbt() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• kbt_ : protocols::cyclic_peptide_predict::PNearCalculator , protocols::mainchain_potential::GenerateMainchainPotentialOptions
• KbT_ : protocols::make_rot_lib::MakeRotLibMover , protocols::make_rot_lib::MakeRotLibOptionsData
• KCluster() : protocols::toolbox::KCluster
• KClusterData() : protocols::toolbox::KClusterData
• KClusterElement() : protocols::toolbox::KClusterElement
• keep_ : protocols::simple_filters::SecretionPredictionFilter
• keep_1st_child_pos() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• keep_aas() : core::pack::task::operation::RestrictAbsentCanonicalAAS , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• keep_aas_ : core::pack::task::operation::RestrictAbsentCanonicalAAS , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• keep_adding_to_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• keep_all_protocol() : protocols::frag_picker::FragmentPicker
• keep_base_fixed_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• keep_bb : protocols::protein_interface_design::movers::VLBInstruction
• keep_center : protocols::toolbox::ClusterOptions
• keep_chain_and_cutpoint_open_matched() : core::pose::full_model_info::FullModelParameters
• keep_checkpoint_file() : protocols::monte_carlo::GenericSimulatedAnnealer
• keep_checkpoint_file_ : protocols::monte_carlo::GenericSimulatedAnnealer
• keep_covalent_ : protocols::enzdes::AddOrRemoveMatchCsts
• keep_current_ds_ : protocols::denovo_design::DisulfidizeMover
• keep_disulfide_cys_ : protocols::pose_creation::MakePolyXMover
• keep_dof_fixed() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• keep_existing_networks_ : protocols::hbnet::HBNet
• keep_filters() : protocols::monte_carlo::GenericMonteCarloMover
• keep_filters_ : protocols::monte_carlo::GenericMonteCarloMover
• keep_fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• keep_gly_ : protocols::pose_creation::MakePolyXMover
• keep_history() : protocols::moves::PyMOLMover
• keep_history_ : protocols::moves::PyMOLMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• keep_input_foldtree_ : protocols::forge::remodel::RemodelLoopMover
• keep_input_protonation_state() : core::io::StructFileRepOptions
• keep_input_protonation_state_ : core::io::StructFileRepOptions
• keep_input_scores() : core::io::silent::SilentFileOptions
• keep_input_scores_ : core::io::silent::SilentFileOptions
• keep_known_bb_torsions_at_junctions() : protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild
• 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_mover_state_ : protocols::rosetta_scripts::MultipleOutputWrapper
• keep_nas_ : core::pack::task::PIKNA
• keep_native() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::task_operations::SeqprofConsensusOperation
• keep_native_ : protocols::protein_interface_design::filters::FilterScanFilter , protocols::task_operations::SeqprofConsensusOperation
• keep_pdb_info_labels_ : protocols::symmetry::DetectSymmetry , protocols::symmetry::SetupForSymmetryMover
• keep_pdb_remarks_ : protocols::symmetry::DetectSymmetry
• keep_pose_constraint_ : protocols::hybridization::HybridizeProtocol
• keep_pose_in_memory_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• keep_pose_in_memory_hydrid_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• keep_pro_ : protocols::pose_creation::MakePolyXMover
• keep_rnl_pose_ : protocols::enzdes::EnzdesScorefileFilter
• keep_rotamer() : protocols::motifs::BuildPosition
• keep_sequence_symmetry() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• keep_sequence_symmetry_ : core::pack::task::PackerTask_
• keep_sidechains_ : protocols::cryst::RecomputeDensityMapMover
• keep_start_selector_rotamers_fixed_ : protocols::hbnet::HBNet
• keep_stats_type() : protocols::moves::TrialMover
• keep_stub_in_residue() : core::kinematics::Edge
• keep_top_pose() : protocols::forge::remodel::RemodelAccumulator
• keep_trying() : protocols::matdes::MatDesGreedyOptMutationMover
• keep_trying_ : protocols::matdes::MatDesGreedyOptMutationMover
• keep_virtual_residues_ : protocols::symmetry::ExtractAsymmetricUnitMover
• KeepLigandContactsRequirement() : protocols::sewing::requirements::KeepLigandContactsRequirement
• KeepLigandContactsRequirementCreator() : protocols::sewing::requirements::KeepLigandContactsRequirementCreator
• KeepRegionMover() : protocols::grafting::simple_movers::KeepRegionMover
• KeepSequenceSymmetry() : core::pack::task::operation::KeepSequenceSymmetry
• kept_match() : protocols::match::output::BestMatchesCollection
• kept_match_dspos1() : protocols::match::output::BestMatchesCollection
• Keq() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary
• Keq_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary
• Key : core::scoring::motif::MotifHash , core::scoring::motif::MotifHashManager , core::scoring::motif::ResPairMotifMetaBinner , core::scoring::motif::XformScore , core::scoring::motif::XfragSet , core::scoring::packing::HolesParams
• key() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::VallChunk , protocols::frag_picker::VallResidue , protocols::loophash::LeapIndex , protocols::pose_metric_calculators::MetricValueGetter
• key_ : protocols::frag_picker::VallResidue , protocols::multistate_design::MetricCalculatorFitnessFunction , protocols::pose_metric_calculators::MetricValueGetter
• key_mask_BB_BB_ : core::scoring::motif::MotifHashManager
• key_set_ : core::scoring::motif::MotifHash
• keyname() : core::chemical::rotamers::BasicRotamerLibrarySpecification , core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator , core::chemical::rotamers::NCAARotamerLibrarySpecification , core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator , core::chemical::rotamers::PDBRotamerLibrarySpecification , core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator , core::chemical::rotamers::RotamerLibrarySpecification , core::chemical::rotamers::RotamerLibrarySpecificationCreator , core::chemical::rotamers::StoredRotamerLibrarySpecification , core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator , core::import_pose::PDBSilentStructCreator , core::io::silent::BinarySilentStructCreator , core::io::silent::ProteinSilentStruct_SinglePrecCreator , core::io::silent::ProteinSilentStructCreator , core::io::silent::RigidBodySilentStructCreator , core::io::silent::RNA_SilentStructCreator , core::io::silent::ScoreFileSilentStructCreator , core::io::silent::ScoreJumpFileSilentStructCreator , core::io::silent::SilentStructCreator , core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator , core::pack::dunbrack::DunbrackConstraintCreator , core::pack::dunbrack::SingleResidueDunbrackLibraryCreator , core::pack::palette::CustomBaseTypePackerPaletteCreator , core::pack::palette::DefaultPackerPaletteCreator , core::pack::palette::NCAADefaultPackerPaletteCreator , core::pack::palette::NoDesignPackerPaletteCreator , core::pack::palette::PackerPaletteCreator , core::pack::rotamers::SingleBasicRotamerLibraryCreator , core::pack::rotamers::SingleLigandRotamerLibraryCreator , core::pack::rotamers::SingleNCAARotamerLibraryCreator , core::pack::rotamers::SingleResidueRotamerLibraryCreator , core::pack::rotamers::StoredRotamerLibraryCreator , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AddBehaviorRLTCreator , core::pack::task::operation::AllResFilter , core::pack::task::operation::AllResFilterCreator , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AnyResFilterCreator , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendResidueRotamerSetCreator , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerCreator , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::AppendRotamerSetCreator , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsCreator , core::pack::task::operation::ChainIsnt , core::pack::task::operation::ChainIsntCreator , core::pack::task::operation::ClashBasedRepackShell , core::pack::task::operation::ClashBasedRepackShellCreator , core::pack::task::operation::DesignRestrictions , core::pack::task::operation::DesignRestrictionsCreator , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeCreator , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::DisallowIfNonnativeRLTCreator , core::pack::task::operation::EnableMultiCoolAnnealer , core::pack::task::operation::EnableMultiCoolAnnealerCreator , core::pack::task::operation::EnableSmartAnnealer , core::pack::task::operation::EnableSmartAnnealerCreator , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffCreator , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraChiCutoffRLTCreator , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersCreator , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericCreator , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::operation::ExtraRotamersGenericRLTCreator , core::pack::task::operation::FillAUTOTaskOperation , core::pack::task::operation::FillAUTOTaskOperationCreator , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::IncludeCurrentCreator , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::IncludeCurrentRLTCreator , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromCommandlineCreator , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::InitializeFromOptionCollectionCreator , core::pack::task::operation::KeepSequenceSymmetry , core::pack::task::operation::KeepSequenceSymmetryCreator , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::NoRepackDisulfidesCreator , core::pack::task::operation::NoResFilter , core::pack::task::operation::NoResFilterCreator , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnCertainResiduesCreator , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OperateOnResidueSubsetCreator , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptCysHGCreator , core::pack::task::operation::OptH , core::pack::task::operation::OptHCreator , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaCreator , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreserveCBetaRLTCreator , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingCreator , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::PreventRepackingRLTCreator , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitResiduePropertiesCreator , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator , core::pack::task::operation::ReadResfileCreator , core::pack::task::operation::ResFilterCreator , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueHasPropertyCreator , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsCreator , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueIndexIsntCreator , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueLacksPropertyCreator , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3IsCreator , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResidueName3IsntCreator , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsCreator , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBIndexIsntCreator , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoHasLabelCreator , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResiduePDBInfoLacksLabelCreator , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResidueTypeFilterCreator , core::pack::task::operation::ResLvlTaskOperationCreator , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASCreator , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLTCreator , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator , core::pack::task::operation::RestrictInteractionGraphThreadsOperation , core::pack::task::operation::RestrictInteractionGraphThreadsOperationCreator , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictResidueToRepackingCreator , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingCreator , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictToRepackingRLTCreator , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToResiduePropertiesCreator , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypesCreator , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RestrictYSDesignCreator , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::RotamerExplosionCreator , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerCouplingsCreator , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::SetRotamerLinksCreator , core::pack::task::operation::TaskOperationCreator , core::pack::task::operation::UseMultiCoolAnnealer , core::pack::task::operation::UseMultiCoolAnnealerCreator , core::pack::task::residue_selector::ClashBasedShellSelectorCreator , core::scoring::constraints::AmbiguousConstraintCreator , core::scoring::constraints::AmbiguousNMRConstraintCreator , core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator , core::scoring::constraints::AngleConstraintCreator , core::scoring::constraints::AtomPairConstraintCreator , core::scoring::constraints::BasePairConstraintCreator , core::scoring::constraints::BigBinConstraintCreator , core::scoring::constraints::ConstraintCreator , core::scoring::constraints::CoordinateConstraintCreator , core::scoring::constraints::DihedralConstraintCreator , core::scoring::constraints::DihedralPairConstraintCreator , core::scoring::constraints::FabConstraintCreator , core::scoring::constraints::KofNConstraintCreator , core::scoring::constraints::LocalCoordinateConstraintCreator , core::scoring::constraints::MultiConstraintCreator , core::scoring::constraints::NamedAngleConstraintCreator , core::scoring::constraints::NamedAtomPairConstraintCreator , core::scoring::constraints::SequenceProfileConstraintCreator , core::scoring::constraints::SiteConstraintCreator , core::scoring::constraints::SiteConstraintResiduesCreator , core::select::jump_selector::AndJumpSelectorCreator , core::select::jump_selector::InterchainJumpSelectorCreator , core::select::jump_selector::JumpIndexSelectorCreator , core::select::jump_selector::JumpSelectorCreator , core::select::jump_selector::NotJumpSelectorCreator , core::select::jump_selector::OrJumpSelectorCreator , core::select::residue_selector::AndResidueSelectorCreator , core::select::residue_selector::AsymmetricUnitSelectorCreator , core::select::residue_selector::BinSelectorCreator , core::select::residue_selector::BondedResidueSelectorCreator , core::select::residue_selector::ChainSelectorCreator , core::select::residue_selector::CloseContactResidueSelectorCreator , core::select::residue_selector::DensityFitResidueSelectorCreator , core::select::residue_selector::FalseResidueSelectorCreator , core::select::residue_selector::GlycanLayerSelectorCreator , core::select::residue_selector::GlycanPositionSelectorCreator , core::select::residue_selector::GlycanResidueSelectorCreator , core::select::residue_selector::GlycanSequonsSelectorCreator , core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator , core::select::residue_selector::JumpDownstreamSelectorCreator , core::select::residue_selector::JumpUpstreamSelectorCreator , core::select::residue_selector::LayerSelectorCreator , core::select::residue_selector::NeighborhoodResidueSelectorCreator , core::select::residue_selector::NotResidueSelectorCreator , core::select::residue_selector::NumNeighborsSelectorCreator , core::select::residue_selector::OrResidueSelectorCreator , core::select::residue_selector::PhiSelectorCreator , core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator , core::select::residue_selector::RandomGlycanFoliageSelectorCreator , core::select::residue_selector::RandomResidueSelectorCreator , core::select::residue_selector::ResidueIndexSelectorCreator , core::select::residue_selector::ResidueInMembraneSelectorCreator , core::select::residue_selector::ResidueInSequenceMotifSelectorCreator , core::select::residue_selector::ResidueNameSelectorCreator , core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator , core::select::residue_selector::ResiduePropertySelectorCreator , core::select::residue_selector::ResidueSelectorCreator , core::select::residue_selector::ResidueSpanSelectorCreator , core::select::residue_selector::ScoreTermValueBasedSelectorCreator , core::select::residue_selector::SecondaryStructureSelectorCreator , core::select::residue_selector::SliceResidueSelectorCreator , core::select::residue_selector::SSElementSelectorCreator , core::select::residue_selector::SymmetricalResidueSelectorCreator , core::select::residue_selector::TrueResidueSelectorCreator , core::sequence::ChemicalShiftSequenceCreator , core::sequence::CompositeSequenceCreator , core::sequence::SequenceCouplingCreator , core::sequence::SequenceCreator , core::sequence::SequenceProfileCreator , core::sequence::SimpleSequenceCreator , core::simple_metrics::composite_metrics::CompositeEnergyMetricCreator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetricCreator , core::simple_metrics::composite_metrics::ProtocolSettingsMetricCreator , core::simple_metrics::metrics::CalculatorMetricCreator , core::simple_metrics::metrics::DihedralDistanceMetricCreator , core::simple_metrics::metrics::InteractionEnergyMetricCreator , core::simple_metrics::metrics::ResidueSummaryMetricCreator , core::simple_metrics::metrics::RMSDMetricCreator , core::simple_metrics::metrics::SasaMetricCreator , core::simple_metrics::metrics::SecondaryStructureMetricCreator , core::simple_metrics::metrics::SelectedResidueCountMetricCreator , core::simple_metrics::metrics::SelectedResiduesMetricCreator , core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator , core::simple_metrics::metrics::SequenceMetricCreator , core::simple_metrics::metrics::SequenceSimilarityMetricCreator , core::simple_metrics::metrics::TimingProfileMetricCreator , core::simple_metrics::metrics::TotalEnergyMetricCreator , core::simple_metrics::per_residue_metrics::HbondMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueClashMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueSasaMetricCreator , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetricCreator , core::simple_metrics::SimpleMetricCreator , core::simple_metrics::TestCompositeRealMetricCreator , core::simple_metrics::TestCompositeStringMetricCreator , core::simple_metrics::TestPerResidueRealMetricCreator , core::simple_metrics::TestPerResidueStringMetricCreator , core::simple_metrics::TestRealMetricCreator , core::simple_metrics::TestStringMetricCreator , protocols::aa_composition::AddCompositionConstraintMoverCreator , protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator , protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator , protocols::aa_composition::AddNetChargeConstraintMoverCreator , protocols::aa_composition::ClearCompositionConstraintsMoverCreator , 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::burial_metrics::PolarGroupBurialPyMolStringMetricCreator , protocols::analysis::GlycanInfoMoverCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::analysis::LoopAnalyzerMoverCreator , protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator , protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator , protocols::antibody::AntibodyCDRGrafterCreator , protocols::antibody::AntibodyNumberingConverterMoverCreator , protocols::antibody::constraints::CDRDihedralConstraintMoverCreator , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator , protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator , protocols::antibody::design::AntibodyDesignMoverCreator , protocols::antibody::design::MutateFrameworkForClusterCreator , protocols::antibody::residue_selector::AntibodyRegionSelectorCreator , protocols::antibody::residue_selector::CDRResidueSelectorCreator , protocols::antibody::snugdock::SnugDockCreator , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfileSetsOperationCreator , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::AddCDRProfilesOperationCreator , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperationCreator , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::DisableCDRsOperationCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::antibody::task_operations::RestrictToCDRsAndNeighborsCreator , protocols::backbone_moves::local_backbone_mover::LocalBackboneMoverCreator , protocols::backbone_moves::RandomizeBBByRamaPreProCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubProtocolCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::calc_taskop_filters::ConservedPosMutationFilterCreator , protocols::calc_taskop_filters::MultipleSigmoidsFilterCreator , protocols::calc_taskop_filters::OperatorFilterCreator , protocols::calc_taskop_filters::RelativePoseFilterCreator , protocols::calc_taskop_filters::RotamerBoltzmannWeight2Creator , protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCreator , protocols::calc_taskop_filters::SigmoidFilterCreator , protocols::calc_taskop_movers::ConsensusDesignMoverCreator , protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator , protocols::calc_taskop_movers::ForceDisulfidesMoverCreator , 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::carbohydrates::CreateGlycanSequonMoverCreator , protocols::carbohydrates::GlycanSamplerCreator , protocols::carbohydrates::GlycanTreeMinMoverCreator , protocols::carbohydrates::GlycanTreeModelerCreator , protocols::carbohydrates::IdealizeAnomericHydrogensCreator , protocols::carbohydrates::LinkageConformerMoverCreator , protocols::carbohydrates::RingPlaneFlipMoverCreator , protocols::carbohydrates::SimpleGlycosylateMoverCreator , protocols::carbohydrates::TautomerizeAnomerMoverCreator , protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCreator , protocols::comparative_modeling::GenericJobInputterCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::comparative_modeling::ThreadingJobInputterCreator , protocols::constraint_filters::ConstraintScoreCutoffFilterCreator , protocols::constraint_filters::ConstraintScoreFilterCreator , protocols::constraint_filters::SavePoseConstraintToFileFilterCreator , protocols::constraint_filters::ShowConstraintsFilterCreator , protocols::constraint_generator::AddConstraintsCreator , protocols::constraint_generator::AtomPairConstraintGeneratorCreator , protocols::constraint_generator::ConstraintGeneratorCreator , protocols::constraint_generator::CoordinateConstraintGeneratorCreator , protocols::constraint_generator::DihedralConstraintGeneratorCreator , protocols::constraint_generator::DistanceConstraintGeneratorCreator , protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator , protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator , protocols::constraint_generator::MetalContactsConstraintGeneratorCreator , protocols::constraint_generator::RemoveConstraintsCreator , protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator , protocols::constraint_generator::TerminiConstraintGeneratorCreator , protocols::constraint_movers::AddConstraintsToCurrentConformationMoverCreator , protocols::constraint_movers::ClearConstraintsMoverCreator , protocols::constraint_movers::ConstraintSetMoverCreator , protocols::constraint_movers::CstInfoMoverCreator , protocols::constraint_movers::ResidueTypeConstraintMoverCreator , protocols::constraints_additional::BindingSiteConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator , protocols::constraints_additional::SequenceCoupling1BDConstraintCreator , protocols::constraints_additional::SequenceCouplingConstraintCreator , protocols::contact_map::ContactMapCreator , protocols::coupled_moves::CoupledMovesProtocolCreator , protocols::cryst::CrystRMSCreator , protocols::cryst::DockLatticeMoverCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::MakeLatticeMoverCreator , protocols::cryst::MakeLayerMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::ReportGradientsMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateCrystInfoCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cutoutdomain::CutOutDomainCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::CrosslinkerMoverCreator , protocols::cyclic_peptide::CycpepSymmetryFilterCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::FlipChiralityMoverCreator , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator , protocols::cyclic_peptide::PeptideCyclizeMoverCreator , protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator , protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::cyclic_peptide::RamaMutationSelectorCreator , protocols::cyclic_peptide::SymmetricCycpepAlignCreator , protocols::cyclic_peptide::TryDisulfPermutationsCreator , protocols::denovo_design::architects::BetaSheetArchitectCreator , protocols::denovo_design::architects::BlueprintArchitectCreator , protocols::denovo_design::architects::CompoundArchitectCreator , protocols::denovo_design::architects::DeNovoArchitectCreator , protocols::denovo_design::architects::HelixArchitectCreator , protocols::denovo_design::architects::PoseArchitectCreator , protocols::denovo_design::architects::StrandArchitectCreator , protocols::denovo_design::components::StructureDataCreator , protocols::denovo_design::constraints::FileConstraintGeneratorCreator , protocols::denovo_design::DisulfidizeMoverCreator , protocols::denovo_design::filters::CavityVolumeFilterCreator , protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::denovo_design::filters::PreProlineFilterCreator , protocols::denovo_design::filters::SSPredictionFilterCreator , protocols::denovo_design::filters::SSShapeComplementarityFilterCreator , protocols::denovo_design::movers::AddSegmentDataMoverCreator , protocols::denovo_design::movers::AlignResiduesMoverCreator , protocols::denovo_design::movers::BridgeChainsCreator , protocols::denovo_design::movers::BridgeChainsMoverCreator , protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator , protocols::denovo_design::movers::ExtendChainMoverCreator , protocols::denovo_design::movers::FastDesignCreator , protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator , protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator , protocols::denovo_design::movers::RotateSegmentMoverCreator , protocols::denovo_design::movers::SealFoldTreeMoverCreator , protocols::denovo_design::movers::SetResidueAliasMoverCreator , protocols::denovo_design::residue_selectors::NamedSegmentSelectorCreator , protocols::denovo_design::residue_selectors::PairedSheetResidueSelectorCreator , protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::dna::WatsonCrickRotamerCouplings , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::dna_dock::DNAClashCheckFilterCreator , protocols::dna_dock::PropagateClashCheckFilterCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingHighResLegacyCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingPrepackProtocolCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockingSlideIntoContactCreator , protocols::docking::DockMCMProtocolCreator , protocols::docking::DockMinMoverCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::membrane::MPFindInterfaceMoverCreator , protocols::docking::membrane::QuickRelaxPartnersSeparatelyCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::electron_density::VoxelSpacingRefinementMoverCreator , protocols::environment::AutoCutDataCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::AddRigidBodyLigandConfsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::DetectProteinLigandInterface , 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::ProteinLigandInterfaceUpweighter , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , protocols::enzdes::RemoveLigandFilterCreator , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::enzdes::ResidueConformerFilterCreator , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator , protocols::enzymatic_movers::GlycosyltransferaseMoverCreator , protocols::enzymatic_movers::KinaseMoverCreator , protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator , protocols::evolution::AASynthesisFitnessCostFilterCreator , protocols::evolution::AlignmentAAFinderFilterCreator , protocols::evolution::AlignmentGapInserterFilterCreator , protocols::evolution::EvolutionaryDynamicsMoverCreator , protocols::evolution::NucleotideMutationCreator , protocols::farnesyl::InstallFarnesylMoverCreator , protocols::farnesyl::SampleFarnesylMoverCreator , protocols::features::DatabaseJobInputterCreator , protocols::features::DatabaseJobOutputterCreator , protocols::features::InterfaceDdGMoverCreator , 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::FilterValueMetricCreator , 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::HelixBendFilterCreator , 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::filters::StrandCurvatureByLevelsCreator , protocols::fldsgn::filters::StrandHelixGeometryFilterCreator , protocols::fldsgn::MatchResiduesMoverCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetConstraintGeneratorCreator , protocols::fldsgn::SheetRemodelConstraintGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::flxbb::LayerDesignOperation , protocols::flxbb::LayerDesignOperationCreator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGeneratorCreator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGeneratorCreator , protocols::fold_from_loops::filters::ConstraintFulfilmentFilterCreator , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilterCreator , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilterCreator , protocols::fold_from_loops::movers::AlignByResidueSelectorMoverCreator , protocols::fold_from_loops::movers::DisplayPoseLabelsMoverCreator , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMoverCreator , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMoverCreator , protocols::fold_from_loops::movers::NubInitioLoopClosureMoverCreator , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMoverCreator , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMoverCreator , protocols::fold_from_loops::movers::SavePDBInfoMoverCreator , protocols::fold_from_loops::movers::SplitAndMixPoseMoverCreator , protocols::fold_from_loops::NubInitioMoverCreator , protocols::fold_from_loops::selectors::ConstraintResidueSelectorCreator , protocols::fold_from_loops::selectors::CutpointResidueSelectorCreator , protocols::fold_from_loops::selectors::ProteinResidueSelectorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCConstraintGeneratorCreator , protocols::forge::constraints::RemoveRemodelCstsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::frag_picker::FragmentScoreFilterCreator , 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::hbnet::ConstrainHBondNetwork , protocols::hbnet::ConstrainHBondNetworkCreator , protocols::hbnet::HBNetCreator , protocols::hbnet::HBNetScoreFilterCreator , protocols::hbnet::HBNetStapleInterfaceCreator , protocols::hbnet::UnsatSelectorCreator , protocols::helical_bundle::BackboneGridSamplerCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::BundleReporterFilterCreator , 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::CartesianSamplerCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::idealize::IdealizeMoverCreator , protocols::indexed_structure_store::filters::FragmentLookupFilterCreator , protocols::indexed_structure_store::movers::DirectSegmentLookupMoverCreator , protocols::indexed_structure_store::movers::SegmentSequenceProfileMoverCreator , protocols::jd2::AtomTreeDiffJobInputterCreator , protocols::jd2::AtomTreeDiffJobOutputterCreator , protocols::jd2::EmptyPoseJobInputterCreator , protocols::jd2::EnsembleJobInputterCreator , protocols::jd2::JobInputterCreator , protocols::jd2::JobOutputterCreator , protocols::jd2::LargeNstructJobInputterCreator , protocols::jd2::LazySilentFileJobInputterCreator , protocols::jd2::mmCIFJobOutputterCreator , protocols::jd2::mmtfJobOutputterCreator , protocols::jd2::NoOutputJobOutputterCreator , protocols::jd2::PDBJobInputterCreator , protocols::jd2::PDBJobOutputterCreator , protocols::jd2::PoseInputStreamJobInputterCreator , protocols::jd2::RNA_DeNovoJobOutputterCreator , protocols::jd2::ScoreOnlyJobOutputterCreator , protocols::jd2::ScreeningJobInputterCreator , protocols::jd2::SerializedPoseJobInputterCreator , protocols::jd2::SerializedPoseJobOutputterCreator , protocols::jd2::SilentFileJobInputterCreator , protocols::jd2::SilentFileJobOutputterCreator , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterCreator , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator , protocols::jd3::full_model_inputters::FullModelInputterCreator , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputterCreator , protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator , protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PDBPoseInputterCreator , protocols::jd3::pose_inputters::PoseInputterCreator , protocols::jd3::pose_inputters::SilentFilePoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputterCreator , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator , protocols::jd3::pose_outputters::mmTFPoseOutputter , protocols::jd3::pose_outputters::mmTFPoseOutputterCreator , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputterCreator , protocols::jd3::pose_outputters::PoseOutputterCreator , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::ScoreFileOutputterCreator , protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator , protocols::jd3::pose_outputters::SilentFilePoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator , protocols::kinematic_closure::KicMoverCreator , protocols::legacy_sewing::LegacyAddStartnodeFragmentsCreator , protocols::legacy_sewing::LegacyAppendAssemblyMoverCreator , protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCreator , protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCreator , protocols::legacy_sewing::LegacyGivenPathAssemblyMoverCreator , protocols::legacy_sewing::LegacyGreedyAssemblyMoverCreator , protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCreator , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator , protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator , 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::ga_ligand_dock::GALigandDockCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::ligand_docking::HBondDonorFilterCreator , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::HighResEnsembleCreator , 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::ProtLigEnsembleCreator , 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::TransformEnsembleCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loop_build::LoopmodelWrapperCreator , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::loop_grower::FragmentExtensionCreator , protocols::loop_modeler::LoopModelerCreator , protocols::loop_modeling::LoopBuilderCreator , 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::filters::LoopAnalyzerFilterCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator , 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::BuildingBlockInterfaceOperation , 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::mean_field::GenMeanFieldMoverCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::AddMembraneSpanConstraintCreator , protocols::membrane::AddMembraneSpanTermZConstraintCreator , protocols::membrane::AddMPLigandMoverCreator , protocols::membrane::AqueousPoreFinderCreator , protocols::membrane::benchmark::MakeCanonicalHelixCreator , protocols::membrane::benchmark::SampleTiltAnglesCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::HelixFromSequenceCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::MPLipidAccessibilityCreator , protocols::membrane::MPMutateRelaxMoverCreator , protocols::membrane::MPQuickRelaxMoverCreator , protocols::membrane::OptimizeMembranePositionMoverCreator , protocols::membrane::OptimizeProteinEmbeddingMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::SpinAroundPartnerMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TiltMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::membrane_benchmark::MembraneEnergyLandscapeSamplerCreator , protocols::membrane_benchmark::PeptideOrientationMoverCreator , protocols::minimization_packing::BoltzmannRotamerMoverCreator , protocols::minimization_packing::DisulfideOptimizationMoverCreator , protocols::minimization_packing::MinMoverCreator , protocols::minimization_packing::MinPackMoverCreator , protocols::minimization_packing::PackRotamersMoverCreator , protocols::minimization_packing::PertMinMoverCreator , protocols::minimization_packing::RepackSidechainsMoverCreator , protocols::minimization_packing::RotamerTrialsMinMoverCreator , protocols::minimization_packing::RotamerTrialsMoverCreator , protocols::minimization_packing::SaneMinMoverCreator , protocols::minimization_packing::symmetry::SymMinMoverCreator , protocols::minimization_packing::symmetry::SymPackRotamersMoverCreator , protocols::minimization_packing::symmetry::SymRotamerTrialsMoverCreator , protocols::minimization_packing::symmetry::TaskAwareSymMinMoverCreator , protocols::minimization_packing::TaskAwareMinMoverCreator , protocols::monte_carlo::GenericMonteCarloMoverCreator , protocols::monte_carlo::GenericSimulatedAnnealerCreator , protocols::monte_carlo::MonteCarloRecoverCreator , protocols::monte_carlo::MonteCarloResetCreator , protocols::monte_carlo::MonteCarloTestCreator , protocols::monte_carlo::ResetBaselineMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::FilterReportAsPoseExtraScoresMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::moves::PyMOLMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::moves::SwitchMoverCreator , protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetricCreator , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetricCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::ncbb::ResidueReplacementRebuildMoverCreator , protocols::ncbb::SecStructFinderCreator , protocols::ncbb::SecStructMinimizeMoverCreator , protocols::nmr::ParaNMRScoreMoverCreator , protocols::nmr::pcs::PCSLigandTransformMoverCreator , protocols::nmr::pre::PREMoverCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::normalmode::NormalModeRelaxMoverCreator , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::pack_interface::ProteinProteinInterfaceUpweighterTaskOperationCreator , protocols::parser::ConstraintGeneratorLoaderCreator , protocols::parser::DatabaseSessionLoaderCreator , protocols::parser::DataLoaderCreator , protocols::parser::FragSetLoaderCreator , protocols::parser::JumpSelectorLoaderCreator , protocols::parser::MonteCarloLoaderCreator , protocols::parser::MoveMapFactoryLoaderCreator , protocols::parser::PackerPaletteLoaderCreator , protocols::parser::ResidueSelectorLoaderCreator , protocols::parser::ResLvlTaskOperationLoaderCreator , protocols::parser::ScoreFunctionLoaderCreator , protocols::parser::SimpleMetricLoaderCreator , protocols::parser::TaskOperationLoaderCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator , protocols::peptide_deriver::PeptideDeriverFilterCreator , protocols::pockets::PocketConstraintCreator , protocols::pose_creation::ExtendedPoseMoverCreator , protocols::pose_creation::MakeJunctionsMoverCreator , protocols::pose_creation::MakePolyXMoverCreator , protocols::pose_creation::MergePDBatOverlapMoverCreator , protocols::pose_creation::MergePDBMoverCreator , protocols::pose_creation::PoseFromSequenceMoverCreator , protocols::pose_creation::SliceToMiniProteinMoverCreator , protocols::pose_length_moves::AnalyzeLoopModelingCreator , protocols::pose_length_moves::ConnectChainsMoverCreator , protocols::pose_length_moves::FixAllLoopsMoverCreator , protocols::pose_length_moves::InsertResMoverCreator , protocols::pose_length_moves::NearNativeLoopCloserCreator , 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::HbaGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::PCSMultiGridCreator , protocols::qsar::scoring_grid::PCSSingleGridCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ScoringGridLoaderCreator , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SiteGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGridCreator , protocols::quantum_annealing::ExternalPackerResultLoaderCreator , protocols::quantum_annealing::InteractionGraphSummaryMetricCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::recces::scratch::ThermalMinimizerCreator , protocols::recces::scratch::ThermalSamplingMoverCreator , protocols::recon_design::FindConsensusSequenceCreator , protocols::recon_design::FitnessFilterCreator , protocols::recon_design::MSDMoverCreator , protocols::relax::AcceptToBestMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::LocalRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::relax::RepeatProteinRelaxCreator , protocols::residue_selectors::HBondSelectorCreator , protocols::residue_selectors::LigandMetalContactSelectorCreator , protocols::residue_selectors::NativeSelectorCreator , protocols::residue_selectors::StoredResidueSubsetSelectorCreator , protocols::residue_selectors::StoreResidueSubsetMoverCreator , protocols::residue_selectors::TaskSelectorCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTiltMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rna::denovo::movers::RNA_DeNovoProtocolMoverCreator , protocols::rna::denovo::RNA_DeNovoProtocolCreator , protocols::rna::movers::ERRASER2ProtocolCreator , protocols::rna::movers::ErraserMinimizerMoverCreator , protocols::rna::movers::RNAIdealizeMoverCreator , protocols::rna::movers::RNAThreadAndMinimizeMoverCreator , 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::score_filters::GeometryFilterCreator , protocols::score_filters::ScoreCutoffFilterCreator , protocols::score_filters::ScoreTypeFilterCreator , 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::sewing::hashing::AlignmentFileGeneratorMoverCreator , protocols::sewing::movers::AppendAssemblyMoverCreator , protocols::sewing::movers::AssemblyMoverCreator , protocols::sewing::movers::LigandBindingAssemblyMoverCreator , protocols::sewing::requirements::AssemblyRequirementCreator , protocols::sewing::requirements::ClashRequirementCreator , protocols::sewing::requirements::DsspSpecificLengthRequirementCreator , protocols::sewing::requirements::KeepLigandContactsRequirementCreator , protocols::sewing::requirements::LengthInResiduesRequirementCreator , protocols::sewing::requirements::LigandClashRequirementCreator , protocols::sewing::requirements::NonTerminalStartingSegmentRequirementCreator , protocols::sewing::requirements::SizeInSegmentsRequirementCreator , protocols::sewing::scoring::AssemblyScorerCreator , protocols::sewing::scoring::InterModelMotifScorerCreator , protocols::sewing::scoring::IntraDesignTerminusMotifScorerCreator , protocols::sewing::scoring::LigandScorerCreator , protocols::sewing::scoring::MotifScorerCreator , protocols::sewing::scoring::PartnerMotifScorerCreator , protocols::sewing::scoring::SegmentContactOrderScorerCreator , protocols::sewing::scoring::StartingNodeMotifScorerCreator , protocols::sewing::scoring::SubsetPartnerMotifScorerCreator , protocols::sewing::scoring::TerminusMotifScorerCreator , protocols::sewing::scoring::TopNMotifScorerCreator , protocols::simple_ddg::AlaScanFilterCreator , protocols::simple_ddg::ddGCreator , protocols::simple_ddg::DdgFilterCreator , protocols::simple_ddg::DdGScanCreator , protocols::simple_ddg::InterfaceBindingEnergyDensityFilterCreator , protocols::simple_ddg::SSElementBisectddGFilterCreator , protocols::simple_filters::AngleToVectorFilterCreator , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::AveragePathLengthFilterCreator , protocols::simple_filters::BuriedSurfaceAreaFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::ChainBreakFilterCreator , protocols::simple_filters::ChainCountFilterCreator , protocols::simple_filters::ContactMolecularSurfaceFilterCreator , 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::HelixHelixAngleFilterCreator , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::InterfaceHbondsFilterCreator , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilterCreator , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterRepeatContactFilterCreator , protocols::simple_filters::IntraRepeatContactFilterCreator , protocols::simple_filters::LeastNativeLike9merFilterCreator , protocols::simple_filters::LongestContinuousApolarSegmentFilterCreator , protocols::simple_filters::LongestContinuousPolarSegmentFilterCreator , protocols::simple_filters::MembAccesResidueLipophilicityFilterCreator , protocols::simple_filters::MotifScoreFilterCreator , protocols::simple_filters::MPSpanAngleFilterCreator , 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::PackStatFilterCreator , protocols::simple_filters::PoseCommentFilterCreator , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::ReadPoseExtraScoreFilterCreator , protocols::simple_filters::RepeatParameterFilterCreator , protocols::simple_filters::ReportFilterCreator , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ResidueChiralityFilterCreator , protocols::simple_filters::ResidueCountFilterCreator , protocols::simple_filters::ResidueDepthFilterCreator , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::simple_filters::ResidueIEFilterCreator , protocols::simple_filters::ResidueLipophilicityFilterCreator , protocols::simple_filters::ResidueSelectionDistanceFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::simple_filters::SaveResfileToDiskFilterCreator , protocols::simple_filters::SecretionPredictionFilterCreator , protocols::simple_filters::SequenceDistanceFilterCreator , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::simple_filters::SimpleHbondsToAtomFilterCreator , protocols::simple_filters::SimpleMetricFilterCreator , protocols::simple_filters::SpanTopologyMatchPoseFilterCreator , protocols::simple_filters::SSElementLengthFilterCreator , protocols::simple_filters::SSElementMotifContactFilterCreator , protocols::simple_filters::SSMotifFinderFilterCreator , protocols::simple_filters::StemFinderFilterCreator , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::TaskAwareSASAFilterCreator , protocols::simple_filters::TaskAwareScoreTypeFilterCreator , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::TMsAACompFilterCreator , protocols::simple_filters::TMsSpanMembraneFilterCreator , protocols::simple_filters::TotalSasaFilterCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AddPDBInfoMoverCreator , protocols::simple_moves::AddResidueCouplingConstraintCreator , protocols::simple_moves::AddResidueLabelMoverCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMoverCreator , protocols::simple_moves::BBDihedralSamplerMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ConcatenatePosesMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::ConvertRealToVirtualMoverCreator , protocols::simple_moves::ConvertVirtualToRealMoverCreator , protocols::simple_moves::CopyRotamerMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::DeleteChainMoverCreator , protocols::simple_moves::DeleteChainsMoverCreator , protocols::simple_moves::DisulfideInsertionMoverCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::DumpSingleResidueRotamersCreator , protocols::simple_moves::ExplicitWaterMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FoldTreeFromMotifCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PeriodicBoxMoverCreator , protocols::simple_moves::PoseFromPoseResourceMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ReportXYZCreator , protocols::simple_moves::ResetFoldTreeCreator , protocols::simple_moves::ResetFullModelInfoMoverCreator , protocols::simple_moves::RingConformationMoverCreator , protocols::simple_moves::SaveSequenceToCommentsMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::SetupMetalsMoverCreator , 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::SimpleThreadingMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::StorePoseSnapshotCreator , protocols::simple_moves::StructProfileMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::simple_moves::WriteFiltersToPoseCreator , protocols::simple_moves::WriteSSEMoverCreator , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::InterfaceTaskOperation , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToInterfaceCreator , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::simple_task_operations::RestrictToLoopsAndNeighborsCreator , protocols::simple_task_operations::RestrictToLoopsCreator , protocols::splice::AlignEndsMoverCreator , protocols::splice::DesignInterfacesOperation , protocols::splice::DesignInterfacesOperationCreator , protocols::splice::FindEndpointsOperation , protocols::splice::FindEndpointsOperationCreator , protocols::splice::RBInMoverCreator , protocols::splice::RBOutMoverCreator , protocols::splice::RotLibOutCreator , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDBCreator , protocols::splice::SpliceCreator , protocols::splice::SpliceInAntibodyCreator , protocols::splice::SpliceInCreator , protocols::splice::SpliceInTailCreator , protocols::splice::SpliceOutAntibodyCreator , protocols::splice::SpliceOutCreator , protocols::splice::SpliceOutTailCreator , protocols::splice::TailSegmentMoverCreator , protocols::stepwise::monte_carlo::mover::AddMoverCreator , protocols::stepwise::monte_carlo::mover::DeleteMoverCreator , protocols::stepwise::monte_carlo::mover::FromScratchMoverCreator , protocols::stepwise::monte_carlo::mover::ResampleMoverCreator , protocols::struct_fragment::StructFragmentMoverCreator , protocols::switches::GraftSwitchMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::symmetry::DetectSymmetryMoverCreator , protocols::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::symmetry::SetupForSequenceSymmetryMoverCreator , protocols::symmetry::SetupForSymmetryMoverCreator , protocols::symmetry::SetupNCSMoverCreator , protocols::task_operations::AlignedThreadOperation , protocols::task_operations::AlignedThreadOperationCreator , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::ConservativeDesignOperationCreator , protocols::task_operations::CrystalContactsOperation , protocols::task_operations::CrystalContactsOperationCreator , protocols::task_operations::DatabaseThread , protocols::task_operations::DatabaseThreadCreator , protocols::task_operations::DesignAroundOperation , protocols::task_operations::DesignAroundOperationCreator , protocols::task_operations::DsspDesignOperation , protocols::task_operations::DsspDesignOperationCreator , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::ImportUnboundRotamersOperationCreator , protocols::task_operations::InteractingRotamerExplosion , protocols::task_operations::InteractingRotamerExplosionCreator , protocols::task_operations::JointSequenceOperation , protocols::task_operations::JointSequenceOperationCreator , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LimitAromaChi2OperationCreator , protocols::task_operations::LinkResidues , protocols::task_operations::LinkResiduesCreator , protocols::task_operations::ModifyAnnealer , protocols::task_operations::ModifyAnnealerCreator , protocols::task_operations::MutationSetDesignOperation , protocols::task_operations::pHVariantTaskOperation , protocols::task_operations::pHVariantTaskOperationCreator , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventChainFromRepackingOperationCreator , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::task_operations::ProteinCore , protocols::task_operations::ProteinCoreFilterCreator , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::ProteinInterfaceDesignOperationCreator , protocols::task_operations::PruneBuriedUnsatsOperation , protocols::task_operations::PruneBuriedUnsatsOperationCreator , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::ReadResfileFromDBCreator , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::ResfileCommandOperationCreator , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::ResidueProbDesignOperationCreator , protocols::task_operations::RestrictByCalculatorsOperation , protocols::task_operations::RestrictByCalculatorsOperationCreator , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictChainToRepackingOperationCreator , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictConservedLowDdgOperationCreator , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictIdentitiesOperationCreator , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictInterGroupVectorOperationCreator , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNativeResiduesOperationCreator , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::task_operations::RestrictToCDRH3Loop , protocols::task_operations::RestrictToCDRH3LoopCreator , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToInterfaceOperationCreator , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::task_operations::RestrictToNeighborhoodOperation , protocols::task_operations::RestrictToNeighborhoodOperationCreator , protocols::task_operations::RestrictToTerminiOperation , protocols::task_operations::RestrictToTerminiOperationCreator , protocols::task_operations::RetrieveStoredTaskOperation , protocols::task_operations::RetrieveStoredTaskOperationCreator , protocols::task_operations::SelectByDeltaScoreOperation , protocols::task_operations::SelectByDeltaScoreOperationCreator , protocols::task_operations::SelectByDensityFitOperation , protocols::task_operations::SelectByDensityFitOperationCreator , protocols::task_operations::SelectBySASAOperation , protocols::task_operations::SelectBySASAOperationCreator , protocols::task_operations::SelectResiduesWithinChainOperation , protocols::task_operations::SelectResiduesWithinChainOperationCreator , protocols::task_operations::SeqprofConsensusOperation , protocols::task_operations::SeqprofConsensusOperationCreator , protocols::task_operations::SequenceMotifTaskOperation , protocols::task_operations::SequenceMotifTaskOperationCreator , protocols::task_operations::SetIGTypeOperation , protocols::task_operations::SetIGTypeOperationCreator , protocols::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::task_operations::StoreCompoundTaskMoverCreator , protocols::task_operations::StoreTaskMoverCreator , protocols::task_operations::ThreadSequenceOperation , protocols::task_operations::ThreadSequenceOperationCreator , protocols::testing::BenchmarkBuildRotamersMoverCreator , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMoverCreator
• keys() : core::scoring::motif::MotifHash
• KeySet : core::scoring::motif::MotifHash
• keyword_in_progress() : core::io::HeaderInformation
• keyword_in_progress_ : core::io::HeaderInformation
• Keywords : core::io::HeaderInformation
• keywords() : core::io::HeaderInformation
• keywords_ : core::io::HeaderInformation
• kic_ : protocols::seeded_abinitio::CloseFold
• kic_closure() : protocols::pose_length_moves::PossibleLoop
• 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_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• kic_modeler_if_relevant() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• kic_modeler_if_relevant_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• kic_mover_ : protocols::loop_modeling::LoopBuilder
• kic_res1_ : protocols::cyclic_peptide::DeclareBond
• kic_res2_ : protocols::cyclic_peptide::DeclareBond
• kic_sampling() : protocols::recces::scratch::ThermalMinimizer
• kic_sampling_ : protocols::recces::scratch::ThermalMinimizer
• kick_out_pose_at_idx() : protocols::stepwise::modeler::align::StepWiseClusterer
• KicMover() : protocols::kinematic_closure::KicMover
• kill_antiparallel() : core::scoring::SS_Killhairpins_Info
• kill_antiparallel_ : core::scoring::SS_Killhairpins_Info
• kill_parallel() : core::scoring::SS_Killhairpins_Info
• kill_parallel_ : core::scoring::SS_Killhairpins_Info
• KinaseMover() : protocols::enzymatic_movers::KinaseMover
• kind : core::scoring::packstat::Event
• kinemage_file_name_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• kinematic_control_ : protocols::abinitio::Protocol
• kinematic_mover_ : protocols::enzdes::EnzdesFlexBBProtocol , protocols::protein_interface_design::movers::PlaceOnLoop
• 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
• kinetic_energy() : protocols::md::MDBase
• kinetic_energy_ : protocols::md::MDBase
• 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
• kinked_ : protocols::antibody_legacy::Antibody
• kinmover() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• kinmover_ : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• kmax_ : core::scoring::electron_density::ElectronDensity
• KMedoid() : protocols::toolbox::KMedoid
• kmin_ : core::scoring::electron_density::ElectronDensity
• known_atoms_ : core::scoring::saxs::FormFactorManager
• known_links_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• KofNConstraint() : core::scoring::constraints::KofNConstraint
• KofNConstraintCreator() : core::scoring::constraints::KofNConstraintCreator
• KromerMann() : core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::KromerMann
• KRSQuery() : protocols::kinmatch::KRSQuery
• Ks_spline_ : core::scoring::methods::BBDepCartBondedParameters
• kstep_ : core::scoring::electron_density::ElectronDensity
• kT() : core::sequence::MCAligner
• kT_ : core::sequence::MCAligner
• kt_ : protocols::carbohydrates::GlycanSampler
• kT_ : protocols::cryst::DockLatticeMover , protocols::mpi_refinement::StructAvrgMover , protocols::optimize_weights::PNatLigPoseOptEData , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• Ktheta() : core::scoring::mm::MMBondAngleResidueTypeParam
• Ktheta_ : core::scoring::mm::MMBondAngleResidueTypeParam
• kurtosis() : protocols::toolbox::InteratomicVarianceMatrix