Rosetta  2021.16
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  A  
DisulfideMatchingNeighborIterator (core::scoring::disulfides)   LegacyClashScorer (protocols::legacy_sewing::scoring)   PointWaterPotential (core::scoring)   SelectedResiduesMetricCreator (core::simple_metrics::metrics)   
DisulfideMatchingPotential (core::scoring::disulfides)   LegacyEnumerateAssemblyMover (protocols::legacy_sewing)   PoissonBoltzmannEnergy (core::energy_methods)   SelectedResiduesPyMOLMetric (core::simple_metrics::metrics)   
A   DisulfideMover (protocols::protein_interface_design::movers)   LegacyEnumerateAssemblyMoverCreator (protocols::legacy_sewing)   PoissonBoltzmannEnergyCreator (core::energy_methods)   SelectedResiduesPyMOLMetricCreator (core::simple_metrics::metrics)   
A   DisulfideMoverCreator (protocols::protein_interface_design::movers)   LegacyGivenPathAssemblyMover (protocols::legacy_sewing)   PoissonBoltzmannPotential (core::scoring)   SelectedResPredicate (core::scoring)   
A   DisulfideOptimizationMover (protocols::minimization_packing)   LegacyGivenPathAssemblyMoverCreator (protocols::legacy_sewing)   POLAR (core::pack::task)   SelectGdtEvaluator (protocols::simple_filters)   
A   DisulfideOptimizationMoverCreator (protocols::minimization_packing)   LegacyGlobalLengthRequirement (protocols::legacy_sewing::sampling::requirements)   PolarGroupBurialPyMolStringMetric (protocols::analysis::burial_metrics)   SelectMaxsubEvaluator (protocols::simple_filters)   
A   DisulfidizeMover (protocols::denovo_design)   LegacyGlobalLengthRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PolarGroupBurialPyMolStringMetricCreator (protocols::analysis::burial_metrics)   Selector_AA (core::chemical)   
A3BHbsPatcher (protocols::simple_moves::a3b_hbs)   DisulfidizeMoverCreator (protocols::denovo_design)   LegacyGlobalRequirement (protocols::legacy_sewing::sampling::requirements)   PolarHydrogenFilter (core::chemical)   Selector_BASENAME (core::chemical)   
AACompositionConstraint (core::scoring::aa_composition_energy)   DisulfJumpClaimer (protocols::topology_broker)   LegacyGlobalRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PolarHydrogenPacker (protocols::stepwise::modeler::polar_hydrogens)   Selector_CMDFLAG (core::chemical)   
AACompositionEnergy (core::energy_methods)   DisulfMinData (core::energy_methods)   LegacyGreedyAssemblyMover (protocols::legacy_sewing)   Policy (protocols::nonlocal)   Selector_HAS_ATOMS (core::chemical)   
AACompositionEnergy (protocols::fldsgn::potentials)   DisulfPairing (protocols::jumping)   LegacyGreedyAssemblyMoverCreator (protocols::legacy_sewing)   PolicyFactory (protocols::nonlocal)   Selector_MATCH_VARIANTS (core::chemical)   
AACompositionEnergyCreator (core::energy_methods)   DisulfPairingLibrary (protocols::jumping)   LegacyInterModelMotifScorer (protocols::legacy_sewing::scoring)   Poly (protocols::sasa_scores)   Selector_NAME1 (core::chemical)   
AACompositionEnergyCreator (protocols::fldsgn::potentials)   DisulfResNeighbConstIterator (core::scoring::disulfides)   LegacyIntraSegmentRequirement (protocols::legacy_sewing::sampling::requirements)   PolymerBondedEnergyContainer (core::scoring)   Selector_NAME3 (core::chemical)   
AACompositionEnergySetup (core::scoring::aa_composition_energy)   DisulfResNeighbIterator (core::scoring::disulfides)   LegacyIntraSegmentRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PolymerBondedNeighborConstIterator (core::scoring)   Selector_NO_VARIANTS (core::chemical)   
AACompositionPropertiesSet (core::scoring::aa_composition_energy)   DisulfTemplate (protocols::jumping)   LegacyKicSampler (protocols::loop_modeling::samplers)   PolymerBondedNeighborIterator (core::scoring)   Selector_PROPERTY (core::chemical)   
AAFrequencies (protocols::denovo_design::task_operations)   DiversifyCrmsdByClustering (protocols::frag_picker)   LegacyKicSamplerCreator (protocols::loop_modeling::samplers)   Polynomial_1d (core::scoring::hbonds)   Selector_UPPER_ATOM (core::chemical)   
AAFrequency (protocols::denovo_design::task_operations)   DiversifyCrmsdSelector (protocols::frag_picker)   LegacyLeapIndex (protocols::loophash)   Pool_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   Selector_VARIANT_TYPE (core::chemical)   
AAMatrix (protocols::mean_field)   DiversifyDihedralsSelector (protocols::frag_picker)   LegacyMonteCarloAssemblyMover (protocols::legacy_sewing)   Pool_Evaluator (protocols::canonical_sampling::mc_convergence_checks)   SelectorLogicParser (core::select::residue_selector)   
AAProb (protocols::mean_field)   DiversifyStoredRBConfs (protocols::enzdes)   LegacyMonteCarloAssemblyMoverCreator (protocols::legacy_sewing)   Pool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   SelectRDC_Evaluator (protocols::simple_filters)   
AARepeatEnergy (core::energy_methods)   DivideAndConqueror (protocols::denovo_design::components)   LegacyMotifScorer (protocols::legacy_sewing::scoring)   PoolData (protocols::canonical_sampling::mc_convergence_checks)   SelectResiduesByLayer (core::select::util)   
AARepeatEnergyCreator (core::energy_methods)   DME_FilterMover (protocols::simple_moves)   LegacyPartnerMotifScorer (protocols::legacy_sewing::scoring)   PoolEvaluatorCreator (protocols::simple_filters)   SelectResiduesWithinChainOperation (protocols::task_operations)   
AASynthesisFitnessCost (protocols::evolution)   DNA_BaseEnergy (core::energy_methods)   LegacyReadNativeRotamersFile (protocols::legacy_sewing)   Pose (core::pose)   SelectResiduesWithinChainOperationCreator (protocols::task_operations)   
AASynthesisFitnessCostFilterCreator (protocols::evolution)   DNA_BaseEnergyCreator (core::energy_methods)   LegacyReadNativeRotamersFileCreator (protocols::legacy_sewing)   PoseArchitect (protocols::denovo_design::architects)   SelectRmsdEvaluator (protocols::simple_filters)   
Ab_TemplateInfo (protocols::antibody)   DNA_BasePotential (core::scoring::dna)   LegacyReadRepeatNativeRotamersFile (protocols::legacy_sewing)   PoseArchitectCreator (protocols::denovo_design::architects)   SemiExplicitWaterUnsatisfiedPolarsCalculator (protocols::pose_metric_calculators)   
ABEGO (core::sequence)   DNA_DihedralEnergy (core::energy_methods)   LegacyReadRepeatNativeRotamersFileCreator (protocols::legacy_sewing)   PoseBalls (core::scoring::packing)   SemiRotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)   
Abego (core::energy_methods)   DNA_DihedralEnergyCreator (core::energy_methods)   LegacyRepeatAssemblyMover (protocols::legacy_sewing)   PoseBallsLite (core::scoring::packing)   SeparateDnaFromNonDna (protocols::dna)   
ABEGO_SS_Config (protocols::frag_picker::quota)   DNA_DihedralPotential (core::scoring::dna)   LegacyRepeatAssemblyMoverCreator (protocols::legacy_sewing)   PoseBuilder (protocols::denovo_design::components)   SeparateDnaFromNonDnaCreator (protocols::dna)   
ABEGO_SS_Map (protocols::frag_picker::quota)   DNA_EnvPairEnergy (core::energy_methods)   LegacyRequirementFactory (protocols::legacy_sewing::sampling::requirements)   PoseComment (protocols::simple_filters)   SeqprofConsensusOperation (protocols::task_operations)   
ABEGO_SS_Pool (protocols::frag_picker::quota)   DNA_EnvPairEnergyCreator (core::energy_methods)   LegacyRequirementRegistrator (protocols::legacy_sewing::sampling::requirements)   PoseCommentFilterCreator (protocols::simple_filters)   SeqprofConsensusOperationCreator (protocols::task_operations)   
ABEGO_SS_Score (protocols::frag_picker::scores)   DNA_EnvPairPotential (core::scoring::dna)   LegacyRequirementSet (protocols::legacy_sewing::sampling::requirements)   PoseCommentsFeatures (protocols::features)   SeqSymmAnnealerSetup (core::pack::annealer)   
AbegoEnergyCreator (core::energy_methods)   DNA_ReferenceEnergy (core::energy_methods)   LegacyResidueRetentionRequirement (protocols::legacy_sewing::sampling::requirements)   PoseCommentsFeaturesCreator (protocols::features)   Sequence (core::sequence)   
ABEGOEval (core::fragment::picking_old::vall::eval)   DNA_ReferenceEnergyCreator (core::energy_methods)   LegacyResidueRetentionRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PoseCondition (protocols::moves)   SequenceAlignment (core::sequence)   
ABEGOManager (core::sequence)   DNABase (protocols::dna)   LegacyRootClaim (protocols::topology_broker::claims)   PoseConformationFeatures (protocols::features)   SequenceAlignmentHasher (core::sequence)   
AbinitioBaseFilter (protocols::simple_filters)   DNABasepair (protocols::dna)   LegacySegmentDsspRequirement (protocols::legacy_sewing::sampling::requirements)   PoseConformationFeaturesCreator (protocols::features)   SequenceAnnotation (core::environment)   
AbinitioMoverWeight (protocols::topology_broker::weights)   DNABasestep (protocols::dna)   LegacySegmentDsspRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PoseEvaluator (protocols::evaluation)   SequenceClaim (protocols::topology_broker::claims)   
AbrelaxApplication (protocols::abinitio)   DNABFormPotential (core::scoring::dna)   LegacySegmentLengthRequirement (protocols::legacy_sewing::sampling::requirements)   PoseFolder (protocols::denovo_design::components)   SequenceClaimer (protocols::topology_broker)   
AbrelaxMover (protocols::abinitio)   DnaChains (protocols::dna)   LegacySegmentLengthRequirementCreator (protocols::legacy_sewing::sampling::requirements)   PoseForPoseID (protocols::multistage_rosetta_scripts)   SequenceComparison (protocols::pose_metric_calculators)   
AbscriptLoopCloserCM (protocols::abinitio::abscript)   DNAChiEnergy (core::energy_methods)   LeGrandSasa (core::scoring::sasa)   PoseFoundResiduesCombination (protocols::enzdes)   SequenceConstraint (core::scoring::aa_composition_energy)   
AbscriptLoopCloserCMCreator (protocols::abinitio::abscript)   DNAChiEnergyCreator (core::energy_methods)   LengthChecker (core::environment)   PoseFromPoseResourceMover (protocols::simple_moves)   SequenceCoupling (core::sequence)   
AbscriptMover (protocols::abinitio::abscript)   DNAClashCheckFilter (protocols::dna_dock)   LengthEvent (core::conformation::signals)   PoseFromPoseResourceMoverCreator (protocols::simple_moves)   SequenceCoupling1BDConstraint (protocols::constraints_additional)   
AbscriptMoverCreator (protocols::abinitio::abscript)   DNAClashCheckFilterCreator (protocols::dna_dock)   LengthEventCollector (core::pose::datacache)   PoseFromSequenceMover (protocols::pose_creation)   SequenceCoupling1BDConstraintCreator (protocols::constraints_additional)   
AbscriptStageMover (protocols::abinitio::abscript)   DnaDesignDef (protocols::dna)   LengthGen (core::fragment::picking_old::vall::gen)   PoseFromSequenceMoverCreator (protocols::pose_creation)   SequenceCouplingConstraint (protocols::constraints_additional)   
AbstractArchiveBase (protocols::jd2::archive)   DnaInterfaceFinder (protocols::dna)   LengthInResiduesRequirement (protocols::sewing::requirements)   PoseFromSFRBuilder (core::io::pose_from_sfr)   SequenceCouplingConstraintCreator (protocols::constraints_additional)   
AbstractRotamerTrie (core::conformation)   DnaInterfaceMinMover (protocols::dna)   LengthInResiduesRequirementCreator (protocols::sewing::requirements)   PoseInfoFilter (protocols::simple_filters)   SequenceCouplingCreator (core::sequence)   
AcceptanceCheck (protocols::loop_modeling::utilities)   DnaInterfaceMinMoverCreator (protocols::dna)   LHRepulsiveRamp (protocols::antibody)   PoseInfoFilterCreator (protocols::simple_filters)   SequenceCreator (core::sequence)   
AcceptedScores (protocols::monte_carlo)   DnaInterfaceMultiStateDesign (protocols::dna)   LHRepulsiveRampLegacy (protocols::antibody)   PoseInputSource (protocols::jd3::pose_inputters)   SequenceDependentRefEnergy (core::energy_methods)   
AcceptorAtomFilter (core::chemical)   DnaInterfaceMultiStateDesignCreator (protocols::dna)   LHSnugFitLegacy (protocols::antibody)   PoseInputStream (core::import_pose::pose_stream)   SequenceDependentRefEnergyCreator (core::energy_methods)   
AcceptToBestMover (protocols::relax)   DnaInterfacePacker (protocols::dna)   Librarian (core::fragment::picking_old::concepts)   PoseInputStreamJobInputter (protocols::jd2)   SequenceDistance (protocols::simple_filters)   
AcceptToBestMoverCreator (protocols::relax)   DnaInterfacePackerCreator (protocols::dna)   Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary (core::fragment::picking_old::concepts)   PoseInputStreamJobInputterCreator (protocols::jd2)   SequenceDistanceFilterCreator (protocols::simple_filters)   
Accumulator (core::scoring::packstat)   DNAMethyltransferaseMover (protocols::enzymatic_movers)   Library (core::fragment::picking_old::concepts)   PoseInputter (protocols::jd3::pose_inputters)   SequenceFactory (core::sequence)   
ActiveSiteGrid (protocols::match::downstream)   DNAMethyltransferaseMoverCreator (protocols::enzymatic_movers)   Library_VallSections (core::fragment::picking_old::concepts)   PoseInputterCreator (protocols::jd3::pose_inputters)   SequenceIdentity (protocols::frag_picker::scores)   
AdaptiveScoreHistogram (protocols::frag_picker::scores)   DnaNeighbor (protocols::dna)   Ligand_info (protocols::ligand_docking)   PoseInputterFactory (protocols::jd3::pose_inputters)   SequenceMapping (core::id)   
AddAllPositionsMPM (protocols::match)   DNAParameters (protocols::dna)   LigandAligner (protocols::ligand_docking::ga_ligand_dock)   PoseInputterRegistrator (protocols::jd3::pose_inputters)   SequenceMetric (core::simple_metrics::metrics)   
AddAssemblyConstraints (protocols::domain_assembly)   DnaPosition (protocols::dna)   LigandArea (protocols::ligand_docking)   PoseInserter (protocols::match::output)   SequenceMetric (protocols::multistage_rosetta_scripts::cluster::metrics)   
AddAtom (core::chemical)   DNATorsionEnergy (core::energy_methods)   LigandAreaLoader (protocols::ligand_docking)   PoseJobResult (protocols::jd3::job_results)   SequenceMetricCreator (protocols::multistage_rosetta_scripts::cluster::metrics)   
AddAtomAlias (core::chemical)   DNATorsionEnergyCreator (core::energy_methods)   LigandAreaLoaderCreator (protocols::ligand_docking)   PoseMatchOutputWriter (protocols::match::output)   SequenceMetricCreator (core::simple_metrics::metrics)   
AddBehaviorRLT (core::pack::task::operation)   DNATorsionPotential (core::scoring::dna)   LigandAssemblyRequirement (protocols::sewing::requirements)   PoseMetricCalculator (core::pose::metrics)   SequenceMotifTaskOperation (protocols::task_operations)   
AddBehaviorRLTCreator (core::pack::task::operation)   DockAndRetrieveSidechains (protocols::protein_interface_design::movers)   LigandAssemblyScorer (protocols::sewing::scoring)   PoseMetricContainer (core::pose::metrics)   SequenceMotifTaskOperationCreator (protocols::task_operations)   
AddBond (core::chemical)   DockAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   LigandBaseProtocol (protocols::ligand_docking)   PoseMetricEvaluator (protocols::simple_filters)   SequenceMover (protocols::moves)   
AddBondType (core::chemical)   DockingEnsemble (protocols::docking)   LigandBindingAssemblyMover (protocols::sewing::movers)   PoseNumberedLoopFileReader (protocols::loops)   SequenceNumberResolver (protocols::topology_broker)   
AddCavitiesMover (protocols::simple_moves)   DockingEnsemblePrepackProtocol (protocols::docking)   LigandBindingAssemblyMoverCreator (protocols::sewing::movers)   PoseOutputSpecification (protocols::jd3::pose_outputters)   SequenceProfile (core::sequence)   
AddCDRProfileSetsOperation (protocols::antibody::task_operations)   DockingHighRes (protocols::docking)   LigandBindingResPlacer (protocols::sewing::hashing)   PoseOutputSpecification (protocols::jd3::standard)   SequenceProfileConstraint (core::scoring::constraints)   
AddCDRProfileSetsOperationCreator (protocols::antibody::task_operations)   DockingHighResFactory (protocols::docking)   LigandClashRequirement (protocols::sewing::requirements)   PoseOutputter (protocols::jd3::pose_outputters)   SequenceProfileConstraintCreator (core::scoring::constraints)   
AddCDRProfilesOperation (protocols::antibody::task_operations)   DockingHighResFilter (protocols::docking)   LigandClashRequirementCreator (protocols::sewing::requirements)   PoseOutputterCreator (protocols::jd3::pose_outputters)   SequenceProfileCreator (core::sequence)   
AddCDRProfilesOperationCreator (protocols::antibody::task_operations)   DockingHighResLegacy (protocols::docking)   LigandConformer (protocols::ligand_docking::ga_ligand_dock)   PoseOutputterFactory (protocols::jd3::pose_outputters)   SequenceProfileMover (protocols::simple_moves)   
AddChainBreak (protocols::protein_interface_design::movers)   DockingHighResLegacyCreator (protocols::docking)   LigandConformer (protocols::toolbox::match_enzdes_util)   PoseOutputterRegistrator (protocols::jd3::pose_outputters)   SequenceProfileMoverCreator (protocols::simple_moves)   
AddChainBreakCreator (protocols::protein_interface_design::movers)   DockingInitialPerturbation (protocols::docking)   LigandConformerBuilder (protocols::match::downstream)   PosePackData (core::scoring::packstat)   SequenceRecoveryFilter (protocols::protein_interface_design::filters)   
AddChainMover (protocols::simple_moves)   DockingInitialPerturbationCreator (protocols::docking)   LigandContact (protocols::sewing::data_storage)   PosePropertyReporter (protocols::rosetta_scripts)   SequenceRecoveryFilterCreator (protocols::protein_interface_design::filters)   
AddChainMoverCreator (protocols::simple_moves)   DockingLowRes (protocols::docking)   LigandCoordInfo (protocols::sewing::hashing)   PosePropertyReporterCreator (protocols::rosetta_scripts)   SequenceRecoveryMetric (protocols::analysis::simple_metrics)   
AddChi (core::chemical)   DockingLowResEnsemble (protocols::docking)   LigandDescription (protocols::sewing::data_storage)   PosePropertyReporterFactory (protocols::rosetta_scripts)   SequenceRecoveryMetricCreator (protocols::analysis::simple_metrics)   
AddChiRotamer (core::chemical)   DockingLowResFilter (protocols::docking)   LigandDesign (protocols::ligand_docking)   PosePropertyReporterRegistrator (protocols::rosetta_scripts)   SequenceRegistrator (core::sequence)   
AddCompositionConstraintMover (protocols::aa_composition)   DockingNoRepack1 (protocols::simple_task_operations)   LigandDesignCreator (protocols::ligand_docking)   PoseResidueTypeSet (core::chemical)   SequenceShiftMover (protocols::rbsegment_relax)   
AddCompositionConstraintMoverCreator (protocols::aa_composition)   DockingNoRepack2 (protocols::simple_task_operations)   LigandDockMain (protocols::ligand_docking)   PoseResource (core::import_pose)   SequenceSimilarityMetric (core::simple_metrics::metrics)   
AddConnect (core::chemical)   DockingPrepackProtocol (protocols::docking)   LigandDockProtocol (protocols::ligand_docking)   PoseResourceLoader (core::import_pose)   SequenceSimilarityMetricCreator (core::simple_metrics::metrics)   
AddConnectAndTrackingVirt (core::chemical)   DockingPrepackProtocolCreator (protocols::docking)   LigandMetalContactSelector (protocols::residue_selectors)   PoseResourceLoaderCreator (core::import_pose)   SequenceSpecification (protocols::pdbinfo_manipulations)   
AddConnectDeleteChildProton (core::chemical)   DockingProtocol (protocols::docking)   LigandMetalContactSelectorCreator (protocols::residue_selectors)   PoseSelectionScreener (protocols::stepwise::screener)   SequenceSymmetricAnnealer (core::pack::annealer)   
AddConstraints (protocols::constraint_generator)   DockingProtocolCreator (protocols::docking)   LigandMotifSearch (protocols::motifs)   PoseSelector (protocols::rosetta_scripts)   SequentialSymmetrySlider (protocols::symmetry)   
AddConstraintsCreator (protocols::constraint_generator)   DockingScoreFunction (core::scoring)   LigandPropertyScore (protocols::qsar::scoring_grid)   PoseSelectorCreator (protocols::rosetta_scripts)   Serial_Refine (protocols::mpi_refinement)   
AddConstraintsToCurrentConformationMover (protocols::constraint_movers)   DockingSlideIntoContact (protocols::docking)   LigandPropertyScoreCreator (protocols::qsar::scoring_grid)   PoseSelectorFactory (protocols::rosetta_scripts)   SerializedLoop (protocols::loops)   
AddConstraintsToCurrentConformationMoverCreator (protocols::constraint_movers)   DockingSlideIntoContactCreator (protocols::docking)   LigandResidue (protocols::sewing::data_storage)   PoseSelectorRegistrator (protocols::rosetta_scripts)   SerializedPoseJobInputter (protocols::jd2)   
AddEdgeVisitor (core::conformation)   DockIntoDensityMover (protocols::electron_density)   LigandScorer (protocols::sewing::scoring)   PoseSequence (core::energy_methods)   SerializedPoseJobInputterCreator (protocols::jd2)   
AddGood2BPairEnergyRotamers (protocols::toolbox::rotamer_set_operations)   DockLatticeMover (protocols::cryst)   LigandScorerCreator (protocols::sewing::scoring)   PoseToStructFileRepConverter (core::io::pose_to_sfr)   SerializedPoseJobOutputter (protocols::jd2)   
AddHelixSequenceConstraintsMover (protocols::aa_composition)   DockLatticeMoverCreator (protocols::cryst)   LigandSegment (protocols::sewing::data_storage)   PoseUtilityPlaceholder (protocols::indexed_structure_store)   SerializedPoseJobOutputterCreator (protocols::jd2)   
AddHelixSequenceConstraintsMoverCreator (protocols::aa_composition)   DockMCMCycle (protocols::docking)   LigBurialFilter (protocols::enzdes)   PositionConservedResiduesStore (core::pose::datacache)   SeriesJacobians (core::kinematics::jacobian)   
AddHydrogen (protocols::ligand_docking)   DockMCMProtocol (protocols::docking)   LigBurialFilterCreator (protocols::enzdes)   PositionDdGInfo (core::io::PositionDdGInfo)   NetworkQueue::ServerAddress (protocols::network)   
AddHydrogens (protocols::ligand_docking)   DockMCMProtocolCreator (protocols::docking)   LigDSasaFilter (protocols::enzdes)   PositionSpecificRandomizer (protocols::genetic_algorithm)   Set_AA (core::chemical)   
AddHydrogensCreator (protocols::ligand_docking)   DockMinMover (protocols::docking)   LigDSasaFilterCreator (protocols::enzdes)   PositionType (protocols::dna)   SetAACompositionPotential (protocols::fldsgn::potentials)   
AdditionalBackgroundNodesInteractionGraph (core::pack::interaction_graph)   DockMinMoverCreator (protocols::docking)   LigInterfaceEnergyFilter (protocols::enzdes)   PossibleAtomTypesForAtom (core::chemical::gasteiger)   SetAACompositionPotentialCreator (protocols::fldsgn::potentials)   
AdditionalOutputWrapper (protocols::rosetta_scripts)   DockSetupMover (protocols::docking)   LigInterfaceEnergyFilterCreator (protocols::enzdes)   PossibleLoop (protocols::pose_length_moves)   SetAllAtomsRepulsive (core::chemical)   
AdditionalOutputWrapperCreator (protocols::rosetta_scripts)   DockSetupMoverCreator (protocols::docking)   LimitAromaChi2_RotamerSetOperation (protocols::task_operations)   PostDockAssemblyScorer (protocols::domain_assembly)   SetAtomicCharge (core::chemical)   
AddJobPairData (protocols::simple_moves)   DockTaskFactory (protocols::docking)   LimitAromaChi2Operation (protocols::task_operations)   PosType (protocols::multistate_design)   SetAtomTree (protocols::protein_interface_design::movers)   
AddJobPairDataCreator (protocols::simple_moves)   DockWithHotspotMover (protocols::protein_interface_design::movers)   LimitAromaChi2OperationCreator (protocols::task_operations)   PosTypeCreator (protocols::multistate_design)   SetAtomTreeCreator (protocols::protein_interface_design::movers)   
AddLigandMotifRotamers (protocols::enzdes)   DockWithHotspotMoverCreator (protocols::protein_interface_design::movers)   LimitHitsPerRotamerFilter (protocols::match::output)   PowerDiagram (core::scoring::power_diagram)   SetAtomType (core::chemical)   
AddLigandMotifRotamersOperationCreator (protocols::enzdes)   DOF_Constraint (core::scoring::constraints)   Line (core::sequence)   PowExpression (protocols::pack_daemon)   SetBackboneHeavyatom (core::chemical)   
AddMembraneMover (protocols::membrane)   DOF_DataPoint (core::optimization)   LinearBranchEnergy (core::energy_methods)   PPoly (protocols::sasa_scores)   SetBaseName (core::chemical)   
AddMembraneMoverCreator (protocols::membrane)   DOF_ID (core::id)   LinearBranchEnergyCreator (core::energy_methods)   PQR (core::scoring)   SetCatalyticResPackBehavior (protocols::enzdes)   
AddMembraneSpanConstraint (protocols::membrane)   DOF_ID_Map (core::id)   LinearChainbreakEnergy (core::energy_methods)   PrecomputedFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   SetCatalyticResPackBehaviorCreator (protocols::enzdes)   
AddMembraneSpanConstraintCreator (protocols::membrane)   DOF_ID_Range (core::id)   LinearChainbreakEnergyCreator (core::energy_methods)   PrecomputedLibraryMover (protocols::stepwise::modeler::precomputed)   SetChiMover (protocols::simple_moves::sidechain_moves)   
AddMembraneSpanTermZConstraint (protocols::membrane)   DOF_Node (core::optimization)   LinearFunc (protocols::moves)   PrecomputedPairEnergiesEdge (core::pack::interaction_graph)   SetChiMoverCreator (protocols::simple_moves::sidechain_moves)   
AddMembraneSpanTermZConstraintCreator (protocols::membrane)   DofClaim (protocols::topology_broker::claims)   LinearMemEdge (core::pack::interaction_graph)   PrecomputedPairEnergiesInteractionGraph (core::pack::interaction_graph)   SetCrystWeightMover (protocols::cryst)   
AddMHCEpitopeConstraintMover (protocols::aa_composition)   DOFElement (protocols::environment::claims)   LinearMemNode (core::pack::interaction_graph)   PrecomputedPairEnergiesNode (core::pack::interaction_graph)   SetCrystWeightMoverCreator (protocols::cryst)   
AddMHCEpitopeConstraintMoverCreator (protocols::aa_composition)   DOFHistogramRecorder (protocols::simple_moves)   LinearMemoryInteractionGraph (core::pack::interaction_graph)   PREData (core::scoring::nmr::pre)   SetDisulfideAtomName (core::chemical)   
AddMover (protocols::stepwise::monte_carlo::mover)   DofPassport (core::environment)   LinearPenaltyFunction (core::scoring::func)   PredesignPerturbMover (protocols::enzdes)   SetFormalCharge (core::chemical)   
AddMoverCreator (protocols::stepwise::monte_carlo::mover)   DofUnlock (protocols::environment)   LineMinimizationAlgorithm (core::optimization)   PredesignPerturbMoverCreator (protocols::enzdes)   SetICoor (core::chemical)   
AddMPLigandMover (protocols::membrane)   DomainAssembly (protocols::abinitio)   LineObject (protocols::forge::remodel)   Predicate (core::scoring)   SetIGTypeOperation (protocols::task_operations)   
AddMPLigandMoverCreator (protocols::membrane)   DomainAssembly (protocols::hybridization)   LinkageConformerData (core::chemical::carbohydrates)   PredictedBurialEvaluator (protocols::simple_filters)   SetIGTypeOperationCreator (protocols::task_operations)   
AddNetChargeConstraintMover (protocols::aa_composition)   DomainAssemblyCreator (protocols::abinitio)   LinkageConformerMover (protocols::carbohydrates)   PredictedBurialFnEvaluatorCreator (protocols::simple_filters)   SetInterchangeabilityGroup_String (core::chemical)   
AddNetChargeConstraintMoverCreator (protocols::aa_composition)   DomainInterfaceFilter (protocols::simple_filters)   LinkageConformerMoverCreator (protocols::carbohydrates)   PREDistanceRecord (protocols::nmr::pre)   SetIO_String (core::chemical)   
AddOrDeleteMover (protocols::stepwise::monte_carlo::mover)   DotSphere (core::pack::interaction_graph)   LinkerScore (protocols::sic_dock)   PREEnergy (protocols::nmr::pre)   SetMembraneCenterMover (protocols::membrane)   
AddOrRemoveMatchCsts (protocols::enzdes)   DoubleDenseIGRepacker (protocols::pack_daemon)   LinkInformation (core::io)   PREEnergyCreator (protocols::nmr::pre)   SetMembraneCenterMoverCreator (protocols::membrane)   
AddOrRemoveMatchCstsCreator (protocols::enzdes)   DoubleDensePDEdge (core::pack::interaction_graph)   LinkResidues (protocols::task_operations)   PreliminaryLarvalJob (protocols::jd3::standard)   SetMembraneNormalMover (protocols::membrane)   
AddPDBInfoMover (protocols::simple_moves)   DoubleDensePDInteractionGraph (core::pack::interaction_graph)   LinkResiduesCreator (protocols::task_operations)   PreliminaryLarvalJobTracker (protocols::jd3::standard)   SetMembraneNormalMoverCreator (protocols::membrane)   
AddPDBInfoMoverCreator (protocols::simple_moves)   DoubleDensePDNode (core::pack::interaction_graph)   LK_Ball_BB_BB_E_Invoker (core::scoring::lkball)   PreloadedPDB (protocols::cluster::calibur)   SetMembranePositionMover (protocols::membrane)   
AddProperty (core::chemical)   DoubleLayerKinematicAbinitio (protocols::abinitio)   LK_Ball_BB_SC_E_Invoker (core::scoring::lkball)   PREMover (protocols::nmr::pre)   SetMembranePositionMoverCreator (protocols::membrane)   
AddProtonChi (core::chemical)   DoubleLazyEdge (core::pack::interaction_graph)   LK_Ball_RPE_Invoker (core::scoring::lkball)   PREMoverCreator (protocols::nmr::pre)   SetMMAtomType (core::chemical)   
AddResidueCouplingConstraint (protocols::simple_moves)   DoubleLazyInteractionGraph (core::pack::interaction_graph)   LK_Ball_SC_SC_E_Invoker (core::scoring::lkball)   PREMultiSet (core::scoring::nmr::pre)   SetNbrAtom (core::chemical)   
AddResidueCouplingConstraintCreator (protocols::simple_moves)   DoubleLazyNode (core::pack::interaction_graph)   LK_BallEnergy (core::scoring::lkball)   PrepackMover (protocols::protein_interface_design::movers)   SetNbrRadius (core::chemical)   
AddResidueLabelMover (protocols::simple_moves)   DownJumpSRFD (core::fragment)   LK_BallEnergyCreator (core::scoring::lkball)   PrepackMoverCreator (protocols::protein_interface_design::movers)   SetNetFormalCharge (core::chemical)   
AddResidueLabelMoverCreator (protocols::simple_moves)   DownstreamAlgorithm (protocols::match::downstream)   LK_BallInvoker (core::scoring::lkball)   PrepareForCentroid (protocols::loop_modeling::utilities)   SetOrientAtom (core::chemical)   
AddResiduesRotamerSetOperation (core::pack::rotamer_set)   DownstreamBuilder (protocols::match::downstream)   LK_hack (core::energy_methods)   PrepareForCentroidCreator (protocols::loop_modeling::utilities)   SetPolymerConnectAtom (core::chemical)   
AddRigidBodyLigandConfs (protocols::enzdes)   DownstreamCoordinateKinemageWriter (protocols::match::output)   LK_hackCreator (core::energy_methods)   PrepareForFullatom (protocols::loop_modeling::utilities)   SetPoseSecstructFromStructureDataMover (protocols::denovo_design::movers)   
AddRigidBodyLigandConfsCreator (protocols::enzdes)   DownstreamRMSEvaluator (protocols::match::output)   LK_PolarNonPolarEnergy (core::energy_methods)   PrepareForFullatomCreator (protocols::loop_modeling::utilities)   SetRefinementOptionsMover (protocols::cryst)   
AddSapConstraintMover (protocols::simple_moves)   DP_Matrix (core::sequence)   LK_PolarNonPolarEnergyCreator (core::energy_methods)   PrependMainchainAtom (core::chemical)   SetRefinementOptionsMoverCreator (protocols::cryst)   
AddSapConstraintMoverCreator (protocols::simple_moves)   DPScoringScheme (core::sequence)   LK_SigmoidalFunc (core::energy_methods)   PreProlineFilter (protocols::denovo_design::filters)   SetResidueAliasMover (protocols::denovo_design::movers)   
AddSapMathConstraintMover (protocols::simple_moves)   Dssp (core::scoring::dssp)   LKB_ResidueInfo (core::scoring::lkball)   PreProlineFilterCreator (protocols::denovo_design::filters)   SetResidueAliasMoverCreator (protocols::denovo_design::movers)   
AddSapMathConstraintMoverCreator (protocols::simple_moves)   DsspDesignOperation (protocols::task_operations)   LKB_ResiduesInfo (core::scoring::lkball)   PreSelectedResidRange (core::select)   SetReturningPackRotamersMover (protocols::minimization_packing)   
AddSearchPatternRotSetOp (protocols::hotspot_hashing)   DsspDesignOperationCreator (protocols::task_operations)   LKB_ResPairMinData (core::scoring::lkball)   PresenceCommon (protocols::constel)   SetRotamerCouplings (core::pack::task::operation)   
AddSegmentDataMover (protocols::denovo_design::movers)   DsspMover (protocols::moves)   LKBallDatabase (core::scoring::lkball)   PreserveCBeta (core::pack::task::operation)   SetRotamerCouplingsCreator (core::pack::task::operation)   
AddSegmentDataMoverCreator (protocols::denovo_design::movers)   DsspMoverCreator (protocols::moves)   LKBAtom (core::scoring::lkball::lkbtrie)   PreserveCBetaCreator (core::pack::task::operation)   SetRotamerLinks (core::pack::task::operation)   
AddSidechainConstraintsToHotspots (protocols::protein_interface_design::movers)   DsspSpecificLengthRequirement (protocols::sewing::requirements)   LKBTrieEvaluator (core::scoring::lkball::lkbtrie)   PreserveCBetaRLT (core::pack::task::operation)   SetRotamerLinksCreator (core::pack::task::operation)   
AddSidechainConstraintsToHotspotsCreator (protocols::protein_interface_design::movers)   DsspSpecificLengthRequirementCreator (protocols::sewing::requirements)   LKHBondInfo (core::scoring::hbonds::graph)   PreserveCBetaRLTCreator (core::pack::task::operation)   SetSecStructEnergies (protocols::fldsgn::potentials)   
Adduct (core::chemical)   DualMonteCarlo (protocols::moves)   PCSLigandTransformMover::LMMinPCSDataRef (protocols::nmr::pcs)   PRESingle (core::scoring::nmr::pre)   SetSecStructEnergiesCreator (protocols::fldsgn::potentials)   
AddZincSiteConstraints (protocols::metal_interface)   DummyClass (protocols::toolbox)   LnExpression (protocols::pack_daemon)   PRESingleSet (core::scoring::nmr::pre)   SetTemperatureFactor (protocols::protein_interface_design::movers)   
AdjacentList (protocols::cluster::calibur)   DumpPdb (protocols::simple_moves)   LoadDensityMapMover (protocols::cryst)   PreventChainFromRepackingOperation (protocols::task_operations)   SetTemperatureFactorCreator (protocols::protein_interface_design::movers)   
AlaScan (protocols::simple_ddg)   DumpPdbCreator (protocols::simple_moves)   LoadDensityMapMoverCreator (protocols::cryst)   PreventChainFromRepackingOperationCreator (protocols::task_operations)   SetTorsion (protocols::simple_moves)   
AlaScanFilterCreator (protocols::simple_ddg)   DumpSingleResidueRotamers (protocols::simple_moves)   LoadPDBMover (protocols::simple_moves)   PreventRepacking (core::pack::task::operation)   SetTorsionCreator (protocols::simple_moves)   
Alias (protocols::denovo_design::components)   DumpSingleResidueRotamersCreator (protocols::simple_moves)   LoadPDBMoverCreator (protocols::simple_moves)   PreventRepackingCreator (core::pack::task::operation)   SetupForDensityScoringMover (protocols::electron_density)   
Align_RmsdEvaluator (protocols::comparative_modeling)   DumpTrajectoryEnergy (core::energy_methods)   LoadUnboundRotMover (protocols::simple_moves)   PreventRepackingRLT (core::pack::task::operation)   SetupForDensityScoringMoverCreator (protocols::electron_density)   
Align_RotamerEvaluator (protocols::comparative_modeling)   DumpTrajectoryEnergyCreator (core::energy_methods)   LoadUnboundRotMoverCreator (protocols::simple_moves)   PreventRepackingRLTCreator (core::pack::task::operation)   SetupForFibrilMover (protocols::fibril)   
AlignByResidueSelectorMover (protocols::fold_from_loops::movers)   DunbrackAAParameterSet (core::pack::dunbrack)   LoadVarSolDistSasaCalculatorMover (protocols::vardist_solaccess)   PreventResiduesFromRepackingOperation (protocols::task_operations)   SetupForSequenceSymmetryMover (protocols::symmetry)   
AlignByResidueSelectorMoverCreator (protocols::fold_from_loops::movers)   DunbrackConstraint (core::pack::dunbrack)   LoadVarSolDistSasaCalculatorMoverCreator (protocols::vardist_solaccess)   PreventResiduesFromRepackingOperationCreator (protocols::task_operations)   SetupForSequenceSymmetryMoverCreator (protocols::symmetry)   
AlignChainMover (protocols::simple_moves)   DunbrackConstraintCreator (core::pack::dunbrack)   LocalBackboneMover (protocols::backbone_moves::local_backbone_mover)   PrimarySequenceNeighborhoodSelector (core::select::residue_selector)   SetupForSymmetryMover (protocols::symmetry)   
AlignChainMoverCreator (protocols::simple_moves)   DunbrackEnergy (core::pack::dunbrack)   LocalBackboneMoverCreator (protocols::backbone_moves::local_backbone_mover)   PrimarySequenceNeighborhoodSelectorCreator (core::select::residue_selector)   SetupForSymmetryMoverCreator (protocols::symmetry)   
AlignedThreadOperation (protocols::task_operations)   DunbrackEnergyCreator (core::pack::dunbrack)   LocalCoordinateConstraint (core::scoring::constraints)   ProbSortClass (core::pack::dunbrack)   SetupHotspotConstraintsLoopsMover (protocols::protein_interface_design::movers)   
AlignedThreadOperationCreator (protocols::task_operations)   DunbrackRotamer (core::pack::dunbrack)   LocalCoordinateConstraintCreator (core::scoring::constraints)   ProcessorFactory (protocols::match::output)   SetupHotspotConstraintsLoopsMoverCreator (protocols::protein_interface_design::movers)   
AlignEndsMover (protocols::splice)   DunbrackRotamerLibrarySpecification (core::chemical::rotamers)   LocalInserter (protocols::loophash)   ProClosureEnergy (core::energy_methods)   SetupHotspotConstraintsMover (protocols::protein_interface_design::movers)   
AlignEndsMoverCreator (protocols::splice)   DunbrackRotamerLibrarySpecificationCreator (core::chemical::rotamers)   LocalInserter_SimpleMin (protocols::loophash)   ProClosureEnergyCreator (core::energy_methods)   SetupHotspotConstraintsMoverCreator (protocols::protein_interface_design::movers)   
Aligner (core::sequence)   DunbrackRotamerMeanSD (core::pack::dunbrack)   LocalPosition (core::environment)   ProfilerMover (protocols::moves)   SetupMetalsMover (protocols::simple_moves)   
AlignerFactory (core::sequence)   DunbrackRotamerSampleData (core::pack::dunbrack)   LocalRelax (protocols::relax)   ProfileScore (protocols::frag_picker::scores)   SetupMetalsMoverCreator (protocols::simple_moves)   
AlignEvaluator (protocols::evaluation)   DunbrackSCSampler (protocols::match::upstream)   LocalRelaxCreator (protocols::relax)   ProfileScoreBlosum62 (protocols::frag_picker::scores)   SetupNCSMover (protocols::symmetry)   
AlignmentAAFinder (protocols::evolution)   DynamicAggregateFunction (protocols::pack_daemon)   LogFilePerturber (protocols::kinematic_closure::perturbers)   ProfileScoreDistWeight (protocols::frag_picker::scores)   SetupNCSMoverCreator (protocols::symmetry)   
AlignmentAAFinderFilterCreator (protocols::evolution)   DynamicAggregateFunctionDriver (protocols::pack_daemon)   LoggedFragmentMover (protocols::simple_moves)   ProfileScoreL1 (protocols::frag_picker::scores)   SetupPoissonBoltzmannPotential (protocols::pb_potential)   
AlignmentCluster (protocols::comparative_modeling)   
  E  
LogicalSelector (protocols::pose_selectors)   ProfileScoreStructL1 (protocols::frag_picker::scores)   SetupPoissonBoltzmannPotentialCreator (protocols::pb_potential)   
AlignmentClustering (protocols::comparative_modeling)   LogicResidueSelector (core::select::residue_selector)   ProfileScoreSubMatrix (protocols::frag_picker::scores)   SetVirtualShadow (core::chemical)   
AlignmentEnergy (protocols::rna)   E   LogicResidueSelectorCreator (core::select::residue_selector)   ProfSimScoringScheme (core::sequence)   SewAtom (protocols::legacy_sewing)   
AlignmentEnergyCreator (protocols::rna)   Edge (core::kinematics)   LongAxisRotationFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers)   ProgressBarObserver (protocols::canonical_sampling)   SewGraph (protocols::legacy_sewing)   
AlignmentFGMSettings (protocols::sewing::hashing)   EdgeBase (core::pack::interaction_graph)   LongestContinuousApolarSegmentFilter (protocols::simple_filters)   ProgressBarObserverCreator (protocols::canonical_sampling)   SewResidue (protocols::legacy_sewing)   
AlignmentFileGeneratorMover (protocols::sewing::hashing)   EdgeMapGenerator (protocols::sewing::hashing)   LongestContinuousApolarSegmentFilterCreator (protocols::simple_filters)   ProhibitResidueProperties (core::pack::task::operation)   SewSegment (protocols::legacy_sewing)   
AlignmentFileGeneratorMoverCreator (protocols::sewing::hashing)   EdgeStandScore (protocols::sic_dock)   LongestContinuousPolarSegmentFilter (protocols::simple_filters)   ProhibitResiduePropertiesCreator (core::pack::task::operation)   SF_Replica (protocols::toolbox)   
AlignmentGapInserter (protocols::evolution)   EggshellGrid (protocols::pockets)   LongestContinuousPolarSegmentFilterCreator (protocols::simple_filters)   ProhibitSpecifiedBaseResidueTypes (core::pack::task::operation)   SG_Dist_Func (core::scoring::disulfides)   
AlignmentGapInserterFilterCreator (protocols::evolution)   EItem (core::optimization)   LongRangeTwoBodyEnergy (core::scoring::methods)   ProhibitSpecifiedBaseResidueTypesCreator (core::pack::task::operation)   SGSG_Dihedral_Func (core::scoring::disulfides)   
AlignmentGenerator (protocols::sewing::hashing)   ElecAtom (core::scoring::elec::electrie)   Loop (protocols::loops)   ProlineFixMover (protocols::simple_moves)   ShakeStructureMover (protocols::simple_moves)   
AlignmentSet (protocols::comparative_modeling)   ElecDensAllAtomCenEnergy (core::energy_methods)   Loop (protocols::fldsgn::topology)   ProlinePhiScore (protocols::frag_picker::scores)   ShapeComplementarityCalculator (core::scoring::sc)   
AlignmentSettings (protocols::sewing::hashing)   ElecDensAllAtomCenEnergyCreator (core::energy_methods)   Loop (core::scoring::loop_graph)   PropagateClashCheckFilter (protocols::dna_dock)   ShapeComplementarityCalculatorException (core::scoring::sc)   
AlignPDBInfoToSequences (protocols::pdbinfo_manipulations)   ElecDensAtomwiseEnergy (core::energy_methods)   Loop_lt (protocols::loops)   PropagateClashCheckFilterCreator (protocols::dna_dock)   ShapeComplementarityFilter (protocols::simple_filters)   
AlignPDBInfoToSequencesCreator (protocols::pdbinfo_manipulations)   ElecDensAtomwiseEnergyCreator (core::energy_methods)   LoopAnalyzerFilter (protocols::loops::filters)   PROPERTY (core::pack::task)   ShapeComplementarityFilterCreator (protocols::simple_filters)   
AlignPoseToInvrotTreeMover (protocols::toolbox::match_enzdes_util)   ElecDensCenEnergy (core::energy_methods)   LoopAnalyzerFilterCreator (protocols::loops::filters)   ProQ_Energy (core::energy_methods)   ShapeGrid (protocols::qsar::scoring_grid)   
AlignResiduesMover (protocols::denovo_design::movers)   ElecDensCenEnergyCreator (core::energy_methods)   LoopAnalyzerMover (protocols::analysis)   ProQ_EnergyCreator (core::energy_methods)   ShapeGridCreator (protocols::qsar::scoring_grid)   
AlignResiduesMoverCreator (protocols::denovo_design::movers)   ElecDensEnergy (core::energy_methods)   LoopAnalyzerMoverCreator (protocols::analysis)   ProQPotential (core::scoring)   ShapeSimilarityCalculator (core::scoring::sc)   
AlignRMSD_Screener (protocols::stepwise::screener)   ElecDensEnergyCreator (core::energy_methods)   LoopAnchorFeatures (protocols::features)   ProtectedConformation (protocols::environment)   ShapeSimilarityMetric (core::simple_metrics::metrics)   
AlignRmsdTargetEvaluatorCreator (protocols::comparative_modeling)   ElecGroup (core::scoring::elec)   LoopAnchorFeaturesCreator (protocols::features)   ProteinAtrRepChecker (protocols::stepwise::modeler::protein::checker)   ShapeSimilarityMetricCreator (core::simple_metrics::metrics)   
ALLAA (core::pack::task)   ElecTrieEvaluator (core::scoring::elec::electrie)   LoopBuilder (protocols::loop_modeling)   ProteinAtrRepScreener (protocols::stepwise::legacy::screener)   SharedSilentData (core::io::silent)   
ALLAAwc (core::pack::task)   ElectronConfiguration (core::chemical)   LoopBuilderCreator (protocols::loop_modeling)   ProteinBackboneAtomAtomPairFeatures (protocols::features)   ShearFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers)   
ALLAAxc (core::pack::task)   ElectronDensity (core::scoring::electron_density)   LoopBuildMover (protocols::loop_build)   ProteinBackboneAtomAtomPairFeaturesCreator (protocols::features)   ShearMinCCDTrial (protocols::loops::loop_mover::refine)   
AllAtomNormalization (protocols::qsar::scoring_grid)   ElectronDensityAtomwise (core::scoring::electron_density_atomwise)   LoopCloseEnergy (core::energy_methods)   ProteinBackboneBuildPoint (protocols::match::upstream)   ShearMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
AlleleMatrix (core::scoring::mhc_epitope_energy)   ElectrostaticComplementarityCalculator (core::scoring::sc)   LoopCloseEnergyCreator (core::energy_methods)   ProteinBackboneTorsionAngleFeatures (protocols::features)   ShearMover (protocols::simple_moves)   
AllowedSeqposForGeomCst (protocols::toolbox::match_enzdes_util)   ElectrostaticComplementarityMetric (core::simple_metrics::composite_metrics)   LoopClosePotentialEvaluator (core::scoring::loop_graph::evaluator)   ProteinBackboneTorsionAngleFeaturesCreator (protocols::features)   ShearMoverCreator (protocols::simple_moves)   
AllowPdbIdFilter (protocols::frag_picker)   ElectrostaticComplementarityMetricCreator (core::simple_metrics::composite_metrics)   LoopClosure (protocols::loops::loop_closure::ccd)   ProteinBetaAntiParallelStepWiseSampler (protocols::stepwise::sampler::protein)   Sheet (protocols::fldsgn::topology)   
AllResFilter (core::pack::task::operation)   ElectrostaticComplementarityResults (core::scoring::sc)   LoopCM (protocols::loops::loop_mover)   ProteinBondGeometryFeatures (protocols::features)   SheetBuilder (protocols::jumping)   
AllResFilterCreator (core::pack::task::operation)   ElectrostaticpotentialGrid (protocols::pockets)   LoopCMCreator (protocols::loops::loop_mover)   ProteinBondGeometryFeaturesCreator (protocols::features)   SheetConstraintGenerator (protocols::fldsgn)   
AllResiduesChanged (protocols::abinitio)   ElectrostaticSimilarityCalculator (core::scoring::sc)   LoopComparator (protocols::loop_grower)   ProteinCCD_ClosureScreener (protocols::stepwise::screener)   SheetConstraintGeneratorCreator (protocols::fldsgn)   
AllResiduesChanged (protocols::hybridization)   ElectrostaticSimilarityMetric (core::simple_metrics::composite_metrics)   LoopCycle (core::scoring::loop_graph)   ProteinCore (protocols::task_operations)   SheetDB (protocols::denovo_design::components)   
Alternating   ElectrostaticSimilarityMetricCreator (core::simple_metrics::composite_metrics)   LoopFilter (protocols::loop_modeling::utilities)   ProteinCoreFilterCreator (protocols::task_operations)   SheetFilter (protocols::simple_filters)   
AlternativePairings (protocols::abinitio)   ElectrostaticSimilarityResults (core::scoring::sc)   LoopFinder (protocols::protein_interface_design::movers)   ProteinFragmentStepWiseSampler (protocols::stepwise::sampler::protein)   SheetFoldTypeManager (protocols::fldsgn::topology)   
AlterSpecDisruptionDriver (protocols::pmut_scan)   Element (core::chemical)   LoopFinderCreator (protocols::protein_interface_design::movers)   ProteinInterfaceDesignOperation (protocols::task_operations)   SHEETInformation (core::io)   
AmberPeriodicFunc (core::scoring::func)   ElementSet (core::chemical)   LoopFragmentClaimer (protocols::topology_broker)   ProteinInterfaceDesignOperationCreator (protocols::task_operations)   SheetPositions (protocols::loop_grower)   
AmbigCSScore (protocols::frag_picker::scores)   EllipsoidalRandomizationMover (protocols::docking)   LoopFromFileData (protocols::loops)   ProteinInterfaceMultiStateDesignMover (protocols::protein_interface_design::movers)   SheetRemodelConstraintGenerator (protocols::fldsgn)   
AmbiguousConstraint (core::scoring::constraints)   EMapVector (core::scoring)   LoopGraph (core::scoring::loop_graph)   ProteinInterfaceMultiStateDesignMoverCreator (protocols::protein_interface_design::movers)   SheetRemodelConstraintGeneratorCreator (protocols::fldsgn)   
AmbiguousConstraintCreator (core::scoring::constraints)   Embedding (protocols::membrane::geometry)   LoopGrower (protocols::loop_grower)   ProteinLigandInterfaceUpweighter (protocols::enzdes)   SheetSampler (protocols::loop_grower)   
AmbiguousMultiConstraint (protocols::constraints_additional)   EmbeddingDef (protocols::membrane::geometry)   LoopHashDiversifier (protocols::loophash)   ProteinLigandInterfaceUpweighterOperationCreator (protocols::enzdes)   SheetSet (protocols::fldsgn::topology)   
AmbiguousNMRConstraint (core::scoring::constraints)   EmptyPoseJobInputter (protocols::jd2)   LoopHashDiversifierCreator (protocols::loophash)   ProteinMainChainStepWiseSampler (protocols::stepwise::sampler::protein)   SheetTopologyFilter (protocols::fldsgn::filters)   
AmbiguousNMRConstraintCreator (core::scoring::constraints)   EmptyPoseJobInputterCreator (protocols::jd2)   LoopHashLibrary (protocols::loophash)   ProteinProteinInterfaceUpweighter (protocols::pack_interface)   SheetTopologyFilterCreator (protocols::fldsgn::filters)   
AmbiguousNMRDistanceConstraint (core::scoring::constraints)   EmptyVertexData (protocols::pose_metric_calculators)   LoopHashLibraryLoader (protocols::loophash)   ProteinProteinInterfaceUpweighterTaskOperationCreator (protocols::pack_interface)   SheetTranslate (protocols::nonlocal)   
AmbiguousNMRDistanceConstraintCreator (core::scoring::constraints)   EnableMultiCoolAnnealer (core::pack::task::operation)   LoopHashLibraryLoaderCreator (protocols::loophash)   ProteinResidueConformationFeatures (protocols::features)   SHOBuriedUnsatisfiedPolarsCalculator (protocols::pose_metric_calculators)   
AminoAcidNeighborSparseMatrix (core::pack::interaction_graph)   EnableMultiCoolAnnealerCreator (core::pack::task::operation)   LoopHashMap (protocols::loophash)   ProteinResidueConformationFeaturesCreator (protocols::features)   ShortBackrubMover (protocols::simple_moves)   
An   EnableSmartAnnealer (core::pack::task::operation)   LoopHashMoverWrapper (protocols::loophash)   ProteinResidueSelector (protocols::fold_from_loops::selectors)   ShortBackrubMoverCreator (protocols::simple_moves)   
An   EnableSmartAnnealerCreator (core::pack::task::operation)   LoopHashMoverWrapperCreator (protocols::loophash)   ProteinResidueSelectorCreator (protocols::fold_from_loops::selectors)   ShortestPathInFoldTree (core::kinematics)   
AnalyticEtableEnergy (core::scoring::etable)   EndToEndPivots (protocols::kinematic_closure::pivot_pickers)   LoopHashPerturber (protocols::loop_modeler::perturbers)   ProteinRMSDFeatures (protocols::features)   ShortLoopClosure (protocols::loops::loop_closure::ccd)   
AnalyticEtableEvaluator (core::scoring::etable)   Energies (core::scoring)   LoopHashRelaxProtocol (protocols::loophash)   ProteinRMSDFeaturesCreator (protocols::features)   ShortRangeTwoBodyEnergy (core::scoring::methods)   
AnalyzeLoopModeling (protocols::pose_length_moves)   EnergiesByTaskCalculator (protocols::mean_field)   LoopHashSampler (protocols::loophash)   ProteinRMSDNoSuperpositionFeatures (protocols::features)   ShoveResidueMover (protocols::protein_interface_design::movers)   
AnalyzeLoopModelingCreator (protocols::pose_length_moves)   EnergiesData (protocols::pose_metric_calculators)   LoopInfo (protocols::denovo_design::task_operations)   ProteinRMSDNoSuperpositionFeaturesCreator (protocols::features)   ShoveResidueMoverCreator (protocols::protein_interface_design::movers)   
Anchor (protocols::anchored_design)   EnergyBasedClusteringOptions (protocols::energy_based_clustering)   LoopJumpFoldCst (protocols::abinitio)   ProteinSCSampler (protocols::match::upstream)   ShowConstraintsFilter (protocols::constraint_filters)   
AnchoredDesignMover (protocols::anchored_design)   EnergyBasedClusteringProtocol (protocols::energy_based_clustering)   LoopLengthChange (protocols::protein_interface_design::movers)   ProteinSilentReport (protocols::features)   ShowConstraintsFilterCreator (protocols::constraint_filters)   
AnchoredGraftMover (protocols::grafting)   EnergyCutRotamerTrialsMinMover (protocols::minimization_packing)   LoopLengthChangeCreator (protocols::protein_interface_design::movers)   ProteinSilentStruct_SinglePrecCreator (core::io::silent)   ShowViolation (protocols::abinitio)   
AnchoredGraftMoverCreator (protocols::grafting)   EnergyCutRotamerTrialsMover (protocols::minimization_packing)   LoopModeler (protocols::loop_modeler)   ProteinSilentStruct_Template (core::io::silent)   ShuffleFileSystemJobDistributor (protocols::jd2)   
AnchoredPerturbMover (protocols::anchored_design)   EnergyDependentCalculator (core::pose::metrics)   LoopModelerCreator (protocols::loop_modeler)   ProteinSilentStructCreator (core::io::silent)   SICFast (protocols::sic_dock)   
AnchoredRefineMover (protocols::anchored_design)   EnergyEdge (core::scoring)   LoopmodelWrapper (protocols::loop_build)   ProteinUpstreamBuilder (protocols::match::upstream)   SICPatternAtTransform (protocols::hotspot_hashing)   
AnchorMoversData (protocols::anchored_design)   EnergyEval (core::fragment::picking_old::vall::eval)   LoopmodelWrapperCreator (protocols::loop_build)   ProtLigEnsemble (protocols::ligand_docking)   SidechainContactDistCutoff (protocols::frag_picker)   
AnchorSugarScreener (protocols::stepwise::screener)   EnergyEvent (core::pose::signals)   LoopMover (protocols::loop_modeling)   ProtLigEnsembleCreator (protocols::ligand_docking)   SideChainCopier (protocols::stepwise::modeler::packer)   
AndJumpSelector (core::select::jump_selector)   EnergyGraph (core::scoring)   LoopMover (protocols::loops::loop_mover)   ProtLigPair_info (protocols::ligand_docking)   SidechainMCMover (protocols::simple_moves::sidechain_moves)   
AndJumpSelectorCreator (core::select::jump_selector)   EnergyJobSummary (protocols::jd3::job_summaries)   LoopMover_Perturb_CCD (protocols::loops::loop_mover::perturb)   Protocol (protocols::abinitio)   SidechainMCMoverCreator (protocols::simple_moves::sidechain_moves)   
AndResidueSelector (core::select::residue_selector)   EnergyLandscapeEvaluator (protocols::toolbox)   LoopMover_Perturb_CCDCreator (protocols::loops::loop_mover::perturb)   ProtocolFeatures (protocols::features)   SidechainMetropolisHastingsMover (protocols::canonical_sampling)   
AndResidueSelectorCreator (core::select::residue_selector)   EnergyMapContainer (protocols::relax)   LoopMover_Perturb_KIC (protocols::loops::loop_mover::perturb)   ProtocolSettingsMetric (core::simple_metrics::composite_metrics)   SidechainMetropolisHastingsMoverCreator (protocols::canonical_sampling)   
AndSelector (protocols::pose_selectors)   EnergyMethod (core::scoring::methods)   LoopMover_Perturb_KICCreator (protocols::loops::loop_mover::perturb)   ProtocolSettingsMetricCreator (core::simple_metrics::composite_metrics)   SidechainMinMover (protocols::docking)   
AndSelectorCreator (protocols::pose_selectors)   EnergyMethodCreator (core::scoring::methods)   LoopMover_Perturb_QuickCCD (protocols::loops::loop_mover::perturb)   ProtonResonance (protocols::noesy_assign)   SidechainMover (protocols::simple_moves::sidechain_moves)   
AngleConstraint (core::scoring::constraints)   EnergyMethodOptions (core::scoring::methods)   LoopMover_Perturb_QuickCCD_Moves (protocols::loops::loop_mover::perturb)   PruneBuriedUnsats_RotamerSetsOperation (protocols::task_operations)   SidechainMoverBase (protocols::simple_moves::sidechain_moves)   
AngleConstraintCreator (core::scoring::constraints)   EnergyMethodRegistrator (core::scoring::methods)   LoopMover_Perturb_QuickCCD_MovesCreator (protocols::loops::loop_mover::perturb)   PruneBuriedUnsatsOperation (protocols::task_operations)   SidechainMoverCreator (protocols::simple_moves::sidechain_moves)   
AngleToVector (protocols::simple_filters)   EnergyNames (core::io::silent)   LoopMover_Perturb_QuickCCDCreator (protocols::loops::loop_mover::perturb)   PruneBuriedUnsatsOperationCreator (protocols::task_operations)   SidechainNeighborCountMetric (core::simple_metrics::per_residue_metrics)   
AngleToVectorFilterCreator (protocols::simple_filters)   EnergyNode (core::scoring)   LoopMover_Refine_Backrub (protocols::loops::loop_mover::refine)   PseudoBond (core::conformation)   SidechainNeighborCountMetricCreator (core::simple_metrics::per_residue_metrics)   
ANN (protocols::sparta)   EnergyPerResidueFilter (protocols::simple_filters)   LoopMover_Refine_BackrubCreator (protocols::loops::loop_mover::refine)   PseudoBondCollection (core::conformation)   SidechainRmsdFilter (protocols::simple_filters)   
AnnealableGraphBase (core::pack::interaction_graph)   EnergyPerResidueFilterCreator (protocols::simple_filters)   LoopMover_Refine_CCD (protocols::loops::loop_mover::refine)   PseudocontactShiftEnergyController (protocols::topology_broker)   SidechainRmsdFilterCreator (protocols::simple_filters)   
AnnealerFactory (core::pack::annealer)   EnergyReporter (protocols::pose_reporters)   LoopMover_Refine_CCDCreator (protocols::loops::loop_mover::refine)   PseudocontactShiftEnergyController_Ts1 (protocols::topology_broker)   SidechainStateAssignment (core::pack::scmin)   
AnnealerObserver (core::pack::annealer)   EnergyReporterCreator (protocols::pose_reporters)   LoopMover_Refine_KIC (protocols::loops::loop_mover::refine)   PseudocontactShiftEnergyController_Ts2 (protocols::topology_broker)   Sigmoid (protocols::calc_taskop_filters)   
AnnotatedFragData (core::fragment)   EnsembleConstraints (protocols::cluster)   LoopMover_Refine_KICCreator (protocols::loops::loop_mover::refine)   PseudocontactShiftEnergyController_Ts3 (protocols::topology_broker)   SigmoidFilterCreator (protocols::calc_taskop_filters)   
AnnotatedSequence (core::sequence)   EnsembleConstraints_Simple (protocols::cluster)   LoopMover_SlidingWindow (protocols::loop_build)   PseudocontactShiftEnergyController_Ts4 (protocols::topology_broker)   SigmoidFunc (core::scoring::func)   
Antibody (protocols::antibody_legacy)   EnsembleEnergy (protocols::scoring::methods)   LoopMover_SlidingWindowCreator (protocols::loop_build)   PseudocontactShiftEnergyCreator (protocols::scoring::methods::pcs)   SigmoidWeightedCenList (core::scoring)   
AntibodyCDRGrafter (protocols::antibody)   EnsembleEnergyCreator (protocols::scoring::methods)   LoopMoverFactory (protocols::loops)   PseudocontactShiftEnergyCreator_Ts1 (protocols::scoring::methods::pcsTs1)   SilentEnergy (core::io::silent)   
AntibodyCDRGrafterCreator (protocols::antibody)   EnsembleJobInputter (protocols::jd2)   LoopMoverFromCommandLine (protocols::protein_interface_design::movers)   PseudocontactShiftEnergyCreator_Ts2 (protocols::scoring::methods::pcsTs2)   SilentFileData (core::io::silent)   
AntibodyDatabaseManager (protocols::antibody)   EnsembleJobInputterCreator (protocols::jd2)   LoopMoverFromCommandLineCreator (protocols::protein_interface_design::movers)   PseudocontactShiftEnergyCreator_Ts3 (protocols::scoring::methods::pcsTs3)   SilentFileFullModelInputter (protocols::jd3::full_model_inputters)   
AntibodyDesignEnumManager (protocols::antibody::design)   Entity (protocols::genetic_algorithm)   LoopMoverGroup (protocols::loop_modeling::utilities)   PseudocontactShiftEnergyCreator_Ts4 (protocols::scoring::methods::pcsTs4)   SilentFileFullModelInputterCreator (protocols::jd3::full_model_inputters)   
AntibodyDesignMover (protocols::antibody::design)   EntityCorrespondence (protocols::pack_daemon)   LoopOver (protocols::protein_interface_design::movers)   Psi (protocols::frag_picker::scores)   SilentFileJobInputter (protocols::jd2)   
AntibodyDesignMoverCreator (protocols::antibody::design)   EntityElement (protocols::genetic_algorithm)   LoopOverCreator (protocols::protein_interface_design::movers)   PsiPredInterface (core::io::external)   SilentFileJobInputterCreator (protocols::jd2)   
AntibodyEnumManager (protocols::antibody)   EntityElementCreator (protocols::genetic_algorithm)   LoopPartialSolution (protocols::loop_grower)   PsiPredResult (core::io::external)   SilentFileJobOutputter (protocols::jd2)   
AntibodyFeatures (protocols::antibody)   EntityElementFactory (protocols::genetic_algorithm)   LoopPartialSolutionStore (protocols::loop_grower)   PSSM2BfactorMover (protocols::simple_moves)   SilentFileJobOutputterCreator (protocols::jd2)   
AntibodyFeaturesCreator (protocols::antibody)   EntityElementRegistrator (protocols::genetic_algorithm)   LoopPivots (protocols::kinematic_closure::pivot_pickers)   PSSM2BfactorMoverCreator (protocols::simple_moves)   SilentFileOptions (core::io::silent)   
AntibodyInfo (protocols::antibody)   EntityElementsEqual (protocols::genetic_algorithm)   LoopProtocol (protocols::loop_modeling)   PSSMOptEPositionData (protocols::optimize_weights)   SilentFilePoseInputStream (core::import_pose::pose_stream)   
AntibodyModeler (protocols::antibody_legacy)   EntityFunc (protocols::pack_daemon)   LoopProtocolCreator (protocols::loop_modeling)   PValuedFragmentScoreManager (protocols::frag_picker::scores)   SilentFilePoseInputter (protocols::jd3::pose_inputters)   
AntibodyModelerProtocol (protocols::antibody)   EntityFuncExpressionCreator (protocols::pack_daemon)   LoopRebuild (protocols)   PyEnergyMethodRegistrator (core::scoring::methods)   SilentFilePoseInputterCreator (protocols::jd3::pose_inputters)   
AntibodyNumbering (protocols::antibody)   EntityHistoryLT (protocols::pack_daemon)   LoopRefine (protocols)   PyMOLMover (protocols::moves)   SilentFilePoseOutputSpecification (protocols::jd3::pose_outputters)   
AntibodyNumberingConverterMover (protocols::antibody)   EntityRandomizer (protocols::genetic_algorithm)   LoopRefineInnerCycle (protocols::loops::loop_mover::refine)   PyMOLMoverCreator (protocols::moves)   SilentFilePoseOutputter (protocols::jd3::pose_outputters)   
AntibodyNumberingConverterMoverCreator (protocols::antibody)   EntropyEstimator (protocols::ligand_docking::ga_ligand_dock)   LoopRefineInnerCycleContainer (protocols::loops::loop_mover::refine)   PyMOLObserver (protocols::moves)   SilentFilePoseOutputterCreator (protocols::jd3::pose_outputters)   
AntibodyNumberingParser (protocols::antibody)   Enumerate1WithSelector (core::select)   LoopRefineInnerCycleContainerCreator (protocols::loops::loop_mover::refine)   PyRotamerEliminator (core::pack::rotamer_set)   SilentObserver (protocols::viewer)   
AntibodyRegionSelector (protocols::antibody::residue_selector)   EnumeratedVectorSelector (protocols::denovo_design::components)   LoopRefineInnerCycleFactory (protocols::loops::loop_mover::refine)   PyRotamerEliminatorTaskOperation (core::pack::rotamer_set)   SilentStruct (core::io::silent)   
AntibodyRegionSelectorCreator (protocols::antibody::residue_selector)   EnumInfo (update_ResidueType_enum_files)   LoopRelaxMover (protocols::relax::loop)   
  Q  
SilentStructCreator (core::io::silent)   
AntibodySeqDesignTFCreator (protocols::antibody::design)   EnvClaim (protocols::environment::claims)   LoopRelaxMoverCreator (protocols::relax::loop)   SilentStructFactory (core::io::silent)   
AnyResFilter (core::pack::task::operation)   EnvClaimBroker (protocols::environment)   LoopRelaxThreadingMover (protocols::comparative_modeling)   Quat (protocols::simple_filters)   SilentStructRegistrator (core::io::silent)   
AnyResFilterCreator (core::pack::task::operation)   EnvCore (core::environment)   LoopRemodel (protocols::protein_interface_design::movers)   QuickRelaxPartnersSeparately (protocols::docking::membrane)   SilentStructStore (protocols::wum)   
APBSConfig (core::scoring)   EnvEnergy (core::energy_methods)   LoopRemodelCreator (protocols::protein_interface_design::movers)   QuickRelaxPartnersSeparatelyCreator (protocols::docking::membrane)   SilentStructureStoreBackend (protocols::indexed_structure_store)   
APBSResult (core::scoring)   EnvEnergyCreator (core::energy_methods)   LoopRlxMover (protocols::antibody_legacy)   QuickRepacker (protocols::pack_daemon)   SilentTrajectoryRecorder (protocols::canonical_sampling)   
APBSWrapper (core::scoring)   Environment (protocols::environment)   LoopRmsdEvaluator (protocols::simple_filters)   QuotaCollector (protocols::frag_picker::quota)   SilentTrajectoryRecorderCreator (protocols::canonical_sampling)   
APCluster (protocols::cluster)   EnvLabelSelector (protocols::environment::claims)   Loops (protocols::loops)   QuotaConfig (protocols::frag_picker::quota)   SimAnnealerBase (core::pack::annealer)   
APOLA (core::pack::task)   EnvMover (protocols::environment)   LoopsDatabaseDefiner (protocols::loops::loops_definers)   QuotaDebug (protocols::frag_picker)   SimPDB (protocols::cluster::calibur)   
APOLAR (core::pack::task)   EnvMoverCreator (protocols::environment)   LoopsDatabaseDefinerCreator (protocols::loops::loops_definers)   QuotaPool (protocols::frag_picker::quota)   Simple   
APolarHydrogenFilter (core::chemical)   EnvPairPotential (core::scoring)   LoopsDefiner (protocols::loops::loops_definers)   QuotaSelector (protocols::frag_picker::quota)   SimpleCycpepPredictApplication (protocols::cyclic_peptide_predict)   
AppendAssemblyMover (protocols::sewing::movers)   EnvSmoothEnergy (core::energy_methods)   LoopsDefinerCreator (protocols::loops::loops_definers)   
  R  
SimpleDerivCheckResult (core::optimization)   
AppendAssemblyMoverCreator (protocols::sewing::movers)   EnvSmoothEnergyCreator (core::energy_methods)   LoopsDefinerFactory (protocols::loops::loops_definers)   SimpleEdge (core::pack::interaction_graph)   
AppendMainchainAtom (core::chemical)   EnzConstraintIO (protocols::toolbox::match_enzdes_util)   LoopsDefinerLoader (protocols::loops::loops_definers)   APBSConfig::R_PARAM (core::scoring)   SimpleGlycosylateMover (protocols::carbohydrates)   
AppendResidueRotamerSet (core::pack::task::operation)   EnzConstraintParameters (protocols::toolbox::match_enzdes_util)   LoopsDefinerLoaderCreator (protocols::loops::loops_definers)   RadiusOfGyrationFeatures (protocols::features)   SimpleGlycosylateMoverCreator (protocols::carbohydrates)   
AppendResidueRotamerSetCreator (core::pack::task::operation)   EnzCstTemplateRes (protocols::toolbox::match_enzdes_util)   LoopsDefinerRegistrator (protocols::loops::loops_definers)   RadiusOfGyrationFeaturesCreator (protocols::features)   SimpleHbondsToAtomFilter (protocols::simple_filters)   
AppendRotamer (core::pack::task::operation)   EnzCstTemplateResAtoms (protocols::toolbox::match_enzdes_util)   LoopsExplicitDefiner (protocols::loops::loops_definers)   Rama2bPerturber (protocols::kinematic_closure::perturbers)   SimpleHbondsToAtomFilterCreator (protocols::simple_filters)   
AppendRotamerCreator (core::pack::task::operation)   EnzCstTemplateResCache (protocols::toolbox::match_enzdes_util)   LoopsExplicitDefinerCreator (protocols::loops::loops_definers)   Ramachandran (core::scoring)   SimpleInteractionGraph (core::pack::interaction_graph)   
AppendRotamerSet (core::pack::task::operation)   EnzdesBaseProtocol (protocols::enzdes)   LoopsFileData (protocols::loops)   Ramachandran2B (core::scoring)   SimpleMetric (core::simple_metrics)   
AppendRotamerSetCreator (core::pack::task::operation)   EnzdesCacheableObserver (protocols::toolbox::match_enzdes_util)   LoopsFileDefiner (protocols::loops::loops_definers)   RamachandranEnergy (core::energy_methods)   SimpleMetricCreator (core::simple_metrics)   
ApplyRandomStoredRBConf (protocols::enzdes)   EnzdesConstraintReporter (protocols::enzdes)   LoopsFileDefinerCreator (protocols::loops::loops_definers)   RamachandranEnergy2B (core::energy_methods)   SimpleMetricData (core::simple_metrics)   
ApproximateBuriedUnsatPenalty (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty)   EnzdesCstCache (protocols::toolbox::match_enzdes_util)   LoopsFileIO (protocols::loops)   RamachandranEnergy2BCreator (core::energy_methods)   SimpleMetricFactory (core::simple_metrics)   
ApproximateBuriedUnsatPenaltyCreator (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty)   EnzdesCstParamCache (protocols::toolbox::match_enzdes_util)   LoopsFileLoader (protocols::loops)   RamachandranEnergyCreator (core::energy_methods)   SimpleMetricFeatures (protocols::features)   
AqueousPoreFinder (protocols::membrane)   EnzdesFixBBProtocol (protocols::enzdes)   LoopsFileLoaderCreator (protocols::loops)   RamaCheck1B (protocols::loops::loop_closure::ccd)   SimpleMetricFeaturesCreator (protocols::features)   
AqueousPoreFinderCreator (protocols::membrane)   EnzdesFlexBBProtocol (protocols::enzdes)   LoopsStringDefiner (protocols::loops::loops_definers)   RamaCheck2B (protocols::loops::loop_closure::ccd)   SimpleMetricFilter (protocols::simple_filters)   
AqueousPoreParameters (core::conformation::membrane)   EnzdesFlexibleRegion (protocols::enzdes)   LoopsStringDefinerCreator (protocols::loops::loops_definers)   RamaCheckBase (protocols::loops::loop_closure::ccd)   SimpleMetricFilterCreator (protocols::simple_filters)   
ArchiveBase (protocols::jd2::archive)   EnzdesJobInputter (protocols::enzdes)   LR_AtomData (core::scoring::packstat)   RamaMutationSelector (protocols::cyclic_peptide)   SimpleMetricLoader (protocols::parser)   
ArchiveManager (protocols::jd2::archive)   EnzdesJobInputterCreator (protocols::enzdes)   LR_MP_AtomData (core::scoring::packstat)   RamaMutationSelectorCreator (protocols::cyclic_peptide)   SimpleMetricLoaderCreator (protocols::parser)   
AreaAccumulator (core::scoring::packstat)   EnzdesJobOutputter (protocols::enzdes)   LREnergyContainer (core::scoring)   RamaPerturber (protocols::kinematic_closure::perturbers)   SimpleMetricRegistrator (core::simple_metrics)   
AreConnectablePredicate (protocols::denovo_design::connection)   EnzdesJobOutputterCreator (protocols::enzdes)   LRmsdFilter (protocols::protein_interface_design::filters)   RamaPrePro (core::scoring)   SimpleMetricSelector (core::select::residue_selector)   
ArgCationPiEnergy (core::energy_methods)   EnzdesLoopInfo (protocols::toolbox::match_enzdes_util)   LRmsdFilterCreator (protocols::protein_interface_design::filters)   RamaPreProEnergy (core::energy_methods)   SimpleMetricSelectorCreator (core::select::residue_selector)   
ArgCationPiEnergyCreator (core::energy_methods)   EnzdesLoopsFile (protocols::toolbox::match_enzdes_util)   LSMSearchPattern (protocols::hotspot_hashing)   RamaPreProEnergyCreator (core::energy_methods)   SimpleMetricStruct (core::simple_metrics)   
ArmijoLineMinimization (core::optimization)   EnzdesScorefileFilter (protocols::enzdes)   
  M  
RamaPreproFilename (core::chemical)   SimpleNode (core::pack::interaction_graph)   
AROMATIC (core::pack::task)   EnzdesScorefileFilterCreator (protocols::enzdes)   RamaPreproResname (core::chemical)   SimpleNodeManager (protocols::jd3::dag_node_managers)   
AromaticAtomFilter (core::chemical)   EnzdesSeqRecoveryCache (protocols::toolbox::match_enzdes_util)   MainchainScoreTable (core::chemical::mainchain_potential)   RamaScore (protocols::frag_picker::scores)   SimplePDB (core::scoring::packstat)   
AromaticBackboneRestraintEnergy (core::energy_methods)   EnzRepackMinimize (protocols::enzdes)   MainchainTorsionReporter (core::pack::dunbrack)   RampingFunc (protocols::moves)   SimplePDB_Atom (core::scoring::packstat)   
AromaticBackboneRestraintEnergyCreator (core::energy_methods)   EnzRepackMinimizeCreator (protocols::enzdes)   MainChainTorsionSet (protocols::stepwise::modeler::protein)   RampingMover (protocols::moves)   SimplePoseSelection (protocols::stepwise::legacy::screener)   
Array2D (core::scoring::packstat)   EnzScoreFilter (protocols::enzdes)   MakeABEGO_SS_Score (protocols::frag_picker::scores)   RampingMoverCreator (protocols::moves)   SimpleRMSD_Screener (protocols::stepwise::legacy::screener)   
AspartimidePenaltyEnergy (core::energy_methods)   EnzScoreFilterCreator (protocols::enzdes)   MakeAmbigCSScore (protocols::frag_picker::scores)   RandomConformerMover (protocols::ligand_docking)   SimpleScoringScheme (core::sequence)   
AspartimidePenaltyEnergyCreator (core::energy_methods)   EnzymaticMover (protocols::enzymatic_movers)   MakeAsymmetricStructureDataMover (protocols::denovo_design::movers)   RandomConformers (protocols::ligand_docking)   SimpleSequenceCreator (core::sequence)   
AssembleLinkerMover (protocols::domain_assembly)   EnzymeData (core::enzymes)   MakeAsymmetricStructureDataMoverCreator (protocols::denovo_design::movers)   RandomConformersCreator (protocols::ligand_docking)   SimpleSequenceData (core::io::silent)   
Assembly (protocols::legacy_sewing)   EnzymeManager (core::enzymes)   MakeAtomPairConstraintsScore (protocols::frag_picker::scores)   RandomGapSolutionPicker (protocols::backbone_moves::local_backbone_mover::gap_solution_pickers)   SimpleThreadingMover (protocols::simple_moves)   
AssemblyFactory (protocols::legacy_sewing)   EPRSpinLabel (core::scoring::epr_deer)   MakeBFactor (protocols::frag_picker::scores)   RandomGlycanFoliageSelector (core::select::residue_selector)   SimpleThreadingMoverCreator (protocols::simple_moves)   
AssemblyMover (protocols::sewing::movers)   ERRASER2Protocol (protocols::rna::movers)   MakeBundle (protocols::helical_bundle)   RandomGlycanFoliageSelectorCreator (core::select::residue_selector)   SimpleTreeBuilder (protocols::nonlocal)   
AssemblyMoverCreator (protocols::sewing::movers)   ERRASER2ProtocolCreator (protocols::rna::movers)   MakeBundleCreator (protocols::helical_bundle)   RandomizeBBByRamaPrePro (protocols::backbone_moves)   Simulated4PDEERTrace (core::scoring::epr_deer)   
AssemblyRequirement (protocols::sewing::requirements)   ErraserMinimizerMover (protocols::rna::movers)   MakeBundleHelix (protocols::helical_bundle)   RandomizeBBByRamaPreProCreator (protocols::backbone_moves)   Simulated4PDEERTraceFactory (core::scoring::epr_deer)   
AssemblyRequirementCreator (protocols::sewing::requirements)   ErraserMinimizerMoverCreator (protocols::rna::movers)   MakeBundleHelixCreator (protocols::helical_bundle)   RandomMover (protocols::moves)   SimulatedTempering (protocols::canonical_sampling)   
AssemblyRequirementFactory (protocols::sewing::requirements)   Etable (core::scoring::etable)   MakeCanonicalHelix (protocols::membrane::benchmark)   RandomMoverCreator (protocols::moves)   SimulatedTempering (protocols::moves)   
AssemblyRequirementRegistrator (protocols::sewing::requirements)   EtableAtom (core::scoring::etable::etrie)   MakeCanonicalHelixCreator (protocols::membrane::benchmark)   RandomMutation (protocols::protein_interface_design::movers)   SimulatedTemperingCreator (protocols::canonical_sampling)   
AssemblyScorer (protocols::sewing::scoring)   EtableClassicIntraEnergyCreator (core::scoring::etable)   MakeConstScore (protocols::frag_picker::scores)   RandomMutationCreator (protocols::protein_interface_design::movers)   SingleBasicRotamerLibrary (core::pack::rotamers)   
AssemblyScorerCreator (protocols::sewing::scoring)   EtableEnergyCreator (core::scoring::etable)   MakeCSScore (protocols::frag_picker::scores)   RandomOmegaFlipMover (protocols::simple_moves)   SingleBasicRotamerLibraryCreator (core::pack::rotamers)   
AssemblyScorerFactory (protocols::sewing::scoring)   EtableEvaluator (core::scoring::etable)   MakeDihedralConstraintsScore (protocols::frag_picker::scores)   RandomOmegaFlipMoverCreator (protocols::simple_moves)   SingleConstraint (protocols::toolbox::match_enzdes_util)   
AssemblyScorerRegistrator (protocols::sewing::scoring)   EtableFunc (core::scoring::func)   MakeDisulfideDistance (protocols::frag_picker::scores)   RandomPositionRotationMover (protocols::membrane)   SingleDownstreamResidueWriter (protocols::match::output)   
AssignmentScaleAndDerivVectID (core::scoring::hbonds)   EtableOptions (core::scoring::etable)   MakeDisulfideIdentity (protocols::frag_picker::scores)   RandomPositionTranslationMover (protocols::membrane)   SingleFileBuffer (protocols::jd2)   
AssignOrbitals (core::chemical::orbitals)   EtableParamsOnePair (core::scoring::etable)   MakeFragmentAllAtomCrmsd (protocols::frag_picker::scores)   RandomResidueSelector (core::select::residue_selector)   SingleFragmentMover (protocols::nonlocal)   
AssignToClustersMover (protocols::cluster)   EulerAngles (protocols::stepwise::sampler::rigid_body)   MakeFragmentChunkCrms (protocols::frag_picker::scores)   RandomResidueSelectorCreator (core::select::residue_selector)   SingleFragmentMoverCreator (protocols::nonlocal)   
AsymFoldandDockClaimer (protocols::topology_broker)   EvaluatedArchive (protocols::jd2::archive)   MakeFragmentCrmsd (protocols::frag_picker::scores)   RandomSheetBuilder (protocols::jumping)   SingleGrid (protocols::qsar::scoring_grid)   
AsymFoldandDockMoveRbJumpMover (protocols::simple_moves::asym_fold_and_dock)   EvaluatedTrialMover (protocols::simple_filters)   MakeFragmentCrmsdResDepth (protocols::frag_picker::scores)   RandomSolutions (protocols::kinematic_closure::solution_pickers)   SingleLigandRotamerLibrary (core::pack::rotamers)   
AsymFoldandDockMoveRbJumpMoverCreator (protocols::simple_moves::asym_fold_and_dock)   EvaluatorCreator (protocols::evaluation)   MakeFragmentDME (protocols::frag_picker::scores)   RandomSymmetrySlider (protocols::symmetry)   SingleLigandRotamerLibraryCreator (core::pack::rotamers)   
AsymFoldandDockRbTrialMover (protocols::simple_moves::asym_fold_and_dock)   EvaluatorFactory (protocols::evaluation)   MakeFragmentScoringMethod (protocols::frag_picker::scores)   RandomTorsionMover (protocols::simple_moves)   SingleMotif (protocols::motifs)   
AsymFoldandDockRbTrialMoverCreator (protocols::simple_moves::asym_fold_and_dock)   EvaluatorRegistrator (protocols::evaluation)   MakeGunnCostScore (protocols::frag_picker::scores)   RandomTorsionMoverCreator (protocols::simple_moves)   SingleNCAARotamerLibraryCreator (core::pack::rotamers)   
AsymmetricUnitSelector (core::select::residue_selector)   EvenlyPartitionedNodeManager (protocols::jd3::dag_node_managers)   MakeHydrophobicityProfileSimilarity (protocols::frag_picker::scores)   RandomTorsionPoseFolder (protocols::denovo_design::components)   SingleQueryExecutor (protocols::indexed_structure_store::search)   
AsymmetricUnitSelectorCreator (core::select::residue_selector)   Event (core::scoring::packstat)   MakeHydrophobicitySimilarity (protocols::frag_picker::scores)   RandomVectorSelector (protocols::denovo_design::components)   SingleQuerySummaryStatistics (protocols::indexed_structure_store::search)   
AsyncMPITemperingBase (protocols::canonical_sampling)   EvolutionaryDynamicsMover (protocols::evolution)   MakeInterbondAngleScore (protocols::frag_picker::scores)   RangeFilter (protocols::simple_filters)   SingleResidueCenrotLibrary (core::pack::dunbrack::cenrot)   
Atom (core::chemical)   EvolutionaryDynamicsMoverCreator (protocols::evolution)   MakeJCoupling (protocols::frag_picker::scores)   RangeFilterCreator (protocols::simple_filters)   SingleResidueCenrotLibraryCreator (core::pack::dunbrack::cenrot)   
Atom (core::scoring::sc)   EX (core::pack::task)   MakeJunctionsMover (protocols::pose_creation)   RangeRelaxMover (protocols::relax)   SingleResidueDunbrackLibrary (core::pack::dunbrack)   
Atom (core::conformation)   EX_CUTOFF (core::pack::task)   MakeJunctionsMoverCreator (protocols::pose_creation)   RationalLoopComparator (protocols::loops)   SingleResidueDunbrackLibraryConcrete (core::pack::dunbrack)   
Atom (core::kinematics::tree)   ExactOccludedHbondSolEnergy (core::energy_methods)   MakeLAMBEGO_Similarity (protocols::frag_picker::scores)   RationalMonteCarlo (protocols::simple_moves::rational_mc)   SingleResidueDunbrackLibraryCreator (core::pack::dunbrack)   
Atom_ (core::kinematics::tree)   ExactOccludedHbondSolEnergyCreator (core::energy_methods)   MakeLatticeMover (protocols::cryst)   Rattle (protocols::md)   SingleResidueFragData (core::fragment)   
Atom_Bin (core::pose::rna)   ExactResidueMatcher (core::conformation)   MakeLatticeMoverCreator (protocols::cryst)   RawFileData (core::io::raw_data)   SingleResidueInvrotTarget (protocols::toolbox::match_enzdes_util)   
AtomAngleSecMatchRPE (protocols::match::downstream)   AsyncMPITemperingBase::ExchangeRequest (protocols::canonical_sampling)   MakeLayerMover (protocols::cryst)   RawStruct (core::io::raw_data)   SingleResidueMultifunc (core::optimization)   
AtomAtomPairFeatures (protocols::features)   ExcludedFilter (protocols::constel)   MakeLayerMoverCreator (protocols::cryst)   RB_lt (protocols::rbsegment_relax)   SingleResidueRotamerLibrary (core::pack::rotamers)   
AtomAtomPairFeaturesCreator (protocols::features)   ExcludedResPredicate (core::scoring)   MakeMidPhiOut (protocols::frag_picker::scores)   RBfitResult (protocols::electron_density)   SingleResidueRotamerLibraryCreator (core::pack::rotamers)   
AtomBasedConstraintsScore (protocols::frag_picker::scores)   EXCN_Archive (protocols::jd2::archive)   MakeMidPsiOut (protocols::frag_picker::scores)   RBfitResultComparitor (protocols::electron_density)   SingleResidueRotamerLibraryFactory (core::pack::rotamers)   
AtomCoordinateCstMover (protocols::relax)   EXCN_AssignmentNotFound (protocols::noesy_assign)   MakePartialSecondarySimilarity (protocols::frag_picker::scores)   RBInMover (protocols::splice)   SingleResidueRotamerLibraryRegistrator (core::pack::rotamers)   
AtomCoordinateCstMoverCreator (protocols::relax)   EXCN_AtomNotFound (core::id)   MakePCS_FragDistance (protocols::frag_picker::scores)   RBInMoverCreator (protocols::splice)   SingleResidueTorsionFragmentLibrary (protocols::frags)   
AtomCountFilter (protocols::ligand_docking)   EXCN_bbdb_Merge_Failed (protocols::loophash)   MakePhi (protocols::frag_picker::scores)   RBOutMover (protocols::splice)   SingleState (protocols::multistate_design)   
AtomCountFilterCreator (protocols::ligand_docking)   EXCN_CalcFailed (core::simple_metrics::composite_metrics)   MakePhiPsiRmsd (protocols::frag_picker::scores)   RBOutMoverCreator (protocols::splice)   SingleStateEntityData (protocols::multistate_design)   
AtomDihedralSecMatchRPE (protocols::match::downstream)   EXCN_CalcFailed (core::simple_metrics::metrics)   MakePhiPsiSquareWell (protocols::frag_picker::scores)   RBResidueRange (protocols::rbsegment_relax)   SingleStateFitnessFunction (protocols::multistate_design)   
AtomDistanceSecMatchRPE (protocols::match::downstream)   EXCN_CalcFailed (protocols::simple_filters)   MakePolyXMover (protocols::pose_creation)   RBSegment (protocols::rbsegment_relax)   SingleStructureData (protocols::optimize_weights)   
AtomGeometrySecMatchRPE (protocols::match::downstream)   EXCN_ConnectionSetupFailed (protocols::denovo_design::connection)   MakePolyXMoverCreator (protocols::pose_creation)   RBSegmentMover (protocols::rbsegment_relax)   SingleValuePoseEvaluator (protocols::evaluation)   
AtomGraphEdgeData (core::conformation)   EXCN_Converged (protocols::moves)   MakeProfileScore (protocols::frag_picker::scores)   RBSegmentRelax (protocols::rbsegment_relax)   SingleValuePoseEvaluator_Size (protocols::evaluation)   
AtomGraphVertexData (core::conformation)   EXCN_DB_IO_Failed (protocols::loophash)   MakeProfileScoreBlosum62 (protocols::frag_picker::scores)   RBSegmentRelaxImpl (protocols)   SingleValuePoseEvaluator_SSize (protocols::evaluation)   
AtomGrid (protocols::nmr::pcs)   EXCN_Env_Exception (core::environment)   MakeProfileScoreDistWeight (protocols::frag_picker::scores)   RDAT (core::io::rna)   SingResCnlCrea (protocols::constel)   
AtomGridPoint (protocols::nmr::pcs)   EXCN_Env_Passport (protocols::environment)   MakeProfileScoreL1 (protocols::frag_picker::scores)   RDC (core::scoring)   SinXOverX (core::scoring::saxs)   
AtomHash (protocols::simple_moves)   EXCN_Env_Security_Exception (protocols::environment)   MakeProfileScoreStructL1 (protocols::frag_picker::scores)   RDC_Evaluator (protocols::simple_filters)   SiteConstraint (core::scoring::constraints)   
AtomHashNode (protocols::simple_moves)   EXCN_FailedBroking (protocols::topology_broker)   MakeProfileScoreSubMatrix (protocols::frag_picker::scores)   RDC_Rohl (core::scoring)   SiteConstraintCreator (core::scoring::constraints)   
AtomicContactCountFilter (protocols::protein_interface_design::filters)   EXCN_FileFormat (protocols::noesy_assign)   MakeProlinePhiScore (protocols::frag_picker::scores)   RDCData (core::scoring::nmr::rdc)   SiteConstraintResidues (core::scoring::constraints)   
AtomicContactCountFilterCreator (protocols::protein_interface_design::filters)   EXCN_FilterFailed (protocols::denovo_design::movers)   MakePsi (protocols::frag_picker::scores)   RDCEnergy (protocols::nmr::rdc)   SiteConstraintResiduesCreator (core::scoring::constraints)   
AtomicContactFilter (protocols::simple_filters)   EXCN_FilterFailed (protocols::topology_broker)   MakeRamaScore (protocols::frag_picker::scores)   RDCEnergyCreator (protocols::nmr::rdc)   SiteGrid (protocols::qsar::scoring_grid)   
AtomicContactFilterCreator (protocols::simple_filters)   EXCN_Fold (protocols::denovo_design::components)   MakeRDCScore (protocols::frag_picker::scores)   RdcEvaluatorCreator (protocols::simple_filters)   SiteGridCreator (protocols::qsar::scoring_grid)   
AtomicDepth (core::scoring::atomic_depth)   EXCN_FTSketchGraph (core::environment)   MakeRotLibJob (protocols::make_rot_lib)   RDCMultiSet (core::scoring::nmr::rdc)   SixDTransRotPotential (core::scoring::loop_graph::evaluator)   
AtomicDistanceFilter (protocols::simple_filters)   EXCN_Heat_Converged (protocols::canonical_sampling::mc_convergence_checks)   MakeRotLibJobInputter (protocols::make_rot_lib)   RDCScore (protocols::frag_picker::scores)   SixDTransRotPotentialEvaluator (core::scoring::loop_graph::evaluator)   
AtomicDistanceFilterCreator (protocols::simple_filters)   EXCN_Illegal_Arguments (core::conformation::membrane)   MakeRotLibJobInputterCreator (protocols::make_rot_lib)   RdcSelectEvaluatorCreator (protocols::simple_filters)   SizeInSegmentsRequirement (protocols::sewing::requirements)   
AtomICoor (core::chemical)   EXCN_InitFailed (core::simple_metrics::composite_metrics)   MakeRotLibMover (protocols::make_rot_lib)   RDCSingle (core::scoring::nmr::rdc)   SizeInSegmentsRequirementCreator (protocols::sewing::requirements)   
AtomID (core::id)   EXCN_InitFailed (core::simple_metrics::metrics)   MakeRotLibOptionsData (protocols::make_rot_lib)   RDCSingleSet (core::scoring::nmr::rdc)   SizeValuedParameter (core::conformation::parametric)   
AtomID_Map (core::id)   EXCN_InitFailed (protocols::simple_filters)   MakeScoreEValuator (protocols::frag_picker::scores)   RdcTargetEvaluatorCreator (protocols::simple_filters)   SizeVectorValuedParameter (core::conformation::parametric)   
AtomID_Map_AtomID (core::id)   EXCN_Input (protocols::topology_broker)   MakeSecondaryIdentity (protocols::frag_picker::scores)   RDCTensor (core::scoring::nmr::rdc)   SkipViolFunc (core::scoring::func)   
AtomID_Map_bool (core::id)   EXCN_Invalid_Hashmap (protocols::loophash)   MakeSecondarySimilarity (protocols::frag_picker::scores)   RDFBase (protocols::ligand_docking::rdf)   Slice (core::scoring::packstat)   
AtomID_Map_Real (core::id)   EXCN_InvalidFoldTree (core::kinematics)   MakeSequenceIdentity (protocols::frag_picker::scores)   RDFBinaryHbondCreator (protocols::ligand_docking::rdf)   SlicedPoseWorkingParameters (protocols::stepwise::legacy::modeler::rna)   
AtomID_Mapper (core::pose::toolbox)   EXCN_Loop_not_closed (protocols::loops)   MakeSolventAccessibility (protocols::frag_picker::scores)   RDFBinaryHbondFunction (protocols::ligand_docking::rdf)   SliceResidueSelector (core::select::residue_selector)   
AtomIDHashFunction (protocols::sic_dock)   EXCN_Membrane (core::conformation::membrane)   MakeStarTopologyMover (protocols::rbsegment_relax)   RDFBinaryOrbitalFunction (protocols::ligand_docking::rdf)   SliceResidueSelectorCreator (core::select::residue_selector)   
AtomInfo (core::scoring::hbonds::graph)   EXCN_Membrane_Bounds (core::conformation::membrane)   MakeStarTopologyMoverCreator (protocols::rbsegment_relax)   RDFBinaryOrbitalFunctionCreator (protocols::ligand_docking::rdf)   SliceToMiniProteinMover (protocols::pose_creation)   
AtomInformation (core::io)   EXCN_MembraneFoldTree (core::conformation::membrane)   MakeTalosSSSimilarity (protocols::frag_picker::scores)   RDFChargeCreator (protocols::ligand_docking::rdf)   SliceToMiniProteinMoverCreator (protocols::pose_creation)   
AtomInfoSet (core::scoring::hbonds::graph)   EXCN_No_Extra_Data_To_Write (protocols::loophash)   MakeTorsionBinSimilarity (protocols::frag_picker::scores)   RDFChargeFunction (protocols::ligand_docking::rdf)   SlideIntoContact (protocols::docking)   
AtomInResidueAtomInResiduePairFeatures (protocols::features)   EXCN_NoesyAssign (protocols::noesy_assign)   MapCacheUnit (core::fragment)   RDFElecCreator (protocols::ligand_docking::rdf)   SlideTogether (protocols::ligand_docking)   
AtomInResidueAtomInResiduePairFeaturesCreator (protocols::features)   EXCN_NonMembrane (core::conformation::membrane)   MapHotspot (protocols::protein_interface_design::movers)   RDFElecFunction (protocols::ligand_docking::rdf)   SlideTogetherCreator (protocols::ligand_docking)   
AtomLevelDomainMap (core::pose::toolbox)   EXCN_NothingToFold (protocols::denovo_design::movers)   MapHotspotCreator (protocols::protein_interface_design::movers)   RDFEtableCreator (protocols::ligand_docking::rdf)   SlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
AtomNeighbor (core::scoring)   EXCN_Pool_Converged (protocols::canonical_sampling::mc_convergence_checks)   AtomPairConstraintGenerator::MappedAtom (protocols::constraint_generator)   RDFEtableFunction (protocols::ligand_docking::rdf)   SmallAtNb (core::scoring)   
AtomPack (protocols::abinitio::abscript)   EXCN_PoseInconsistent (protocols::denovo_design::components)   MasterFilter (protocols::constel)   RDFFunctionCreator (protocols::ligand_docking::rdf)   SmallBBSampler (protocols::simple_moves::bb_sampler)   
AtomPairConstraint (core::scoring::constraints)   EXCN_PreFilterFailed (protocols::denovo_design::architects)   MatchCollisionFilter (protocols::match::output)   RDFFunctionFactory (protocols::ligand_docking::rdf)   SmallFragWeight (protocols::topology_broker::weights)   
AtomPairConstraintCreator (core::scoring::constraints)   EXCN_RemarksNotPresent (protocols::denovo_design::components)   MatchConsolidator (protocols::match::output)   RDFFunctionRegistrator (protocols::ligand_docking::rdf)   SmallMinCCDTrial (protocols::loops::loop_mover::refine)   
AtomPairConstraintGenerator (protocols::constraint_generator)   EXCN_RemoveCstsFailed (protocols::constraint_generator)   MatchConstraintFileInfo (protocols::toolbox::match_enzdes_util)   RDFHbondCreator (protocols::ligand_docking::rdf)   SmallMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
AtomPairConstraintGeneratorCreator (protocols::constraint_generator)   EXCN_RemoveCstsFailed (protocols::forge::remodel)   MatchConstraintFileInfoList (protocols::toolbox::match_enzdes_util)   RDFHbondFunction (protocols::ligand_docking::rdf)   SmallMol (protocols::pockets)   
AtomPairConstraintsData (protocols::frag_picker::scores)   EXCN_Resource_Definition (core::conformation::membrane)   MatchCounter (protocols::match)   RDFOrbitalFunction (protocols::ligand_docking::rdf)   SmallMover (protocols::simple_moves)   
AtomPairConstraintsScore (protocols::frag_picker::scores)   EXCN_TopologyBroker (protocols::topology_broker)   Matcher (protocols::match)   RDFOrbitalFunctionCreator (protocols::ligand_docking::rdf)   SmallMoverCreator (protocols::simple_moves)   
AtomPairData (protocols::ligand_docking::rdf)   EXCN_Unknown (protocols::topology_broker)   MatcherMover (protocols::match)   RDKitMetric (protocols::drug_design)   SmartAssembly (protocols::sewing::data_storage)   
AtomPairEnergy (core::scoring::etable)   EXCN_UnknownAtomname (protocols::noesy_assign)   MatcherMoverCreator (protocols::match)   RDKitMetricCreator (protocols::drug_design)   SmartFixbbSimAnnealer (core::pack::annealer)   
AtomPairFuncList (core::scoring::custom_pair_distance)   EXCN_UnknownResonance (protocols::noesy_assign)   MatcherOutputStats (protocols::match)   RDKitMetricsMover (protocols::drug_design)   SmartSegment (protocols::sewing::data_storage)   
AtomProperties (protocols::ligand_docking::ga_ligand_dock)   EXCN_VirtualRsd (core::conformation::membrane)   MatcherTask (protocols::match)   RDKitMetricsMoverCreator (protocols::drug_design)   SmartSewingResidue (protocols::sewing::data_storage)   
AtomProperties (core::chemical)   EXCN_Wrong_DB_Format (protocols::loophash)   MatchEvaluator (protocols::match::output)   RDMolToRestype (core::chemical::rdkit)   SmoothCenPairEnergy (core::energy_methods)   
AtomPropertiesManager (core::chemical)   Exemplar (protocols::cluster)   MatchFilter (protocols::match::output)   ReadPoseExtraScoreFilter (protocols::simple_filters)   SmoothCenPairEnergyCreator (core::energy_methods)   
AtomRadiusMap (core::scoring::packstat)   ExpExpression (protocols::pack_daemon)   MatchGrafter (protocols::metal_interface)   ReadPoseExtraScoreFilterCreator (protocols::simple_filters)   SmoothEnvEnergy (core::energy_methods)   
PDBInfo::AtomRecord (core::pose)   ExpiryFilter (protocols::simple_filters)   MatchGrouper (protocols::match::output)   ReadResfile (core::pack::task::operation)   SmoothEnvEnergyCreator (core::energy_methods)   
AtomRefMapping (core::chemical)   ExpiryFilterCreator (protocols::simple_filters)   MatchOutputter (protocols::match::output)   ReadResfileAndObeyLengthEvents (core::pack::task::operation)   SmoothEnvPairPotential (core::scoring)   
AtomSelection (core::io::nmr)   ExplicitWaterMover (protocols::simple_moves)   MatchOutputTracker (protocols::match)   ReadResfileAndObeyLengthEventsCreator (core::pack::task::operation)   SmoothFragmentMover (protocols::simple_moves)   
AtomToAxisConstraint (core::scoring::constraints)   ExplicitWaterMoverCreator (protocols::simple_moves)   MatchPositionModifier (protocols::match)   ReadResfileCreator (core::pack::task::operation)   SmoothFragWeight (protocols::topology_broker::weights)   
AtomTree (core::kinematics)   ExposedHydrophobicsFilter (protocols::denovo_design::filters)   MatchProcessor (protocols::match::output)   ReadResfileFromDB (protocols::task_operations)   SmoothPolicy (protocols::nonlocal)   
AtomTreeCollection (core::pack::scmin)   ExposedHydrophobicsFilterCreator (protocols::denovo_design::filters)   MatchResidues (protocols::fldsgn)   ReadResfileFromDBCreator (protocols::task_operations)   SmoothScoreTermCoeffs (core::scoring)   
AtomTreeDiff (core::import_pose::atom_tree_diffs)   ExtendChainMover (protocols::denovo_design::movers)   MatchResiduesMover (protocols::fldsgn)   ReadResidueCoordinatesFromPDB (protocols::chromophore)   SmoothStepFunc (core::scoring::func)   
AtomTreeDiffJobDistributor (protocols::jobdist)   ExtendChainMoverCreator (protocols::denovo_design::movers)   MatchResiduesMoverCreator (protocols::fldsgn)   RealFilter (core::chemical)   SmoothSymmetricFragmentMover (protocols::simple_moves)   
AtomTreeDiffJobInputter (protocols::jd2)   ExtendedPoseBuilder (protocols::denovo_design::components)   MatchScoreWriter (protocols::match::output)   RealMetric (core::simple_metrics)   SmotifFeatures (protocols::features)   
AtomTreeDiffJobInputterCreator (protocols::jd2)   ExtendedPoseInputStream (core::import_pose::pose_stream)   MatDesGreedyOptMutationMover (protocols::matdes)   RealValuedParameter (core::conformation::parametric)   SmotifFeaturesCreator (protocols::features)   
AtomTreeDiffJobOutputter (protocols::jd2)   ExtendedPoseMover (protocols::pose_creation)   MatDesGreedyOptMutationMoverCreator (protocols::matdes)   RealVectorValuedParameter (core::conformation::parametric)   SnugDock (protocols::antibody::snugdock)   
AtomTreeDiffJobOutputterCreator (protocols::jd2)   ExtendedPoseMoverCreator (protocols::pose_creation)   MatDesPointMutationCalculator (protocols::matdes)   RECCES_Mover (protocols::recces)   SnugDockCreator (protocols::antibody::snugdock)   
AtomTreeMinimizer (core::optimization)   Extender (protocols::star)   MatrixScoringScheme (core::sequence)   RECCES_Options (protocols::recces::options)   SnugDockProtocol (protocols::antibody::snugdock)   
AtomTreeMultifunc (core::optimization)   Extent (core::fragment::picking_old::concepts)   MaxSeqSepConstraintSet (protocols::constraints_additional)   RECCES_Parameters (protocols::recces::params)   SoedingFunc (core::scoring::func)   
AtomTreeSCMinMinimizerMap (core::pack::scmin)   ExternalEvaluator (protocols::simple_filters)   MC_Any (protocols::recces::sampler)   RecomputeDensityMapMover (protocols::cryst)   SOGFunc (core::scoring::func)   
AtomType (core::chemical)   ExternalGeomSampler (protocols::toolbox::match_enzdes_util)   MC_Comb (protocols::recces::sampler)   RecomputeDensityMapMoverCreator (protocols::cryst)   SOGFunc_Impl (core::scoring::func)   
AtomTypeData   ExternalPackerResultLoader (protocols::quantum_annealing)   MC_Loop (protocols::recces::sampler)   RecordCollection (core::io::pdb)   SolutionPicker (protocols::kinematic_closure::solution_pickers)   
AtomTypeDatabaseIO (core::chemical)   ExternalPackerResultLoaderCreator (protocols::quantum_annealing)   MC_OneTorsion (protocols::recces::sampler)   RecoverSideChainsMover (protocols::comparative_modeling)   SolutionPredicate (protocols::denovo_design::components)   
AtomTypeSet (core::chemical)   ExtraChiCutoff (core::pack::task::operation)   MC_RNA_KIC_Sampler (protocols::recces::sampler::rna)   RedefineChi (core::chemical)   SolutionSorter (protocols::denovo_design::components)   
AtomTypesFeatures (protocols::features)   ExtraChiCutoffCreator (core::pack::task::operation)   MC_RNA_MultiSuite (protocols::recces::sampler::rna)   RefConvert (core::chemical)   SolvationGrid (protocols::qsar::scoring_grid)   
AtomTypesFeaturesCreator (protocols::features)   ExtraChiCutoffRLT (core::pack::task::operation)   MC_RNA_OneJump (protocols::recces::sampler::rna)   RefConvert< core::Size > (core::chemical)   SolvationGridCreator (protocols::qsar::scoring_grid)   
AtomVDW (core::scoring)   ExtraChiCutoffRLTCreator (core::pack::task::operation)   MC_RNA_Sugar (protocols::recces::sampler::rna)   RefConvert< std::string > (core::chemical)   SolvationMetaGrid (protocols::qsar::scoring_grid)   
AtomWithDOFChange (core::kinematics)   ExtractAsymmetricPoseMover (protocols::symmetry)   MC_RNA_Suite (protocols::recces::sampler::rna)   RefConvert< VD > (core::chemical)   SolvationMetaGridCreator (protocols::qsar::scoring_grid)   
AtrGrid (protocols::qsar::scoring_grid)   ExtractAsymmetricPoseMoverCreator (protocols::symmetry)   MC_Sampler (protocols::recces::sampler)   ReferenceEnergy (core::energy_methods)   SolventAccessibility (protocols::frag_picker::scores)   
AtrGridCreator (protocols::qsar::scoring_grid)   ExtractAsymmetricUnitMover (protocols::symmetry)   MCAligner (core::sequence)   ReferenceEnergyCreator (core::energy_methods)   SortByLowEnergy (protocols::multistage_rosetta_scripts)   
Attachment (protocols::stepwise::monte_carlo::mover)   ExtractAsymmetricUnitMoverCreator (protocols::symmetry)   MCShowMover (protocols::moves)   ReferenceEnergyNoncanonical (core::energy_methods)   SortPredicate (protocols::jd2::archive)   
AUTO (core::pack::task)   ExtractSubposeMover (protocols::matdes)   MD_Angle (protocols::cartesian)   ReferenceEnergyNoncanonicalCreator (core::energy_methods)   SourcePositions (protocols::rna::denovo::coarse)   
AutoCutData (protocols::environment)   ExtractSubposeMoverCreator (protocols::matdes)   MD_Bond (protocols::cartesian)   ReferencePose (core::pose::reference_pose)   Spacegroup (protocols::cryst)   
AutoCutDataCreator (protocols::environment)   ExtraDataEnumManager (core::io::mmtf)   MD_HarmonicDihedral (protocols::cartesian)   ReferencePoseSet (core::pose::reference_pose)   Span (core::conformation::membrane)   
AutomaticSheetConstraintGenerator (protocols::fold_from_loops::constraint_generator)   ExtraQuadraticRepulsion (core::scoring::etable)   MDBase (protocols::md)   RefineBetaBarrel (protocols::antibody)   SpanInfo (protocols::membrane)   
AutomaticSheetConstraintGeneratorCreator (protocols::fold_from_loops::constraint_generator)   ExtraRotamers (core::pack::task::operation)   MDscheduleData (protocols::md)   RefinementResult (protocols::electron_density)   SpanningTopology (core::conformation::membrane)   
AutomorphismIterator (core::chemical)   ExtraRotamerSamplingData (core::pack::task::operation)   Mean (protocols::pack_daemon)   RefinementResultComparitor (protocols::electron_density)   SpanTopologyMatchPoseFilter (protocols::simple_filters)   
AutoRBMover (protocols::rbsegment_relax)   ExtraRotamersCreator (core::pack::task::operation)   MeanField (protocols::mean_field)   Region (protocols::nonlocal)   SpanTopologyMatchPoseFilterCreator (protocols::simple_filters)   
AverageDegreeFilter (protocols::protein_interface_design::filters)   ExtraRotamersGeneric (core::pack::task::operation)   MeanFieldFactory (protocols::mean_field)   RegionalConnections (protocols::simple_filters)   SparseMatrixIndex (core::pack::interaction_graph)   
AverageDegreeFilterCreator (protocols::protein_interface_design::filters)   ExtraRotamersGenericCreator (core::pack::task::operation)   MedalExchangeMover (protocols::medal)   RelativeConnectRight (protocols::forge::build)   Sparta (protocols::sparta)   
AveragePathLengthFilter (protocols::simple_filters)   ExtraRotamersGenericRLT (core::pack::task::operation)   MedalMover (protocols::medal)   RelativePoseFilter (protocols::calc_taskop_filters)   Sparta::SpartaLib (protocols::sparta)   
AveragePathLengthFilterCreator (protocols::simple_filters)   ExtraRotamersGenericRLTCreator (core::pack::task::operation)   MembAccesResidueLipophilicityFilter (protocols::simple_filters)   RelativePoseFilterCreator (protocols::calc_taskop_filters)   SpecialRotamerEnergy (protocols::scoring::methods)   
  B  
ExtraScoreEvaluatorCreator (protocols::simple_filters)   MembAccesResidueLipophilicityFilterCreator (protocols::simple_filters)   RelativeSegmentFilter (protocols::protein_interface_design::filters)   SpecialRotamerEnergyCreator (protocols::scoring::methods)   
ExtraThreadingMover (protocols::comparative_modeling)   MembEtable (core::scoring::etable)   RelativeSegmentFilterCreator (protocols::protein_interface_design::filters)   SpecialRotamerRSO (protocols::toolbox::rotamer_set_operations)   
BackboneDB (protocols::loophash)   
  F  
Membrane_FAEmbed (core::scoring)   RelativeSequencePosition (protocols::forge::build)   SpecialSegmentsObserver (core::pose::datacache)   
BackboneGridSampler (protocols::helical_bundle)   Membrane_FAPotential (core::scoring)   RelaxProtocolBase (protocols::relax)   SpecificGeometryLibrary (protocols::jumping)   
BackboneGridSamplerCreator (protocols::helical_bundle)   FA_ElecEnergy (core::scoring::elec)   MembraneAbinitio (protocols::abinitio)   RelaxScriptCommand (protocols::relax)   SpecificResiduesNearInterfaceFilter (protocols::protein_interface_design::filters)   
BackboneGridSamplerHelper (protocols::helical_bundle)   FA_ElecEnergyAroAll (core::energy_methods)   MembraneCbetaEnergy (core::energy_methods)   RelaxScriptCommand (protocols::denovo_design::movers)   SpecificResiduesNearInterfaceFilterCreator (protocols::protein_interface_design::filters)   
BackboneMover (protocols::simple_moves)   FA_ElecEnergyAroAllCreator (core::energy_methods)   MembraneCbetaEnergyCreator (core::energy_methods)   RelaxScriptFileContents (protocols::relax)   Sphere (core::scoring::packstat)   
BackboneSampler (protocols::enzdes)   FA_ElecEnergyAroAro (core::energy_methods)   MembraneCenPairEnergy (core::energy_methods)   RelaxScriptManager (protocols::relax)   SphericalRotationSearchPattern (protocols::hotspot_hashing)   
BackboneSamplerCreator (protocols::enzdes)   FA_ElecEnergyAroAroCreator (core::energy_methods)   MembraneCenPairEnergyCreator (core::energy_methods)   ReleaseConstraintFromResidueMover (protocols::fold_from_loops::movers)   CrossPeak::Spin (protocols::noesy_assign)   
BackboneSegment (protocols::loophash)   FA_ElecEnergyCreator (core::scoring::elec)   MembraneCenterPerturbationMover (protocols::rigid)   ReleaseConstraintFromResidueMoverCreator (protocols::fold_from_loops::movers)   SpinAroundPartnerMover (protocols::membrane)   
BackboneStubConstraint (core::scoring::constraints)   FA_GrpElecEnergy (core::energy_methods)   MembraneData (core::scoring::membrane)   RemarkInfo (core::io)   SpinAroundPartnerMoverCreator (protocols::membrane)   
BackboneStubLinearConstraint (core::scoring::constraints)   FA_GrpElecEnergyCreator (core::energy_methods)   MembraneEmbed (core::scoring)   Remarks (core::io)   SpinlabelDatabaseEntry (core::io::nmr)   
BackboneTorsionPerturbation (protocols::hybridization)   Fa_MbenvEnergy (core::energy_methods)   MembraneEnergyLandscapeSampler (protocols::membrane_benchmark)   RemodelAccumulator (protocols::forge::remodel)   SpinlabelDatabaseHandler (core::io::nmr)   
BackboneTorsionPerturbationCreator (protocols::hybridization)   Fa_MbenvEnergyCreator (core::energy_methods)   MembraneEnergyLandscapeSamplerCreator (protocols::membrane_benchmark)   RemodelConstraintGenerator (protocols::forge::remodel)   SpinMover (protocols::protein_interface_design::movers)   
BackboneTorsionSampler (protocols::hybridization)   Fa_MbsolvEnergy (core::energy_methods)   MembraneEnvEnergy (core::energy_methods)   RemodelData (protocols::forge::remodel)   SpinMoverCreator (protocols::protein_interface_design::movers)   
BackboneTorsionSamplerCreator (protocols::hybridization)   Fa_MbsolvEnergyCreator (core::energy_methods)   MembraneEnvEnergyCreator (core::energy_methods)   RemodelDesignMover (protocols::forge::remodel)   Splice (protocols::splice)   
BackgroundNode (core::pack::interaction_graph)   FabConstraint (core::scoring::constraints)   MembraneEnvPenalties (core::energy_methods)   RemodelEnzdesCstModule (protocols::forge::remodel)   SpliceCreator (protocols::splice)   
BackgroundToFirstClassEdge (core::pack::interaction_graph)   FabConstraintCreator (core::scoring::constraints)   MembraneEnvPenaltiesCreator (core::energy_methods)   RemodelGlobalFrame (protocols::forge::remodel)   SpliceIn (protocols::splice)   
BackrubDDMover (protocols::protein_interface_design::movers)   FACTSEnergy (core::energy_methods)   MembraneEnvSmoothEnergy (core::energy_methods)   RemodelLigandHandler (protocols::forge::remodel)   SpliceInAntibody (protocols::splice)   
BackrubDDMoverCreator (protocols::protein_interface_design::movers)   FACTSEnergyCreator (core::energy_methods)   MembraneEnvSmoothEnergyCreator (core::energy_methods)   RemodelLoopMover (protocols::forge::remodel)   SpliceInAntibodyCreator (protocols::splice)   
BackrubMover (protocols::backrub)   FACTSPoseInfo (core::scoring::facts)   MembraneInfo (core::conformation::membrane)   RemodelLoopMoverPoseFolder (protocols::denovo_design::components)   SpliceInCreator (protocols::splice)   
BackrubMoverCreator (protocols::backrub)   FACTSPotential (core::scoring::facts)   MembraneJump (protocols::jumping)   RemodelMover (protocols::forge::remodel)   SpliceInTail (protocols::splice)   
BackrubProtocol (protocols::backrub)   FACTSResidueInfo (core::scoring::facts)   MembraneLipo (core::energy_methods)   RemodelMoverCreator (protocols::forge::remodel)   SpliceInTailCreator (protocols::splice)   
BackrubProtocolCreator (protocols::backrub)   FACTSRotamerSetInfo (core::scoring::facts)   MembraneLipoCreator (core::energy_methods)   RemodelRotamerLinks (protocols::forge::remodel)   SpliceManager (protocols::splice)   
BackrubSegment (protocols::backrub)   FACTSRsdTypeInfo (core::scoring::facts)   MembraneNormalPerturbationMover (protocols::rigid)   RemodelRotamerLinksCreator (protocols::forge::remodel)   SpliceOut (protocols::splice)   
BackrubSidechainMover (protocols::backrub)   FACTSRsdTypeMap (core::scoring::facts)   MembranePositionFromTopologyMover (protocols::membrane)   RemodelWorkingSet (protocols::forge::remodel)   SpliceOutAntibody (protocols::splice)   
BackrubSidechainMoverCreator (protocols::backrub)   FadeFunc (core::scoring::func)   MembranePositionFromTopologyMoverCreator (protocols::membrane)   RemoveConstraints (protocols::constraint_generator)   SpliceOutAntibodyCreator (protocols::splice)   
BalancedKicMover (protocols::kinematic_closure)   FadeInterval (core::scoring::hbonds)   MembranePotential (core::scoring)   RemoveConstraintsCreator (protocols::constraint_generator)   SpliceOutCreator (protocols::splice)   
Ball (core::scoring::packing)   FaDockingSlideIntoContact (protocols::docking)   MembraneSpanConstraint (core::scoring::constraints)   RemoveLigandFilter (protocols::enzdes)   SpliceOutTail (protocols::splice)   
BareMinimumPDEdge (core::pack::hbonds)   FAElecContextData (core::energy_methods)   MembraneSpanConstraintGenerator (protocols::constraint_generator)   RemoveLigandFilterCreator (protocols::enzdes)   SpliceOutTailCreator (protocols::splice)   
Base (protocols::toolbox::py_inheritance_test)   FalseFilter (protocols::filters)   MembraneSpanConstraintGeneratorCreator (protocols::constraint_generator)   RemoveMetalConnectionsMover (protocols::metal_interface)   SpliceSegment (protocols::splice)   
BaseArchiveManager (protocols::jd2::archive)   FalseFilterCreator (protocols::filters)   MembraneSpanTermZConstraint (core::scoring::constraints)   RemoveMetalConnectionsMoverCreator (protocols::metal_interface)   SplineFunc (core::scoring::func)   
BaseBin (protocols::stepwise::modeler::rna::rigid_body)   FalseResidueSelector (core::select::residue_selector)   MembraneTopology (protocols::simple_moves)   RemoveNorCTermMPM (protocols::match)   SplitAndMixPoseMover (protocols::fold_from_loops::movers)   
BaseBinMapUpdater (protocols::stepwise::screener)   FalseResidueSelectorCreator (core::select::residue_selector)   MembraneTopology (core::scoring)   RemoveRemodelCsts (protocols::forge::constraints)   SplitAndMixPoseMoverCreator (protocols::fold_from_loops::movers)   
BaseCacheUnit (core::fragment)   FaMPEnvEnergy (core::energy_methods)   MembraneTopologyClaimer (protocols::topology_broker)   RemoveRemodelCstsCreator (protocols::forge::constraints)   SplitUnfoldedTwoBodyEnergy (core::energy_methods)   
BaseCentroidScreener (protocols::stepwise::screener)   FaMPEnvEnergyCreator (core::energy_methods)   MembraneTopologyCreator (protocols::simple_moves)   RemoveRotamerSpecifications (core::chemical)   SplitUnfoldedTwoBodyEnergyCreator (core::energy_methods)   
BaseDisulfPairingLibrary (protocols::jumping)   FaMPEnvSmoothEnergy (core::energy_methods)   ClosureProblem::Memento (protocols::kinematic_closure)   RenameAtom (core::chemical)   SplitUnfoldedTwoBodyPotential (core::scoring)   
BaseEtableEnergy (core::scoring::etable)   FaMPEnvSmoothEnergyCreator (core::energy_methods)   MEnvAtomParams (protocols::membrane::scoring)   RenderGridsToKinemage (protocols::qsar)   SpringParams (core::scoring)   
BaseJobDistributor (protocols::jobdist)   FaMPSolvEnergy (core::energy_methods)   MergeBehaviorManager (core::chemical)   RenderGridsToKinemageCreator (protocols::qsar)   SquarePlanarMetal_Helper (protocols::cyclic_peptide::crosslinker)   
BaseJumpSetup (protocols::jumping)   FaMPSolvEnergyCreator (core::energy_methods)   MergePDBatOverlapMover (protocols::pose_creation)   RepackingRefiner (protocols::loop_modeling::refiners)   SquarePyramidalMetal_Helper (protocols::cyclic_peptide::crosslinker)   
BasePair (core::pose::rna)   FAScatter (core::scoring::fiber_diffraction)   MergePDBatOverlapMoverCreator (protocols::pose_creation)   RepackingRefinerCreator (protocols::loop_modeling::refiners)   SquareWell2Func (core::scoring::func)   
BasePairConstraint (core::scoring::constraints)   FASelectSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   MergePDBMover (protocols::pose_creation)   RepackLigandSiteWithoutLigandMover (protocols::enzdes)   SquareWellFunc (core::scoring::func)   
BasePairConstraintCreator (core::scoring::constraints)   FastDensEnergy (core::energy_methods)   MergePDBMoverCreator (protocols::pose_creation)   RepackMinimize (protocols::protein_interface_design::movers)   SRelaxPose (protocols::relax)   
BasePairingLibrary (protocols::jumping)   FastDensEnergyCreator (core::energy_methods)   Metal_HelperBase (protocols::cyclic_peptide::crosslinker)   RepackMinimizeCreator (protocols::protein_interface_design::movers)   SS_Base (protocols::fldsgn::topology)   
BasePairStep (core::pose::rna)   FastDesign (protocols::denovo_design::movers)   MetalContactsConstraintGenerator (protocols::constraint_generator)   RepackSidechainsMover (protocols::minimization_packing)   SS_Info (core::scoring)   
BasePairStepLibrary (core::import_pose::libraries)   FastDesignCreator (protocols::denovo_design::movers)   MetalContactsConstraintGeneratorCreator (protocols::constraint_generator)   RepackSidechainsMoverCreator (protocols::minimization_packing)   SS_Info2 (protocols::fldsgn::topology)   
BasePairStepSequence (core::import_pose::libraries)   FASTER_IG_Repacker (protocols::pack_daemon)   MetalloClaimer (protocols::topology_broker)   RepackTrial (protocols::loops::loop_mover::refine)   SS_Killhairpins_Info (core::scoring)   
BasePairType (core::import_pose::libraries)   FASTERAnnealer (core::pack::annealer)   MetalSiteResidue (protocols::metal_interface)   RepackTrialCreator (protocols::loops::loop_mover::refine)   SS_predictor (protocols::ss_prediction)   
BasePartner (core::scoring::dna)   FASTEREdge (core::pack::interaction_graph)   Metapatch (core::chemical)   RepackWithoutLigandFilter (protocols::enzdes)   SSamountFilter (protocols::protein_interface_design::filters)   
BaseStack (core::pose::rna)   FASTERInteractionGraph (core::pack::interaction_graph)   MetapatchEnumeration (protocols::residue_optimization)   RepackWithoutLigandFilterCreator (protocols::enzdes)   SSamountFilterCreator (protocols::protein_interface_design::filters)   
BaseTabooPerturber (protocols::loops::loop_closure::kinematic_closure)   FASTERNode (core::pack::interaction_graph)   MetaPoseEvaluator (protocols::evaluation)   RepeatMover (protocols::moves)   SSBondInformation (core::io)   
BaseTypeList (core::pack::palette)   FastForwardToNextResidueAlternative (protocols::stepwise::screener)   MetaPoseInputStream (core::import_pose::pose_stream)   RepeatParameterFilter (protocols::simple_filters)   SliceToMiniProteinMover::SSElement (protocols::pose_creation)   
BasicCDRClusterSet (protocols::antibody::clusters)   FastForwardToNextRigidBody (protocols::stepwise::screener)   MethodParams (protocols::mpi_refinement)   RepeatParameterFilterCreator (protocols::simple_filters)   SSElementSelector::SSElement (core::select::residue_selector)   
BasicCmdLineInit (protocols::rpc)   FastGapMover (protocols::loophash)   MethylNameLibrary (protocols::noesy_assign)   RepeatPropagationMover (protocols::simple_moves)   SSElementBisectddGFilter (protocols::simple_ddg)   
BasicInit (protocols::rpc)   FastLinearFunc (protocols::moves)   MethylNames (protocols::noesy_assign)   RepeatPropagationMoverCreator (protocols::simple_moves)   SSElementBisectddGFilterCreator (protocols::simple_ddg)   
BasicJob (protocols::jobdist)   FastRelax (protocols::relax)   MetricCalculatorFitnessFunction (protocols::multistate_design)   RepeatProteinRelax (protocols::relax)   SSElementLengthFilter (protocols::simple_filters)   
BasicJumpClaimer (protocols::topology_broker)   FastRelaxCreator (protocols::relax)   MetricData (protocols::features)   RepeatProteinRelaxCreator (protocols::relax)   SSElementLengthFilterCreator (protocols::simple_filters)   
BasicRotamerLibrarySpecification (core::chemical::rotamers)   FastSAXSEnergy (core::energy_methods)   MetricKey (core::simple_metrics)   RepGrid (protocols::qsar::scoring_grid)   SSElementMotifContactEnergy (core::energy_methods)   
BasicRotamerLibrarySpecificationCreator (core::chemical::rotamers)   FastSAXSEnergyCreator (core::energy_methods)   MetricRecorder (protocols::canonical_sampling)   RepGridCreator (protocols::qsar::scoring_grid)   SSElementMotifContactEnergyCreator (core::energy_methods)   
BasicSimAnnealerRepacker (protocols::pack_daemon)   FaSymDockingSlideTogether (protocols::symmetry)   MetricRecorderCreator (protocols::canonical_sampling)   ReplaceMainchainAtom (core::chemical)   SSElementMotifContactFilter (protocols::simple_filters)   
Basis (protocols::legacy_sewing)   FavorNativeResidue (protocols::protein_interface_design)   MetricValueGetter (protocols::pose_metric_calculators)   ReplaceProtonWithBromine (core::chemical)   SSElementMotifContactFilterCreator (protocols::simple_filters)   
Basis (protocols::sewing::data_storage)   FavorNativeResiduePreCycle (protocols::protein_interface_design::movers)   MetropolisHastingsMover (protocols::canonical_sampling)   ReplaceProtonWithChlorine (core::chemical)   SSElementSelector (core::select::residue_selector)   
BasisMapGenerator (protocols::sewing::hashing)   FavorNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MetropolisHastingsMoverCreator (protocols::canonical_sampling)   ReplaceProtonWithEthyl (core::chemical)   SSElementSelectorCreator (core::select::residue_selector)   
Batch (protocols::jd2::archive)   FavorNonNativeResidue (protocols::protein_interface_design)   MgEnergy (core::energy_methods)   ReplaceProtonWithFluorine (core::chemical)   SSFeature (protocols::comparative_modeling::features)   
BatchEvaluator (protocols::simple_filters)   FavorNonNativeResiduePreCycle (protocols::protein_interface_design::movers)   MgEnergyCreator (core::energy_methods)   ReplaceProtonWithHydroxyl (core::chemical)   SSHashedFragmentStore (protocols::indexed_structure_store)   
BatchFeatures (protocols::features)   FavorNonNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MgHydrater (protocols::magnesium)   ReplaceProtonWithIodine (core::chemical)   SSManager (core::sequence)   
BatchJobInputter (protocols::jd2)   FavorSequenceProfile (protocols::simple_moves)   MgKnowledgeBasedPotential (core::scoring::magnesium)   ReplaceProtonWithMethoxy (core::chemical)   SSMotifFinder (protocols::simple_filters)   
BatchNrEvaluator (protocols::simple_filters)   FavorSequenceProfileCreator (protocols::simple_moves)   MgMinimizer (protocols::magnesium)   ReplaceProtonWithMethyl (core::chemical)   SSMotifFinderFilterCreator (protocols::simple_filters)   
BB_BB_EnergyInvoker (core::scoring::etable)   FavorSymmetricSequence (protocols::simple_moves)   MgMonteCarlo (protocols::magnesium)   ReplaceProtonWithTrifluoromethyl (core::chemical)   SSPairPotential (protocols::fldsgn::potentials::sspot)   
BB_Pos (core::scoring)   FavorSymmetricSequenceCreator (protocols::simple_moves)   MgOrbitalFrameFinder (protocols::magnesium)   ReplaceRegionMover (protocols::grafting::simple_movers)   SSPredictionFilter (protocols::denovo_design::filters)   
BB_Pos (protocols::fldsgn::topology)   FaWaterToBilayerEnergy (protocols::membrane::scoring)   MgScanner (protocols::magnesium)   ReplaceRegionMoverCreator (protocols::grafting::simple_movers)   SSPredictionFilterCreator (protocols::denovo_design::filters)   
BBClaim (protocols::topology_broker::claims)   FaWaterToBilayerEnergyCreator (protocols::membrane::scoring)   MgWaterHydrogenPacker (protocols::magnesium)   ReplicaExchangeMC (protocols::moves)   SSShapeComplementarityFilter (protocols::denovo_design::filters)   
BBConRotMover (protocols::simple_moves)   FeaturesReporter (protocols::features)   MHCEpitopeConstraint (core::scoring::mhc_epitope_energy)   ReplicateFilter (protocols::filters)   SSShapeComplementarityFilterCreator (protocols::denovo_design::filters)   
BBData (protocols::loophash)   FeaturesReporterCreator (protocols::features)   MHCEpitopeEnergy (core::energy_methods)   ReplicateFilterCreator (protocols::filters)   SSWeightParameters (core::scoring::hbonds)   
BBDepCartBondedParameters (core::scoring::methods)   FeaturesReporterFactory (protocols::features)   MHCEpitopeEnergyCreator (core::energy_methods)   ReplicateTask (core::pack::task::operation)   StackElecEnergy (core::energy_methods)   
BBDepNRChiSample (core::pack::dunbrack)   FeaturesReporterRegistrator (protocols::features)   MHCEpitopeEnergySetup (core::scoring::mhc_epitope_energy)   Report (protocols::features)   StackElecEnergyCreator (core::energy_methods)   
BBDepScoreInterpData (core::pack::dunbrack)   FiberDiffraction (core::scoring::fiber_diffraction)   MHCEpitopePredictor (core::scoring::mhc_epitope_energy)   ReportEffectivePKA (protocols::simple_moves)   Stage1Sampler (protocols::abinitio)   
BBDepSemiRotamericData (core::pack::dunbrack)   FiberDiffractionEnergy (core::energy_methods)   MHCEpitopePredictorExternal (core::scoring::mhc_epitope_energy)   ReportEffectivePKACreator (protocols::simple_moves)   StagePreparer (protocols::abinitio::abscript)   
BBDihedralSampler (protocols::simple_moves::bb_sampler)   FiberDiffractionEnergyCreator (core::energy_methods)   MHCEpitopePredictorMatrix (core::scoring::mhc_epitope_energy)   ReportFilter (protocols::simple_filters)   AbscriptMover::StageTracker (protocols::abinitio::abscript)   
BBDihedralSampler2D (protocols::simple_moves::bb_sampler)   FiberDiffractionEnergyDens (core::energy_methods)   MHCEpitopePredictorPreLoaded (core::scoring::mhc_epitope_energy)   ReportFilterCreator (protocols::simple_filters)   StandardDisulfPairingLibrary (protocols::jumping)   
BBDihedralSampler3D (protocols::simple_moves::bb_sampler)   FiberDiffractionEnergyDensCreator (core::energy_methods)   MHCEpitopePredictorSVM (core::scoring::mhc_epitope_energy)   ReportFSC (protocols::electron_density)   StandardInnerLarvalJob (protocols::jd3::standard)   
BBDihedralSamplerBase (protocols::simple_moves::bb_sampler)   FibrilModelingClaimer (protocols::topology_broker)   MidPhiOut (protocols::frag_picker::scores)   ReportFSCCreator (protocols::electron_density)   StandardJobQueen (protocols::jd3::standard)   
BBDihedralSamplerMover (protocols::simple_moves)   Field (core::io::pdb)   MidPsiOut (protocols::frag_picker::scores)   ReportGradientsMover (protocols::cryst)   StandardPairingLibrary (protocols::jumping)   
BBDihedralSamplerMoverCreator (protocols::simple_moves)   FileBuffer (protocols::checkpoint)   MinDebug (core::optimization::symmetry)   ReportGradientsMoverCreator (protocols::cryst)   StandardPivots (protocols::kinematic_closure::pivot_pickers)   
BBDihedralSamplerND (protocols::simple_moves::bb_sampler)   FileConstraintGenerator (protocols::denovo_design::constraints)   MinimalFragSet (core::fragment)   ReportPSSMDifferences (protocols::protein_interface_design)   StandardPoseJobSummary (protocols::jd3::job_summaries)   
BBDofs (protocols::splice)   FileConstraintGeneratorCreator (protocols::denovo_design::constraints)   MinimalFragSetIterator_ (core::fragment)   ReportSequenceDifferences (protocols::protein_interface_design)   StandardResultOutputter (protocols::jd3::output)   
BBExtraData (protocols::loophash)   FileExistFilter (protocols::simple_filters)   MinimalistFlexbbEdge (protocols::flexpack::interaction_graph)   ReportToDB (protocols::features)   StarAbinitio (protocols::star)   
BBG8T3AMover (protocols::simple_moves)   FileExistFilterCreator (protocols::simple_filters)   MinimalistFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   ReportToDBCreator (protocols::features)   StartFrom (protocols::ligand_docking)   
BBGaussianMover (protocols::simple_moves)   FileJobOutputter (protocols::jd2)   MinimalistFlexbbNode (protocols::flexpack::interaction_graph)   ReportXYZ (protocols::simple_moves)   StartFromCreator (protocols::ligand_docking)   
BBGaussianMoverCreator (protocols::simple_moves)   FileRemoveFilter (protocols::simple_filters)   MinimalRotamer (protocols::minimization_packing)   ReportXYZCreator (protocols::simple_moves)   StartingNodeMotifScorer (protocols::sewing::scoring)   
BBIndepCartBondedParameters (core::scoring::methods)   FileRemoveFilterCreator (protocols::simple_filters)   MinimizationEdge (core::scoring)   RepulsiveOnlyMover (protocols::simple_moves)   StartingNodeMotifScorerCreator (protocols::sewing::scoring)   
BBIndNRChiSample (core::pack::dunbrack)   FileSystemJobDistributor (protocols::jd2)   MinimizationGraph (core::scoring)   RerootEdgeSorter (core::chemical)   StarTreeBuilder (protocols::nonlocal)   
BBIndSemiRotamericData (core::pack::dunbrack)   FillAUTOTaskOperation (core::pack::task::operation)   MinimizationNode (core::scoring)   RerootRestypeVisitor (core::chemical)   StartStructClaimer (protocols::topology_broker)   
BBMatching (protocols::splice)   FillAUTOTaskOperationCreator (core::pack::task::operation)   MinimizationRefiner (protocols::loop_modeling::refiners)   ResampleMover (protocols::stepwise::monte_carlo::mover)   StateAccumulatingMatchFilter (protocols::match::output)   
BBTorsionAndAnglesSRFD (core::fragment)   Filter (protocols::pose_selectors)   MinimizationRefinerCreator (protocols::loop_modeling::refiners)   ResampleMoverCreator (protocols::stepwise::monte_carlo::mover)   StealLigandMover (protocols::comparative_modeling)   
BBTorsionSRFD (core::fragment)   Filter (protocols::filters)   MinimizeBackbone (protocols::ligand_docking)   ResConnID (core::chemical)   StealSideChainsMover (protocols::comparative_modeling)   
BDR (protocols::forge::components)   FilterBucket (protocols::loophash)   MinimizeBackboneCreator (protocols::ligand_docking)   ResetBaselineMover (protocols::monte_carlo)   StemFinder (protocols::simple_filters)   
BenchmarkBuildRotamersMover (protocols::testing)   FilterByAmphetamine (protocols::constel)   MinimizeLigand (protocols::ligand_docking)   ResetBaselineMoverCreator (protocols::monte_carlo)   StemFinderFilterCreator (protocols::simple_filters)   
BenchmarkBuildRotamersMoverCreator (protocols::testing)   FilterByHistamine (protocols::constel)   Minimizer (core::optimization)   ResetBondLength (core::chemical)   StepWiseBasicModelerOptions (protocols::stepwise::modeler::options)   
BestHotspotCstMover (protocols::protein_interface_design::movers)   FilterByIndoleCOO (protocols::constel)   MinimizerMap (core::optimization)   ResetFoldTree (protocols::simple_moves)   StepWiseBasicOptions (protocols::stepwise::options)   
BestHotspotCstMoverCreator (protocols::protein_interface_design::movers)   FilterByProxTerm (protocols::constel)   MinimizerMapBase (core::kinematics)   ResetFoldTreeCreator (protocols::simple_moves)   StepWiseBasicWorkingParameters (protocols::stepwise::modeler::working_parameters)   
BestMatchesCollection (protocols::match::output)   FilterBySASA (protocols::constel)   MinimizerOptions (core::optimization)   ResetFullModelInfoMover (protocols::simple_moves)   StepWiseClusterer (protocols::stepwise::modeler::align)   
BestTotalScoreSelector (protocols::frag_picker)   FilterByTryptamine (protocols::constel)   MinimizeStoredRBConfs (protocols::enzdes)   ResetFullModelInfoMoverCreator (protocols::simple_moves)   StepWiseConnectionSampler (protocols::stepwise::modeler)   
BetaAlphaBetaMotif (protocols::fldsgn::topology)   FilterCollection (protocols::filters)   MiniPose (core::pose)   ResfileCommand (core::pack::task)   StepWiseLegacyClusterer (protocols::stepwise::modeler::align)   
BetaAlphaBetaMotifSet (protocols::fldsgn::topology)   FilterCreator (protocols::pose_selectors)   MiniRelax (protocols::relax)   ResfileCommandOperation (protocols::task_operations)   StepWiseLegacyClustererSilentBased (protocols::stepwise::modeler::align)   
BetaSheetArchitect (protocols::denovo_design::architects)   FilterCreator (protocols::filters)   MinMover (protocols::minimization_packing)   ResfileCommandOperationCreator (protocols::task_operations)   StepWiseMasterMover (protocols::stepwise::monte_carlo::mover)   
BetaSheetArchitectCreator (protocols::denovo_design::architects)   FilteredSolutions (protocols::kinematic_closure::solution_pickers)   MinMoverCreator (protocols::minimization_packing)   ResfileContents (core::pack::task)   StepWiseMasterPacker (protocols::stepwise::modeler::packer)   
BetaTurnDetection (protocols::features)   Filterer_Count (protocols::stepwise::modeler::rna)   MinMultiHarmonicFunc (core::scoring::func)   ResfileReaderException (core::pack::task)   StepWiseMinimizer (protocols::stepwise::modeler)   
BetaTurnDetectionFeatures (protocols::features)   FilterFactory (protocols::filters)   MinPackMover (protocols::minimization_packing)   ResFilter (core::pack::task::operation)   StepWiseModeler (protocols::stepwise::modeler)   
BetaTurnDetectionFeaturesCreator (protocols::features)   FilterMover (protocols::moves)   MinPackMoverCreator (protocols::minimization_packing)   ResFilterComposition (core::pack::task::operation)   StepWiseModelerOptions (protocols::stepwise::modeler::options)   
BFactor (protocols::frag_picker::scores)   FilterRegistrator (protocols::filters)   MinScoreScoreFunction (core::scoring)   ResFilterCreator (core::pack::task::operation)   StepWiseMonteCarlo (protocols::stepwise::monte_carlo)   
BfactorFittingMover (protocols::electron_density)   FilterReportAsPoseExtraScoresMover (protocols::moves)   MirrorSymmetricConformation (core::conformation::symmetry)   ResFilterFactory (core::pack::task::operation)   StepWiseMonteCarloOptions (protocols::stepwise::monte_carlo::options)   
BfactorFittingMoverCreator (protocols::electron_density)   FilterReportAsPoseExtraScoresMoverCreator (protocols::moves)   MissingDensityToJumpMover (protocols::simple_moves)   ResFilterRegistrator (core::pack::task::operation)   StepWiseMove (protocols::stepwise::monte_carlo::mover)   
BfactorMPM (protocols::match)   FilterReporter (protocols::pose_reporters)   MissingEnergy (core::energy_methods)   ResHasher (protocols::mean_field)   StepWiseMoveSelector (protocols::stepwise::monte_carlo::mover)   
BfactorMultifunc (protocols::electron_density)   FilterReporterCreator (protocols::pose_reporters)   MissingEnergyCreator (core::energy_methods)   ResHashMap (protocols::mean_field)   StepWiseMoveSelectorOptions (protocols::stepwise::monte_carlo::mover::options)   
BiasedFragmentMover (protocols::nonlocal)   FilterReporterMover (protocols::moves)   MixtureFunc (core::scoring::func)   ResId (protocols::moves)   StepWisePacker (protocols::stepwise::modeler::packer)   
BiasedMonteCarlo (protocols::canonical_sampling)   FilterScanFilter (protocols::protein_interface_design::filters)   MMAtomType (core::chemical)   ResidualDipolarCoupling (core::scoring)   StepWisePoseAligner (protocols::stepwise::modeler::align)   
BiasEnergy (protocols::canonical_sampling)   FilterScanFilterCreator (protocols::protein_interface_design::filters)   MMAtomTypeSet (core::chemical)   ResidualDipolarCoupling_Rohl (core::scoring)   StepWiseProteinBackboneSampler (protocols::stepwise::modeler::protein)   
BigBinConstraint (core::scoring::constraints)   FilterStructs (protocols::flxbb)   MMBondAngleEnergy (core::scoring::methods)   ResidualDipolarCouplingEnergy (core::energy_methods)   StepWiseProteinCCD_Closer (protocols::stepwise::modeler::protein::loop_close)   
BigBinConstraintCreator (core::scoring::constraints)   FilterStructs_Packstat (protocols::flxbb)   MMBondAngleEnergyCreator (core::scoring::methods)   ResidualDipolarCouplingEnergy_Rohl (core::energy_methods)   StepWiseProteinCCD_MultiPoseCloser (protocols::stepwise::modeler::protein::loop_close)   
BinaryFragmentStoreBackend (protocols::indexed_structure_store)   FilterStructs_TotalCharge (protocols::flxbb)   MMBondAngleLibrary (core::scoring::mm)   ResidualDipolarCouplingEnergy_RohlCreator (core::energy_methods)   StepWiseProteinKIC_LoopBridger (protocols::stepwise::modeler::protein::loop_close)   
BinarySilentStruct (core::io::silent)   FilterValueMetric (protocols::filters)   MMBondAngleResidueTypeParam (core::scoring::mm)   ResidualDipolarCouplingEnergyCreator (core::energy_methods)   StepWiseProteinMinimizer (protocols::stepwise::legacy::modeler::protein)   
BinarySilentStructCreator (core::io::silent)   FilterValueMetricCreator (protocols::filters)   MMBondAngleResidueTypeParamSet (core::scoring::mm)   ResidualDipolarCouplingEnergyRigidSegments (protocols::scoring::methods)   StepWiseProteinModelerOptions (protocols::stepwise::modeler::options)   
BindingSiteConstraint (protocols::constraints_additional)   FinalMinimizer (protocols::ligand_docking)   MMBondAngleScore (core::scoring::mm)   ResidualDipolarCouplingEnergyRigidSegmentsCreator (protocols::scoring::methods)   StepWiseProteinPoseSetup (protocols::stepwise::legacy::modeler::protein)   
BindingSiteConstraintCreator (protocols::constraints_additional)   FinalMinimizerCreator (protocols::ligand_docking)   MMBondLengthEnergy (core::scoring::methods)   ResidualDipolarCouplingRigidSegments (protocols::scoring)   StepWiseResiduePairScreener (protocols::stepwise::screener)   
BindingStrainFilter (protocols::protein_interface_design::filters)   FinalRMSDComparator (protocols::pose_length_moves)   MMBondLengthEnergyCreator (core::scoring::methods)   Residue (protocols::backbone_moves::local_backbone_mover)   StepWiseRNA_Clusterer (protocols::stepwise::legacy::modeler::rna)   
BindingStrainFilterCreator (protocols::protein_interface_design::filters)   FindConsensusSequence (protocols::recon_design)   MMBondLengthLibrary (core::scoring::mm)   Residue (core::conformation)   StepWiseRNA_CombineLongLoopFilterer (protocols::stepwise::modeler::rna)   
BinSelector (core::select::residue_selector)   FindConsensusSequenceCreator (protocols::recon_design)   MMBondLengthScore (core::scoring::mm)   Residue_info (protocols::stepwise::modeler::rna)   StepWiseRNA_CountStruct (protocols::stepwise::modeler::rna)   
BinSelectorCreator (core::select::residue_selector)   FindEndpointsOperation (protocols::splice)   MMEnergyTableAtom (core::scoring::mm::mmtrie)   ResidueAlternativeSet (protocols::stepwise::sampler::copy_dofs)   StepWiseRNA_ModelerOptions (protocols::stepwise::modeler::options)   
BinTransitionCalculator (core::scoring::bin_transitions)   FindEndpointsOperationCreator (protocols::splice)   MoveMapFactory::MMJumpAction (core::select::movemap)   ResidueAlternativeStepWiseSampler (protocols::stepwise::sampler::copy_dofs)   StepWiseRNA_PoseSelection (protocols::stepwise::legacy::modeler::rna)   
BinTransitionData (core::scoring::bin_transitions)   FingerprintBase (protocols::pockets)   MMLJEnergyInter (core::scoring::methods)   ResidueAlternativeStepWiseSamplerComb (protocols::stepwise::sampler::copy_dofs)   StepWiseRNA_PoseSetup (protocols::stepwise::legacy::modeler::rna)   
BlockParam (core::pack::guidance_scoreterms::sap)   FingerprintMultifunc (protocols::pockets)   MMLJEnergyInterCreator (core::scoring::methods)   ResidueArrayAnnealableEnergy (core::scoring::annealing)   StepWiseSampleAndScreen (protocols::stepwise)   
Blosum62Map (core::sequence)   FirstClassEdge (core::pack::interaction_graph)   MMLJEnergyIntra (core::scoring::methods)   ResidueArrayAnnealingEvaluator (core::pack::interaction_graph)   StepWiseSampler (protocols::stepwise::sampler)   
BluePrint (protocols::parser)   FirstClassNode (core::pack::interaction_graph)   MMLJEnergyIntraCreator (core::scoring::methods)   ResidueAtomOverlaps (core::scoring::methods)   StepWiseSamplerComb (protocols::stepwise::sampler)   
BlueprintArchitect (protocols::denovo_design::architects)   FitBfactorsMover (protocols::cryst)   MMLJEnergyTable (core::scoring::mm)   ResidueAtomTreeCollection (core::pack::scmin)   StepWiseSamplerOneDOF (protocols::stepwise::sampler)   
BlueprintArchitectCreator (protocols::denovo_design::architects)   FitBfactorsMoverCreator (protocols::cryst)   MMLJLibrary (core::scoring::mm)   ResidueAtomTreeCollectionMomento (core::pack::scmin)   StepWiseSamplerOneTorsion (protocols::stepwise::sampler)   
BluePrintBDR (protocols::fldsgn)   FitnessFilter (protocols::recon_design)   MMLJScore (core::scoring::mm)   ResidueBackboneEntry (protocols::indexed_structure_store)   StepWiseSamplerOneValue (protocols::stepwise::sampler)   
BluePrintBDRCreator (protocols::fldsgn)   FitnessFilterCreator (protocols::recon_design)   MoveMapFactory::MMResAction (core::select::movemap)   ResidueBBDofs (protocols::splice)   StepWiseSamplerOneValueComb (protocols::stepwise::sampler)   
Boinc (protocols::boinc)   FitnessFunction (protocols::genetic_algorithm)   MoveMapFactory::MMResIndexAction (core::select::movemap)   ResidueBurialFeatures (protocols::features)   StepWiseSamplerRingConformer (protocols::stepwise::sampler)   
BoincCurrentPoseObserver (protocols::boinc)   FitSimpleHelix (protocols::helical_bundle)   MMTorsionEnergy (core::scoring::methods)   ResidueBurialFeaturesCreator (protocols::features)   StepWiseSamplerSized (protocols::stepwise::sampler)   
BOINCJobDistributor (protocols::jd2)   FitSimpleHelixCreator (protocols::helical_bundle)   MMTorsionEnergyCreator (core::scoring::methods)   ResidueBurialFilter (protocols::simple_filters)   StepWiseSamplerSizedAny (protocols::stepwise::sampler)   
BoincSharedMemory (protocols::boinc)   FitSimpleHelixMultiFunc (protocols::helical_bundle)   MMTorsionLibrary (core::scoring::mm)   ResidueBurialFilterCreator (protocols::simple_filters)   StepWiseSamplerSizedComb (protocols::stepwise::sampler)   
BoltzmannFilter (protocols::protein_interface_design::filters)   FIX_HIS_TAUTOMER (core::pack::task)   MMTorsionScore (core::scoring::mm)   ResidueCartBondedParameters (core::energy_methods)   StepWiseScreener (protocols::stepwise::screener)   
BoltzmannFilterCreator (protocols::protein_interface_design::filters)   FixAllLoopsMover (protocols::pose_length_moves)   Model (protocols::legacy_sewing)   ResidueChiralityFilter (protocols::simple_filters)   StepWiseWorkingParameters (protocols::stepwise::modeler::working_parameters)   
BoltzmannRotamerMover (protocols::minimization_packing)   FixAllLoopsMoverCreator (protocols::pose_length_moves)   ModelConstIterator (protocols::legacy_sewing)   ResidueChiralityFilterCreator (protocols::simple_filters)   StepWiseWorkingParametersSetup (protocols::stepwise::legacy::modeler::rna)   
BoltzmannRotamerMoverCreator (protocols::minimization_packing)   FixbbCoupledRotamerSimAnnealer (core::pack::annealer)   ModelFeatures (protocols::features)   ResidueChunkSelection (protocols::abinitio::abscript)   STMStoredTask (protocols::task_operations)   
Bond (core::chemical)   FixbbLinkingRotamerSimAnnealer (core::pack::annealer)   ModelFeaturesCreator (protocols::features)   ResidueConformationFeatures (protocols::features)   StochasticFilter (protocols::filters)   
BondAnglePerturber (protocols::kinematic_closure::perturbers)   FixbbPwatSimAnnealer (core::pack::annealer)   ModelFileReader (protocols::sewing::hashing)   ResidueConformationFeaturesCreator (protocols::features)   StochasticFilterCreator (protocols::filters)   
BondData (core::chemical::sdf)   FixbbRotamerSets (core::pack::rotamer_set)   ModelIterator (protocols::legacy_sewing)   ResidueConformerFilter (protocols::enzdes)   StoreCombinedStoredTasksMover (protocols::task_operations)   
BondedAtom (core::kinematics::tree)   FixbbSimAnnealer (core::pack::annealer)   ModelNode (protocols::legacy_sewing)   ResidueConformerFilterCreator (protocols::enzdes)   StoreCombinedStoredTasksMoverCreator (protocols::task_operations)   
BondedResidueSelector (core::select::residue_selector)   FixedBBEdge (core::pack::interaction_graph)   ModifiedResidueInformation (core::io)   ResidueConnection (core::chemical)   StoreCompoundTaskMover (protocols::task_operations)   
BondedResidueSelectorCreator (core::select::residue_selector)   FixedBBInteractionGraph (core::pack::interaction_graph)   ModifyAnnealer (protocols::task_operations)   ResidueConstraints (core::scoring::constraints)   StoreCompoundTaskMoverCreator (protocols::task_operations)   
BondID (core::id)   FixedBBNode (core::pack::interaction_graph)   ModifyAnnealerCreator (protocols::task_operations)   ResidueContactScreener (protocols::stepwise::screener)   StoredResidueSubsetSelector (protocols::residue_selectors)   
BondInfo (protocols::denovo_design::components)   FixedOffsetPivots (protocols::kinematic_closure::pivot_pickers)   ModifyStoredRBConfs (protocols::enzdes)   ResidueCoordinateChangeList (core::kinematics)   StoredResidueSubsetSelectorCreator (protocols::residue_selectors)   
BondOrderParser (core::scoring)   FixedOffsetsPivots (protocols::kinematic_closure::pivot_pickers)   ModifyVariantTypeMover (protocols::simple_moves)   ResidueCountFilter (protocols::simple_filters)   StoredRotamerLibraryCreator (core::pack::rotamers)   
Book (core::fragment::picking_old::concepts)   FixedPivots (protocols::kinematic_closure::pivot_pickers)   ModifyVariantTypeMoverCreator (protocols::simple_moves)   ResidueCountFilterCreator (protocols::simple_filters)   StoredRotamerLibrarySpecification (core::chemical::rotamers)   
Book_VallResidues (core::fragment::picking_old::concepts)   FixedTemperatureController (protocols::canonical_sampling)   ModuleType1 (core::kinematics::jacobian)   ResidueCouplingConstraint (core::scoring::constraints)   StoredRotamerLibrarySpecificationCreator (core::chemical::rotamers)   
Bool3DGrid (protocols::match)   FixTemplateJumpSetup (protocols::abinitio)   MolarMassFilter (protocols::ligand_docking)   ResidueDatabaseIO (core::chemical)   StorePoseSnapshot (protocols::simple_moves)   
Bool3DGridKinemageWriter (protocols::match)   FlatHarmonicFunc (core::scoring::func)   MolarMassFilterCreator (protocols::ligand_docking)   ResidueDecompositionByChainCalculator (protocols::pose_metric_calculators)   StorePoseSnapshotCreator (protocols::simple_moves)   
BooleanValuedParameter (core::conformation::parametric)   FlexBBDesignMeanField (protocols::mean_field)   MolecularDynamics (protocols::cartesian)   ResidueDecompositionCalculator (protocols::pose_metric_calculators)   StoreResidueSubsetMover (protocols::residue_selectors)   
BoundedCollector (protocols::frag_picker)   FlexbbEdge (protocols::flexpack::interaction_graph)   MolecularMassFilter (protocols::ligand_docking)   ResidueDepthCalculator (protocols::simple_filters)   StoreResidueSubsetMoverCreator (protocols::residue_selectors)   
BoundedCollector_CompareTotalScore (protocols::frag_picker)   FlexbbIGFactory (protocols::flexpack::interaction_graph)   MolecularMassFilterCreator (protocols::ligand_docking)   ResidueDepthData (protocols::simple_filters)   StoreTaskMover (protocols::task_operations)   
BoundedPriorityQueue (protocols::frag_picker)   FlexbbInteractionGraph (protocols::flexpack::interaction_graph)   MolecularSurfaceCalculator (core::scoring::sc)   ResidueDepthFilter (protocols::simple_filters)   StoreTaskMoverCreator (protocols::task_operations)   
BoundFunc (core::scoring::constraints)   FlexBBMeanField (protocols::mean_field)   MolecularWeightNormalization (protocols::qsar::scoring_grid)   ResidueDepthFilterCreator (protocols::simple_filters)   Strand (protocols::fldsgn::topology)   
BranchAngleOptimizer (protocols::branch_angle)   FlexbbNode (protocols::flexpack::interaction_graph)   MolFileIOAtom (core::chemical::sdf)   ResidueDepthFrag (protocols::simple_filters)   StrandArchitect (protocols::denovo_design::architects)   
BranchCoef1 (protocols::branch_angle)   FlexbbRotamerSet (protocols::flexpack::rotamer_set)   MolFileIOBond (core::chemical::sdf)   ResidueDihedrals (protocols::denovo_design::components)   StrandArchitectCreator (protocols::denovo_design::architects)   
BranchCoef2 (protocols::branch_angle)   FlexbbRotamerSets (protocols::flexpack::rotamer_set)   MolFileIOMolecule (core::chemical::sdf)   ResidueDistanceFilter (protocols::simple_filters)   StrandBundleFeatures (protocols::features::strand_assembly)   
BranchEnergy (core::energy_methods)   FlexbbSimAnnealer (protocols::flexpack::annealer)   MolFileIOReader (core::chemical::sdf)   ResidueDistanceFilterCreator (protocols::simple_filters)   StrandBundleFeaturesCreator (protocols::features::strand_assembly)   
BranchEnergyCreator (core::energy_methods)   FlexbbSparseMatrixIndex (protocols::flexpack::interaction_graph)   MolWriter (core::chemical::sdf)   ResidueDOFReporter (core::pack::dunbrack)   StrandConstraints (protocols::abinitio)   
BranchParam1 (protocols::branch_angle)   FlexPacker (protocols::flexpack)   MonteCarlo (protocols::moves)   ResidueElement (protocols::environment::claims)   StrandCurvatureByLevels (protocols::fldsgn::filters)   
BranchParam2 (protocols::branch_angle)   FlexPepDockingAbInitio (protocols::flexpep_docking)   MonteCarloExceptionConverge (protocols::moves)   ResidueEntry (protocols::indexed_structure_store)   StrandCurvatureByLevelsCreator (protocols::fldsgn::filters)   
BrentLineMinimization (core::optimization)   FlexPepDockingFlags (protocols::flexpep_docking)   MonteCarloInterface (protocols::monte_carlo)   ResidueExclParams (core::scoring)   StrandFragment (protocols::features::strand_assembly)   
Bridge (protocols::forge::build)   FlexPepDockingLowRes (protocols::flexpep_docking)   MonteCarloLoader (protocols::parser)   ResidueFactory (core::conformation)   StrandHelixGeometryFilter (protocols::fldsgn::filters)   
BridgeChainsCreator (protocols::denovo_design::movers)   FlexPepDockingPoseMetrics (protocols::flexpep_docking)   MonteCarloLoaderCreator (protocols::parser)   ResidueFeature (protocols::comparative_modeling::features)   StrandHelixGeometryFilterCreator (protocols::fldsgn::filters)   
BridgeChainsMover (protocols::denovo_design::movers)   FlexPepDockingProtocol (protocols::flexpep_docking)   MonteCarloRecover (protocols::monte_carlo)   ResidueFeatureFactory (protocols::comparative_modeling::features)   StrandPairing (protocols::fldsgn::topology)   
BridgeChainsMoverCreator (protocols::denovo_design::movers)   FlexPepDockingProtocolCreator (protocols::flexpep_docking)   MonteCarloRecoverCreator (protocols::monte_carlo)   ResidueFeatures (protocols::features)   StrandPairing (core::scoring::dssp)   
EnvClaimBroker::BrokeredJumpData (protocols::environment)   FlipChiralityMover (protocols::cyclic_peptide)   MonteCarloReset (protocols::monte_carlo)   ResidueFeaturesCreator (protocols::features)   StrandPairing (protocols::denovo_design::components)   
EnvClaimBroker::BrokerResult (protocols::environment)   FlipChiralityMoverCreator (protocols::cyclic_peptide)   MonteCarloResetCreator (protocols::monte_carlo)   ResidueGridScoresFeatures (protocols::features)   StrandPairingSet (core::scoring::dssp)   
BruteFunGroupTK (protocols::kinmatch)   FlipMover (protocols::membrane)   MonteCarloTest (protocols::monte_carlo)   ResidueGridScoresFeaturesCreator (protocols::features)   StrandPairingSet (protocols::fldsgn::topology)   
BUFFER (core::io::serialization)   FlipMoverCreator (protocols::membrane)   MonteCarloTestCreator (protocols::monte_carlo)   ResidueGroupIGEdgeUpweighter (protocols::toolbox)   Strands (core::scoring)   
BuildAlaPose (protocols::protein_interface_design::movers)   FloatingResonance (protocols::noesy_assign)   MonteCarloUtil (protocols::moves)   ResidueHasProperty (core::pack::task::operation)   StrandTwistingMover (protocols::rbsegment_relax)   
BuildAlaPoseCreator (protocols::protein_interface_design::movers)   FloppyTailMover (protocols::floppy_tail)   Motif (protocols::motifs)   ResidueHasPropertyCreator (core::pack::task::operation)   StringMetric (core::simple_metrics)   
BuildDeNovoBackboneMover (protocols::denovo_design::movers)   FlxbbDesign (protocols::flxbb)   MotifArchitect (protocols::denovo_design::architects)   ResidueIEFilter (protocols::simple_filters)   StrongWolfeLineMinimization (core::optimization)   
BuildDeNovoBackboneMoverCreator (protocols::denovo_design::movers)   FlxbbDesignCreator (protocols::flxbb)   MotifArchitectCreator (protocols::denovo_design::architects)   ResidueIEFilterCreator (protocols::simple_filters)   Stru (protocols::cluster::calibur)   
BuildingBlockInterfaceOperation (protocols::matdes)   FlxbbDesignPack (protocols::flxbb)   MotifDnaPacker (protocols::motifs)   ResidueIndexDescription (core::pose)   StructAvrgMover (protocols::mpi_refinement)   
BuildingBlockInterfaceOperationCreator (protocols::matdes)   FNatFilter (protocols::protein_interface_design::filters)   MotifDnaPackerCreator (protocols::motifs)   ResidueIndexDescriptionChainEnd (core::pose)   StructFileReaderOptions (core::io)   
BuildInstruction (protocols::forge::build)   FNatFilterCreator (protocols::protein_interface_design::filters)   MotifDockEnergy (core::energy_methods)   ResidueIndexDescriptionLastResidue (core::pose)   StructFileRep (core::io)   
BuildManager (protocols::forge::build)   FoldandDockClaimer (protocols::topology_broker)   MotifDockEnergyCreator (core::energy_methods)   ResidueIndexDescriptionPDB (core::pose)   StructFileRepOptions (core::io)   
BuildPhases (protocols::denovo_design::components)   FoldArchitectMover (protocols::denovo_design::movers)   MotifGraftCreator (protocols::motif_grafting::movers)   ResidueIndexDescriptionPoseNum (core::pose)   StructFragmentMover (protocols::struct_fragment)   
BuildPosition (protocols::motifs)   FoldArchitectMoverCreator (protocols::denovo_design::movers)   MotifGraftMover (protocols::motif_grafting::movers)   ResidueIndexDescriptionRefPose (core::pose)   StructFragmentMoverCreator (protocols::struct_fragment)   
BuildSet (protocols::match::upstream)   FoldConstraints (protocols::abinitio)   MotifHash (core::scoring::motif)   ResidueIndexIs (core::pack::task::operation)   StructInfo (protocols::ligand_docking::ga_ligand_dock)   
BulgeApplier (protocols::stepwise::screener)   FoldGraph (protocols::denovo_design::components)   MotifHashManager (core::scoring::motif)   ResidueIndexIsCreator (core::pack::task::operation)   StructInfoComp (protocols::ligand_docking::ga_ligand_dock)   
BulgeApplyMover (protocols::stepwise::modeler::rna::bulge)   FoldResonance (protocols::noesy_assign)   MotifHashRigidScore (protocols::sic_dock::scores)   ResidueIndexIsnt (core::pack::task::operation)   StructPerturberCM (protocols::abinitio::abscript)   
BulgeUnApplyMover (protocols::stepwise::modeler::rna::bulge)   FoldTree (core::kinematics)   MotifHit (protocols::motifs)   ResidueIndexIsntCreator (core::pack::task::operation)   StructPerturberCMCreator (protocols::abinitio::abscript)   
BumpGrid (protocols::match)   FoldTreeFromFoldGraphMover (protocols::denovo_design::movers)   MotifHit (core::scoring::motif)   ResidueIndexSelector (core::select::residue_selector)   StructProfileMover (protocols::simple_moves)   
BumpSelector (core::pack::rotamer_set)   FoldTreeFromFoldGraphMoverCreator (protocols::denovo_design::movers)   MotifHits (core::scoring::motif)   ResidueIndexSelectorCreator (core::select::residue_selector)   StructProfileMoverCreator (protocols::simple_moves)   
BundleGridSampler (protocols::helical_bundle)   FoldTreeFromLoops (protocols::loops)   MotifHitsRotamersOperation (protocols::matdes)   ResidueInformation (core::io)   StructuralSimilarityEvaluator (protocols::simple_filters)   
BundleGridSamplerCreator (protocols::helical_bundle)   FoldTreeFromLoopsCreator (protocols::loops)   MotifHitStats (core::scoring::motif)   ResidueInMembraneSelector (core::select::residue_selector)   StructureArchitect (protocols::denovo_design::architects)   
BundleGridSamplerHelper (protocols::helical_bundle)   FoldTreeFromMotif (protocols::simple_moves)   MotifLibrary (protocols::motifs)   ResidueInMembraneSelectorCreator (core::select::residue_selector)   StructureData (protocols::indexed_structure_store::search)   
BundleParameters (protocols::helical_bundle::parameters)   FoldTreeFromMotifCreator (protocols::simple_moves)   MotifMatch (protocols::motif_grafting::movers)   ResidueInSequenceMotifSelector (core::select::residue_selector)   StructureData (protocols::denovo_design::components)   
BundleParametersSet (protocols::helical_bundle::parameters)   FoldTreeHybridize (protocols::hybridization)   MotifScoreFilter (protocols::simple_filters)   ResidueInSequenceMotifSelectorCreator (core::select::residue_selector)   StructureDatabase (protocols::indexed_structure_store::search)   
BundleParametrizationCalculator (protocols::helical_bundle)   FoldTreeSketch (core::environment)   MotifScoreFilterCreator (protocols::simple_filters)   PDBPoseMap::ResidueKey (core::pose)   StructureDataCreator (protocols::denovo_design::components)   
BundleReporterFilter (protocols::helical_bundle)   ForceDisulfidesMover (protocols::calc_taskop_movers)   MotifScorer (protocols::sewing::scoring)   ResidueKinemageWriter (protocols::match::output)   StructureDataFactory (protocols::denovo_design::components)   
BundleReporterFilterCreator (protocols::helical_bundle)   ForceDisulfidesMoverCreator (protocols::calc_taskop_movers)   MotifScorerCreator (protocols::sewing::scoring)   ResidueKinWriter (core::conformation)   StructureDataObserver (protocols::denovo_design::components)   
Burial_v2Energy (core::energy_methods)   FormFactor (core::scoring::saxs)   MotifSearch (protocols::motifs)   ResidueLabelsToPymolSelectionMover (protocols::fold_from_loops::movers)   StructureDataPerturber (protocols::denovo_design::components)   
Burial_v2EnergyCreator (core::energy_methods)   FormFactorManager (core::scoring::saxs)   MoveBeforeFilter (protocols::filters)   ResidueLabelsToPymolSelectionMoverCreator (protocols::fold_from_loops::movers)   StructureDependentCalculator (core::pose::metrics)   
BurialEnergy (core::energy_methods)   FourAtomsConstraintData (protocols::frag_picker::scores)   MoveBeforeFilterCreator (protocols::filters)   ResidueLacksProperty (core::pack::task::operation)   StructureDependentPeakCalibrator (protocols::noesy_assign)   
BurialEnergyCreator (core::energy_methods)   FourPointsFunc (core::scoring::func)   MoveMap (core::kinematics)   ResidueLacksPropertyCreator (core::pack::task::operation)   StructureEntry (protocols::indexed_structure_store)   
BuriedPolarScore (protocols::sic_dock)   FragCache (core::fragment)   MoveMapBuilder (protocols::ligand_docking)   ResidueLevelTask (core::pack::task)   StructureFeatures (protocols::features)   
BuriedSurfaceAreaFilter (protocols::simple_filters)   FragData (core::fragment)   MoveMapBuilderLoader (protocols::ligand_docking)   ResidueLevelTask_ (core::pack::task)   StructureFeaturesCreator (protocols::features)   
BuriedSurfaceAreaFilterCreator (protocols::simple_filters)   FragFactory (core::fragment)   MoveMapBuilderLoaderCreator (protocols::ligand_docking)   ResidueLipophilicityFilter (protocols::simple_filters)   StructureFileNames (protocols::pack_daemon)   
BuriedUnsatHbondFilter (protocols::simple_filters)   FragID (core::fragment)   MoveMapFactory (core::select::movemap)   ResidueLipophilicityFilterCreator (protocols::simple_filters)   StructureIndependentPeakCalibrator (protocols::noesy_assign)   
BuriedUnsatHbondFilter2 (protocols::buns)   FragID_Iterator (core::fragment)   MoveMapFactoryLoader (protocols::parser)   ResidueListStepWiseSampler (protocols::stepwise::sampler::copy_dofs)   StructurePairQuery (protocols::indexed_structure_store::search)   
BuriedUnsatHbondFilter2Creator (protocols::buns)   FragInsertAndAlignMover (protocols::rbsegment_relax)   MoveMapFactoryLoaderCreator (protocols::parser)   ResidueMask (protocols::constel)   StructurePairQueryResult (protocols::indexed_structure_store::search)   
BuriedUnsatHbondFilterCreator (protocols::simple_filters)   FragLib (protocols::frags)   MoveMapFactoryToNamedMoveMapMover (protocols::fold_from_loops::movers)   ResidueMatcher (core::conformation)   StructureRecord (protocols::indexed_structure_store)   
BuriedUnsatisfiedPolarsCalculator (protocols::simple_pose_metric_calculators)   FragmentAllAtomCrmsd (protocols::frag_picker::scores)   MoveMapFactoryToNamedMoveMapMoverCreator (protocols::fold_from_loops::movers)   ResidueName3Is (core::pack::task::operation)   StructureRestrictor (protocols::moves)   
BuriedUnsatisfiedPolarsCalculator2 (protocols::buns)   FragmentBiasAssigner (protocols::hybridization)   MoveMapMover (protocols::moves)   ResidueName3IsCreator (core::pack::task::operation)   StructureScoresFeatures (protocols::features)   
BuriedUnsatPenalty (core::pack::guidance_scoreterms::buried_unsat_penalty)   FragmentCandidate (protocols::frag_picker)   MovePoseToMembraneCenterMover (protocols::rigid)   ResidueName3Isnt (core::pack::task::operation)   StructureScoresFeaturesCreator (protocols::features)   
BuriedUnsatPenaltyCreator (core::pack::guidance_scoreterms::buried_unsat_penalty)   FragmentChunkCrms (protocols::frag_picker::scores)   Mover (protocols::moves)   ResidueName3IsntCreator (core::pack::task::operation)   StructureSimilarityEvaluatorCreator (protocols::simple_filters)   
BuriedUnsatPenaltyEdge (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentClaimer (protocols::topology_broker)   Mover_LoopHashRefine (protocols::loophash)   ResidueNameSelector (core::select::residue_selector)   StructureSingleQuery (protocols::indexed_structure_store::search)   
BuriedUnsatPenaltyEdgeData (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentCM (protocols::abinitio::abscript)   MoverAndChunkLibraryJob (protocols::jd3::chunk_library)   ResidueNameSelectorCreator (core::select::residue_selector)   StructureSingleQueryResult (protocols::indexed_structure_store::search)   
BuriedUnsatPenaltyGraph (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentCMCreator (protocols::abinitio::abscript)   MoverApplyingMover (protocols::moves)   ResidueNblistData (core::scoring)   StructureSlice (protocols::denovo_design::components)   
BuriedUnsatPenaltyGraphContainer (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentComparatorBase (protocols::frag_picker)   MoverContainer (protocols::moves)   ResidueNeighborConstIterator (core::scoring)   StructureSlicePredicate (protocols::denovo_design::components)   
BuriedUnsatPenaltyGraphHbond (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentContainer (protocols::topology_broker)   MoverCreator (protocols::moves)   ResidueNeighborIterator (core::scoring)   StructureStore (protocols::indexed_structure_store)   
BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentCost (protocols::simple_moves)   MoverFactory (protocols::moves)   ResidueNetwork (protocols::toolbox)   StructureStore (protocols::abinitio)   
BuriedUnsatPenaltyGraphOptions (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentCrmsd (protocols::frag_picker::scores)   MoverForPoseList (protocols::moves)   ResidueOrientEntry (protocols::indexed_structure_store)   StructureStoreManager (protocols::indexed_structure_store)   
BuriedUnsatPenaltyNode (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentCrmsdResDepth (protocols::frag_picker::scores)   MoverJob (protocols::jd3::jobs)   ResiduePair (protocols::fldsgn)   StructureStoreProvider (protocols::indexed_structure_store)   
BuriedUnsatPenaltyNodeData (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)   FragmentDME (protocols::frag_picker::scores)   MoverList (protocols::wum)   ResiduePairJump (protocols::jumping)   Stub (core::kinematics)   
  C  
FragmentExtension (protocols::loop_grower)   MoverRegistrator (protocols::moves)   ResiduePairJumpSetup (protocols::jumping)   StubApplier (protocols::stepwise::screener)   
FragmentExtensionCreator (protocols::loop_grower)   MoverStatistics (protocols::moves)   ResiduePairJumpSingle (protocols::jumping)   StubDistanceScreener (protocols::stepwise::screener)   
CaCbCb_Angle_Func (core::scoring::disulfides)   FragmentIO (core::fragment)   MPCbetaEnergy (core::energy_methods)   ResiduePairNeighborList (core::scoring)   StubGenerator (protocols::hotspot_hashing)   
CaCbCbCa_Dihedral_Func (core::scoring::disulfides)   FragmentJumpClaimer (protocols::topology_broker)   MPCbetaEnergyCreator (core::energy_methods)   ResiduePairXYZ (core::scoring::func)   StubID (core::id)   
CacheableAtomID_MapVector (core::id)   FragmentJumpCM (protocols::abinitio::abscript)   MPDockingMover (protocols::docking::membrane)   ResiduePDBIndexIs (core::pack::task::operation)   StubRMSDComparator (protocols::pose_length_moves)   
CacheableDataType (core::pose::datacache)   FragmentJumpCMCreator (protocols::abinitio::abscript)   MPDockingMoverCreator (protocols::docking::membrane)   ResiduePDBIndexIsCreator (core::pack::task::operation)   StubScoreFilter (protocols::protein_interface_design::filters)   
CacheableObserver (core::pose::datacache)   FragmentLibrary (core::fragment::rna)   MPDockingSetupMover (protocols::docking::membrane)   ResiduePDBIndexIsnt (core::pack::task::operation)   StubScoreFilterCreator (protocols::protein_interface_design::filters)   
CacheablePoseRawPtr (core::pose::datacache)   FragmentLibraryManager (core::fragment::picking_old)   MPDockingSetupMoverCreator (protocols::docking::membrane)   ResiduePDBIndexIsntCreator (core::pack::task::operation)   StubScoreLoopsFilter (protocols::protein_interface_design::filters)   
CacheableResidueTypeSets (core::chemical)   FragmentLookup (protocols::indexed_structure_store)   MPEnvEnergy (core::energy_methods)   ResiduePDBInfoHasLabel (core::pack::task::operation)   StubScoreLoopsFilterCreator (protocols::protein_interface_design::filters)   
CachedResidueSubset (core::select::residue_selector)   FragmentLookupFilter (protocols::indexed_structure_store::filters)   MPEnvEnergyCreator (core::energy_methods)   ResiduePDBInfoHasLabelCreator (core::pack::task::operation)   SubMotifInfo (core::pose::full_model_info)   
CacheWrapper (core::fragment)   FragmentLookupFilterCreator (protocols::indexed_structure_store::filters)   MPFastRelaxMover (protocols::relax::membrane)   ResiduePDBInfoHasLabelSelector (core::select::residue_selector)   SubMotifLibrary (protocols::stepwise::monte_carlo::submotif)   
CachingScoringMethod (protocols::frag_picker::scores)   FragmentLookupResult (protocols::indexed_structure_store)   MPFastRelaxMoverCreator (protocols::relax::membrane)   ResiduePDBInfoHasLabelSelectorCreator (core::select::residue_selector)   SubroutineMover (protocols::protein_interface_design::movers)   
CAcstGenerator (protocols::seeded_abinitio)   FragmentMover (protocols::simple_moves)   MPFindInterfaceMover (protocols::docking::membrane)   ResiduePDBInfoLacksLabel (core::pack::task::operation)   SubroutineMoverCreator (protocols::protein_interface_design::movers)   
CAcstGeneratorCreator (protocols::seeded_abinitio)   FragmentPair (protocols::features::helixAssembly)   MPFindInterfaceMoverCreator (protocols::docking::membrane)   ResiduePDBInfoLacksLabelCreator (core::pack::task::operation)   SubsetPartnerMotifScorer (protocols::sewing::scoring)   
CalcInterNeighborGroup (protocols::toolbox)   FragmentPerturber (protocols::kinematic_closure::perturbers)   MPHelicalityEnergy (core::energy_methods)   ResidueProbDesignOperation (protocols::task_operations)   SubsetPartnerMotifScorerCreator (protocols::sewing::scoring)   
CalculatorFactory (core::pose::metrics)   FragmentPicker (protocols::frag_picker)   MPHelicalityEnergyCreator (core::energy_methods)   ResidueProbDesignOperationCreator (protocols::task_operations)   SuckerEnergy (core::energy_methods)   
CalculatorFilter (protocols::filters)   FragmentReader (protocols::parser)   MPI_LoopHashRefine (protocols::loophash)   ResidueProperties (core::chemical)   SuckerEnergyCreator (core::energy_methods)   
CalculatorFilterCreator (protocols::filters)   FragmentRmsd (core::fragment)   MPI_LoopHashRefine_Emperor (protocols::loophash)   ResiduePropertySelector (core::select::residue_selector)   SugarBackboneEnergy (core::energy_methods)   
CalculatorMetric (core::simple_metrics::metrics)   FragmentSampler (protocols::abinitio)   MPI_LoopHashRefine_Master (protocols::loophash)   ResiduePropertySelectorCreator (core::select::residue_selector)   SugarBackboneEnergyCreator (core::energy_methods)   
CalculatorMetricCreator (core::simple_metrics::metrics)   FragmentScoreFilter (protocols::frag_picker)   MPI_Refine_Emperor (protocols::mpi_refinement)   ResidueRange (core::select::residue_selector)   SugarBBSampler (protocols::simple_moves::bb_sampler)   
CamShiftEvaluator (protocols::simple_filters)   FragmentScoreFilterCreator (protocols::frag_picker)   MPI_Refine_Master (protocols::mpi_refinement)   ResidueRanges (core::select::residue_selector)   SugarInstantiateMover (protocols::stepwise::modeler::rna::sugar)   
CamShiftEvaluatorCreator (protocols::simple_filters)   FragmentScoreManager (protocols::frag_picker::scores)   MPI_Refinement (protocols::mpi_refinement)   PDBInfo::ResidueRecord (core::pose)   SugarInstantiator (protocols::stepwise::screener)   
SmoothPolicy::Candidate (protocols::nonlocal)   FragmentScoreMap (protocols::frag_picker::scores)   MPI_WorkUnitManager (protocols::wum)   ResidueReplacementRebuildMover (protocols::ncbb)   SugarModeling (protocols::stepwise::modeler::rna::sugar)   
CandidatesCollector (protocols::frag_picker)   FragmentScoringMethod (protocols::frag_picker::scores)   MPI_WorkUnitManager_Slave (protocols::wum)   ResidueReplacementRebuildMoverCreator (protocols::ncbb)   SugarModificationsNomenclatureTableRow (core::chemical::carbohydrates)   
CanonicalSamplingMover (protocols::canonical_sampling)   FragmentSelectingRule (protocols::frag_picker)   MPIArchiveJobDistributor (protocols::jd2::archive)   ResidueScoresFeatures (protocols::features)   SugarVirtualizeMover (protocols::stepwise::modeler::rna::sugar)   
CarbohydrateInfo (core::chemical::carbohydrates)   FragmentSetLoader (core::fragment)   MpiFileBuffer (protocols::jd2)   ResidueScoresFeaturesCreator (protocols::features)   SuggestValueMessage (protocols::topology_broker)   
CarbohydrateInfoManager (core::chemical::carbohydrates)   FragmentSetLoaderCreator (core::fragment)   MPIFileBufJobDistributor (protocols::jd2)   ResidueSecondaryStructureFeatures (protocols::features)   SumFunc (core::scoring::func)   
CarbonHBondEnergy (core::scoring::carbon_hbonds)   FragmentSpecification (protocols::indexed_structure_store)   MPIMultiCommJobDistributor (protocols::jd2)   ResidueSecondaryStructureFeaturesCreator (protocols::features)   SuperimposeMover (protocols::simple_moves)   
CarbonHBondEnergyCreator (core::scoring::carbon_hbonds)   FragmentStore (protocols::indexed_structure_store)   MPIMultistateFitnessFunction (protocols::pack_daemon)   ResidueSelectionDistanceFilter (protocols::simple_filters)   SuperimposeMoverCreator (protocols::simple_moves)   
CarbonHBondPotential (core::scoring::carbon_hbonds)   FragmentStoreManager (protocols::indexed_structure_store)   MPIWorkPartitionJobDistributor (protocols::jd2)   ResidueSelectionDistanceFilterCreator (protocols::simple_filters)   SurfaceBackgroundEdge (core::pack::interaction_graph)   
CartBondedParameters (core::scoring::methods)   FragmentStoreProvider (protocols::indexed_structure_store)   MPIWorkPoolJobDistributor (protocols::jd2)   ResidueSelector (core::select::residue_selector)   SurfaceBackgroundNode (core::pack::interaction_graph)   
CartesianAtom (protocols::cartesian)   FragQualCalculator (protocols::pose_metric_calculators)   MPLipidAccessibility (protocols::membrane)   ResidueSelectorCreator (core::select::residue_selector)   SurfaceCalculator (protocols::pose_metric_calculators)   
CartesianBondedEnergy (core::energy_methods)   FragQualFilter (protocols::fldsgn::filters)   MPLipidAccessibilityCreator (protocols::membrane)   ResidueSelectorFactory (core::select::residue_selector)   SurfaceDockingProtocol (protocols::surface_docking)   
CartesianBondedEnergyCreator (core::energy_methods)   FragQualFilterCreator (protocols::fldsgn::filters)   MPMutateRelaxMover (protocols::membrane)   ResidueSelectorLoader (protocols::parser)   SurfaceEdge (core::pack::interaction_graph)   
CartesianHybridize (protocols::hybridization)   FragSet (core::fragment)   MPMutateRelaxMoverCreator (protocols::membrane)   ResidueSelectorLoaderCreator (protocols::parser)   SurfaceEnergies (core::scoring::solid_surface)   
CartesianMD (protocols::md)   FragSetCollection (core::fragment)   MPNonHelixPenalty (core::scoring::membrane)   ResidueSelectorRegistrator (core::select::residue_selector)   SurfaceEnergy (core::pack::interaction_graph)   
CartesianMDCreator (protocols::md)   FragSetLoader (protocols::parser)   MPNonHelixPenaltyCreator (core::scoring::membrane)   ResidueSetChainEnergyFilter (protocols::simple_filters)   SurfaceEnergyCreator (core::pack::interaction_graph)   
CartesianMinimizer (core::optimization)   FragSetLoaderCreator (protocols::parser)   MPPairEnergy (core::energy_methods)   ResidueSetChainEnergyFilterCreator (protocols::simple_filters)   SurfaceInteractionGraph (core::pack::interaction_graph)   
CartesianMinimizerMap (core::optimization)   FragsToAtomDist (protocols::noesy_assign)   MPPairEnergyCreator (core::energy_methods)   ResidueSidechainEntry (protocols::indexed_structure_store)   SurfaceNode (core::pack::interaction_graph)   
CartesianMultifunc (core::optimization)   FragStore (core::fragment)   MPQuickRelaxMover (protocols::membrane)   ResiduesInInterfaceFilter (protocols::simple_filters)   SurfaceOrientMover (protocols::surface_docking)   
CartesianSampler (protocols::hybridization)   DbTrajectoryRecorder::Frame (protocols::canonical_sampling)   MPQuickRelaxMoverCreator (protocols::membrane)   ResiduesInInterfaceFilterCreator (protocols::simple_filters)   SurfaceParameters (protocols::surface_docking)   
CartesianSamplerCreator (protocols::hybridization)   Frame (core::fragment)   MPRangeRelaxMover (protocols::relax::membrane)   ResidueSpanSelector (core::select::residue_selector)   SurfacePotential (core::pack::interaction_graph)   
CartesianSearchPattern (protocols::hotspot_hashing)   DbTrajectoryWriter::Frame (protocols::trajectory)   MPResidueLipophilicityEnergy (core::energy_methods)   ResidueSpanSelectorCreator (core::select::residue_selector)   SurfaceSearchPattern (protocols::hotspot_hashing)   
CartGrid (core::grid)   FrameIterator (core::fragment)   MPResidueLipophilicityEnergyCreator (core::energy_methods)   ResidueSummaryMetric (core::simple_metrics::metrics)   SurfaceVectorLoader (protocols::surface_docking)   
CartSCMinMinimizerMap (core::pack::scmin)   FrameIteratorWorker_ (core::fragment)   MPSpanAngleEnergy (core::energy_methods)   ResidueSummaryMetricCreator (core::simple_metrics::metrics)   SurfaceVectorLoaderCreator (protocols::surface_docking)   
CartSCMinMultifunc (core::pack::scmin)   FrameList (core::fragment)   MPSpanAngleEnergyCreator (core::energy_methods)   ResidueTorsionRestraints (protocols::ligand_docking)   SurfEnergy (core::energy_methods)   
CatPiCalculator (protocols::pose_metric_calculators)   FrameListIterator_ (core::fragment)   MPSpanAngleFilter (protocols::simple_filters)   ResidueTotalScoresFeatures (protocols::features)   SurfEnergyCreator (core::energy_methods)   
CavityBall (core::scoring::packstat)   FrameWork (protocols::antibody)   MPSpanAngleFilterCreator (protocols::simple_filters)   ResidueTotalScoresFeaturesCreator (protocols::features)   SurfVol (core::scoring::packing)   
CavityBallCluster (core::scoring::packstat)   FreeDOF_Energy (core::energy_methods)   MPSpanInsertionEnergy (core::energy_methods)   ResidueType (core::chemical)   SurfVolDeriv (core::scoring::packing)   
CavityCalculator (protocols::denovo_design::calculators)   FreeDOF_EnergyCreator (core::energy_methods)   MPSpanInsertionEnergyCreator (core::energy_methods)   ResidueTypeBase (core::chemical)   SurfVolEnergy (core::energy_methods)   
CavityVolumeFilter (protocols::denovo_design::filters)   FreeDOF_Options (core::scoring::methods)   MPSymDockMover (protocols::symmetric_docking::membrane)   ResidueTypeConstraint (core::scoring::constraints)   SurfVolEnergyCreator (core::energy_methods)   
CavityVolumeFilterCreator (protocols::denovo_design::filters)   FreePeptide (protocols::backbone_moves::local_backbone_mover)   MPSymDockMoverCreator (protocols::symmetric_docking::membrane)   ResidueTypeConstraintGenerator (protocols::constraint_generator)   SurrogateVariableExpression (protocols::pack_daemon)   
CB_Angle_Func (core::scoring::disulfides)   FreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers)   MPTerminiPenalty (core::scoring::membrane)   ResidueTypeConstraintGeneratorCreator (protocols::constraint_generator)   SurroundingSS (protocols::denovo_design::task_operations)   
Cb_Distance_Func (core::scoring::disulfides)   FromScratchMover (protocols::stepwise::monte_carlo::mover)   MPTerminiPenaltyCreator (core::scoring::membrane)   ResidueTypeConstraintMover (protocols::constraint_movers)   SWAligner (core::sequence)   
CBScore (protocols::sic_dock)   FromScratchMoverCreator (protocols::stepwise::monte_carlo::mover)   MPTMProjPenalty (core::scoring::membrane)   ResidueTypeConstraintMoverCreator (protocols::constraint_movers)   SwapSegment (protocols::seeded_abinitio)   
CBScoreVisitor (protocols::sic_dock)   FullatomCustomPairDistanceEnergy (core::scoring::custom_pair_distance)   MPTMProjPenaltyCreator (core::scoring::membrane)   ResidueTypeFilter (core::pack::task::operation)   SwapSegmentCreator (protocols::seeded_abinitio)   
CBSG_Dihedral_Func (core::scoring::disulfides)   FullatomCustomPairDistanceEnergyCreator (core::scoring::custom_pair_distance)   MRMover (protocols::hybridization)   ResidueTypeFilterCreator (core::pack::task::operation)   SwitchChainOrderMover (protocols::simple_moves)   
CCDEndsGraftMover (protocols::grafting)   FullatomDisulfideEnergy (core::energy_methods)   MRSJob (protocols::multistage_rosetta_scripts)   ResidueTypeFinder (core::chemical)   SwitchChainOrderMoverCreator (protocols::simple_moves)   
CCDEndsGraftMoverCreator (protocols::grafting)   FullatomDisulfideEnergyComponents (core::scoring::disulfides)   MRSJobQueen (protocols::multistage_rosetta_scripts)   ResidueTypeKinWriter (core::chemical)   SwitchMover (protocols::moves)   
CCDLoopClosureMover (protocols::loops::loop_closure::ccd)   FullatomDisulfideEnergyContainer (core::scoring::disulfides)   MRSJobQueenChecker (protocols::multistage_rosetta_scripts)   ResidueTypeLinkingConstraint (core::scoring::constraints)   SwitchMoverCreator (protocols::moves)   
CCDLoopClosureMoverCreator (protocols::loops::loop_closure::ccd)   FullatomDisulfideEnergyCreator (core::energy_methods)   MRSJobSummary (protocols::multistage_rosetta_scripts)   ResidueTypeSelector (core::chemical)   SwitchResidueTypeSetMover (protocols::simple_moves)   
CCDMoveWrapper (protocols::rbsegment_relax)   FullatomDisulfideParams13 (core::scoring::disulfides)   MSDMover (protocols::recon_design)   ResidueTypeSelectorSingle (core::chemical)   SwitchResidueTypeSetMoverCreator (protocols::simple_moves)   
CCluster (protocols::pockets)   FullatomDisulfidePotential (core::scoring::disulfides)   MSDMoverCreator (protocols::recon_design)   ResidueTypeSet (core::chemical)   SymAtomTreeMinimizer (core::optimization::symmetry)   
CClusterSet (protocols::pockets)   FullatomRelaxMover (protocols::surface_docking)   MulliganPNearEvaluator (protocols::toolbox)   ResidueTypeSetCache (core::chemical)   SymAtomTreeMultifunc (core::optimization::symmetry)   
CDRCluster (protocols::antibody::clusters)   FullAtomRNA_Fragments (core::fragment::rna)   MultiConstraint (core::scoring::constraints)   ResidueTypesFeatures (protocols::features)   SymDockBaseProtocol (protocols::symmetric_docking)   
CDRClusterEnumManager (protocols::antibody::clusters)   FullChiSampleSet (protocols::match::upstream)   MultiConstraintCreator (core::scoring::constraints)   ResidueTypesFeaturesCreator (protocols::features)   SymDockingHiRes (protocols::symmetric_docking)   
CDRClusterFeatures (protocols::antibody::clusters)   FullModelInfo (core::pose::full_model_info)   MultiCoolAnnealer (core::pack::annealer)   ResidueVector (core::select::residue_selector)   SymDockingInitialPerturbation (protocols::symmetry)   
CDRClusterFeaturesCreator (protocols::antibody::clusters)   FullModelInnerLarvalJob (protocols::jd3::full_model)   Multifunc (core::optimization)   ResidueVicinityCstGeneratorCreator (protocols::forge::remodel)   SymDockingLowRes (protocols::symmetric_docking)   
CDRClusterMatcher (protocols::antibody::clusters)   FullModelInputSource (protocols::jd3::full_model_inputters)   MultiObjective (protocols::mpi_refinement)   ResidueVicinityInfo (protocols::forge::remodel)   SymDockingSlideIntoContact (protocols::symmetry)   
CDRClusterSet (protocols::antibody::clusters)   FullModelInputter (protocols::jd3::full_model_inputters)   MultiPhosphateSampler (protocols::stepwise::modeler::rna::phosphate)   ResidueVicinityRCG (protocols::forge::remodel)   SymDockProtocol (protocols::symmetric_docking)   
CDRDBPose (protocols::antibody)   FullModelInputterCreator (protocols::jd3::full_model_inputters)   MultipleDomainMover (protocols::rna::denovo::coarse)   ResidueXYZ (core::scoring::func)   SymDockProtocolCreator (protocols::symmetric_docking)   
CDRDBSequence (protocols::antibody)   FullModelInputterFactory (protocols::jd3::full_model_inputters)   MultipleOutputSpecification (protocols::jd3::output)   ResInteractions (protocols::toolbox::match_enzdes_util)   SymDof (core::conformation::symmetry)   
CDRDihedralConstraintMover (protocols::antibody::constraints)   FullModelInputterRegistrator (protocols::jd3::full_model_inputters)   MultipleOutputter (protocols::jd3::output)   ResLvlTaskOperation (core::pack::task::operation)   SymDofMover (protocols::matdes)   
CDRDihedralConstraintMoverCreator (protocols::antibody::constraints)   FullModelJobQueen (protocols::jd3::full_model)   MultipleOutputWrapper (protocols::rosetta_scripts)   ResLvlTaskOperationCreator (core::pack::task::operation)   SymDofMoverCreator (protocols::matdes)   
CDRGraftDesignOptions (protocols::antibody::design)   FullModelParameters (core::pose::full_model_info)   MultipleOutputWrapperCreator (protocols::rosetta_scripts)   ResLvlTaskOperationFactory (core::pack::task::operation)   SymDofMoverSampler (protocols::matdes)   
CDRGraftDesignOptionsParser (protocols::antibody::design)   FullModelPoseBuilder (core::import_pose)   MultiplePoseMover (protocols::rosetta_scripts)   ResLvlTaskOperationLoader (protocols::parser)   SymEnergyCutRotamerTrialsMover (protocols::minimization_packing::symmetry)   
CDRH3Modeler (protocols::antibody_legacy)   FullModelPreliminaryLarvalJob (protocols::jd3::full_model)   MultiplePoseMoverCreator (protocols::rosetta_scripts)   ResLvlTaskOperationLoaderCreator (protocols::parser)   SymFoldandDockMoveRbJumpMover (protocols::symmetric_docking)   
CDRResidueSelector (protocols::antibody::residue_selector)   Func (core::scoring::func)   MultipleSigmoids (protocols::calc_taskop_filters)   ResLvlTaskOperationRegistrator (core::pack::task::operation)   SymFoldandDockMoveRbJumpMoverCreator (protocols::symmetric_docking)   
CDRResidueSelectorCreator (protocols::antibody::residue_selector)   FuncFactory (core::scoring::func)   MultipleSigmoidsFilterCreator (protocols::calc_taskop_filters)   ResMut (protocols::constel)   SymFoldandDockRbTrialMover (protocols::symmetric_docking)   
CDRSeqDesignOptions (protocols::antibody::design)   FunGroupTK (protocols::kinmatch)   MultiplexedAnnealableGraph (core::pack::interaction_graph)   DisulfideFile::ResNum (core::io::raw_data)   SymFoldandDockRbTrialMoverCreator (protocols::symmetric_docking)   
CDRSeqDesignOptionsParser (protocols::antibody::design)   
  G  
MultipoleElecEnergy (core::energy_methods)   ResnumFromStringsWithRangesSelector (protocols::antibody::design)   SymFoldandDockSlideTrialMover (protocols::symmetric_docking)   
CDRSetOptions (protocols::antibody)   MultipoleElecEnergyCreator (core::energy_methods)   ResolutionSwitcher (protocols::abinitio)   SymFoldandDockSlideTrialMoverCreator (protocols::symmetric_docking)   
CDRSetOptionsParser (protocols::antibody)   G   MultipoleElecPoseInfo (core::scoring)   Resonance (protocols::noesy_assign)   SymInterfaceSidechainMinMover (protocols::symmetric_docking)   
CDRsMinPackMin (protocols::antibody)   GA_Minimizer (core::optimization)   MultipoleElecPotential (core::scoring)   ResonanceList (protocols::noesy_assign)   SymmData (core::conformation::symmetry)   
Cell (core::sequence)   GADockStageParams (protocols::ligand_docking::ga_ligand_dock)   MultipoleElecResidueInfo (core::scoring)   ResourceDeallocationMessage (protocols::jd3::deallocation)   SymmDataLoader (core::conformation::symmetry)   
Cen_Distance_Func (core::scoring::disulfides)   GALigandDock (protocols::ligand_docking::ga_ligand_dock)   MultipoleElecResPairMinData (core::energy_methods)   RespairInteractions (core::scoring::custom_pair_distance)   SymmDataLoaderCreator (core::conformation::symmetry)   
CenHBEnergy (core::energy_methods)   GALigandDockCreator (protocols::ligand_docking::ga_ligand_dock)   MultipoleElecRotamerSetInfo (core::scoring)   ResPairMinimizationData (core::scoring)   SymmetricAddMembraneMover (protocols::membrane::symmetry)   
CenHBEnergyCreator (core::energy_methods)   GAOptimizer (protocols::ligand_docking::ga_ligand_dock)   MultipoleParameter (core::scoring)   ResPairMotif (core::scoring::motif)   SymmetricAddMembraneMoverCreator (protocols::membrane::symmetry)   
CenHBPotential (core::scoring)   GapCloser (protocols::backbone_moves::local_backbone_mover)   MultiProbePerSphereAccumulator (core::scoring::packstat)   ResPairMotifMetaBinner (core::scoring::motif)   SymmetricalResidueSelector (core::select::residue_selector)   
CenListInfo (core::scoring)   GapSolutionPicker (protocols::backbone_moves::local_backbone_mover::gap_solution_pickers)   MultiProbePoseAccumulator (core::scoring::packstat)   ResPairMotifQuery (core::scoring::motif)   SymmetricalResidueSelectorCreator (core::select::residue_selector)   
CenPairEnergy (core::energy_methods)   GasteigerAtomTypeData (core::chemical::gasteiger)   MultiStateAggregateFunction (protocols::multistate_design)   ResPairMotifs (core::scoring::motif)   SymmetricConformation (core::conformation::symmetry)   
CenPairEnergyCreator (core::energy_methods)   GasteigerAtomTypeSet (core::chemical::gasteiger)   MultistateAggregateFunction (protocols::pack_daemon)   ResPred (protocols::mean_field)   SymmetricCycpepAlign (protocols::cyclic_peptide)   
CenPairMotifDegreeEnergy (core::energy_methods)   GatherPosesMover (protocols::cluster)   MultiStateEntity (protocols::multistate_design)   ResRangePredicate (core::scoring)   SymmetricCycpepAlignCreator (protocols::cyclic_peptide)   
CenPairMotifDegreeEnergyCreator (core::energy_methods)   GaussianChainDoubleFunc (core::scoring::func)   MultistateFitnessFunction (protocols::pack_daemon)   ResResEnergyInvoker (core::scoring::etable)   SymmetricEnergies (core::scoring::symmetry)   
CenPairMotifEnergy (core::energy_methods)   GaussianChainFunc (core::scoring::func)   MultiStateFitnessFunction (protocols::multistate_design)   ResSingleMinimizationData (core::scoring)   SymmetricFragmentMover (protocols::simple_moves)   
CenPairMotifEnergyCreator (core::energy_methods)   GaussianChainFuncPotentialEvaluator (core::scoring::loop_graph::evaluator)   MultiStatePacker (protocols::multistate_design)   ResTorsions (protocols::loop_grower)   SymmetricLigandEnergy (core::energy_methods)   
CenRotDunEnergy (core::pack::dunbrack::cenrot)   GaussianChainGeneralFunc (core::scoring::func)   MultiTemperatureTrialCounter (protocols::canonical_sampling)   RestrictAbsentCanonicalAAS (core::pack::task::operation)   SymmetricLigandEnergyCreator (core::energy_methods)   
CenRotDunEnergyCreator (core::pack::dunbrack::cenrot)   GaussianChainQuadrupleFunc (core::scoring::func)   MultiThreadingJob (protocols::jd2)   RestrictAbsentCanonicalAASCreator (core::pack::task::operation)   SymmetricMotifFilter (protocols::simple_filters)   
CenRotEnvEnergy (core::energy_methods)   GaussianChainSingleFunc (core::scoring::func)   MultiThreadingMover (protocols::comparative_modeling)   RestrictAbsentCanonicalAASExceptNativeRLT (core::pack::task::operation)   SymmetricMotifFilterCreator (protocols::simple_filters)   
CenRotEnvEnergyCreator (core::energy_methods)   GaussianChainTripleFunc (core::scoring::func)   MutableChiRecord (core::chemical)   RestrictAbsentCanonicalAASExceptNativeRLTCreator (core::pack::task::operation)   SymmetricRmsdEvaluator (protocols::simple_filters)   
CenRotEnvPairPotential (core::scoring)   GaussianFunc (core::scoring::func)   MutableICoorRecord (core::chemical)   RestrictAbsentCanonicalAASRLT (core::pack::task::operation)   SymmetricRMSMover (protocols::symmetry)   
CenrotLibrary (core::pack::dunbrack::cenrot)   GaussianOverlapEnergy (core::energy_methods)   MutableResidueConnection (core::chemical)   RestrictAbsentCanonicalAASRLTCreator (core::pack::task::operation)   SymmetricRotamerSet_ (core::pack::rotamer_set::symmetry)   
CenRotPairEnergy (core::energy_methods)   GaussianOverlapEnergyCreator (core::energy_methods)   MutableResidueType (core::chemical)   RestrictByCalculatorsOperation (protocols::task_operations)   SymmetricRotamerSets (core::pack::rotamer_set::symmetry)   
CenRotPairEnergyCreator (core::energy_methods)   GaussianParameter (core::chemical::rna)   Mutant (protocols::pmut_scan)   RestrictByCalculatorsOperationCreator (protocols::task_operations)   SymmetricScoreFunction (core::scoring::symmetry)   
CenrotRotamerLibrarySpecification (core::chemical::rotamers)   GaussianRBSegmentMover (protocols::rbsegment_relax)   MutantPosition (protocols::antibody::design)   RestrictChainToRepackingOperation (protocols::task_operations)   SymmetryClaim (protocols::topology_broker::claims)   
CenrotRotamerLibrarySpecificationCreator (core::chemical::rotamers)   GDB (protocols::sparta)   Mutate1Randomizer (protocols::genetic_algorithm)   RestrictChainToRepackingOperationCreator (protocols::task_operations)   SymmetryClaimer (protocols::topology_broker)   
CentroidDistanceScreener (protocols::stepwise::screener)   GenBondedExclInfo (core::scoring)   MutateFrameworkForCluster (protocols::antibody::design)   RestrictConservedLowDdgOperation (protocols::task_operations)   SymmetryInfo (core::conformation::symmetry)   
CentroidDisulfideEnergy (core::energy_methods)   GenBornEnergy (core::energy_methods)   MutateFrameworkForClusterCreator (protocols::antibody::design)   RestrictConservedLowDdgOperationCreator (protocols::task_operations)   SymmetrySlider (protocols::symmetry)   
CentroidDisulfideEnergyComponents (core::scoring::disulfides)   GenBornEnergyCreator (core::energy_methods)   MutateResidue (protocols::simple_moves)   RestrictDesignToProteinDNAInterface (protocols::dna)   SymmetryTransform (core::conformation::symmetry)   
CentroidDisulfideEnergyContainer (core::scoring::disulfides)   GenBornPoseInfo (core::scoring)   MutateResidueCreator (protocols::simple_moves)   RestrictDesignToProteinDNAInterfaceCreator (protocols::dna)   SymMinimizerMap (core::optimization::symmetry)   
CentroidDisulfideEnergyCreator (core::energy_methods)   GenBornPotential (core::scoring)   MutationData (protocols::pmut_scan)   RestrictIdentitiesAtAlignedPositionsOperation (protocols::task_operations)   SymMinMover (protocols::minimization_packing::symmetry)   
CentroidDisulfideNeighborConstIterator (core::scoring::disulfides)   GenBornResidueInfo (core::scoring)   MutationSetDesignOperation (protocols::task_operations)   RestrictIdentitiesAtAlignedPositionsOperationCreator (protocols::task_operations)   SymMinMoverCreator (protocols::minimization_packing::symmetry)   
CentroidDisulfideNeighborIterator (core::scoring::disulfides)   GenBornRotamerSetInfo (core::scoring)   MutationsFilter (protocols::simple_filters)   RestrictIdentitiesOperation (protocols::task_operations)   SymmLinearMemEdge (core::pack::interaction_graph)   
CentroidDisulfidePotential (core::scoring::disulfides)   GeneralAntibodyModeler (protocols::antibody::design)   MutationsFilterCreator (protocols::simple_filters)   RestrictIdentitiesOperationCreator (protocols::task_operations)   SymmLinearMemNode (core::pack::interaction_graph)   
CentroidRelax (protocols::relax)   GeneralEvent (core::pose::signals)   MyAtom (protocols::fldsgn)   RestrictInteractionGraphThreadsOperation (core::pack::task::operation)   SymmLinearMemoryInteractionGraph (core::pack::interaction_graph)   
CentroidRelaxMover (protocols::surface_docking)   GeneralEvent (core::conformation::signals)   MyHash (core::scoring::motif)   RestrictInteractionGraphThreadsOperationCreator (core::pack::task::operation)   SymmMinimalistEdge (core::pack::interaction_graph)   
CentroidRotamerSampleData (core::pack::dunbrack::cenrot)   GeneralizedKIC (protocols::generalized_kinematic_closure)   MyPred (core::scoring::motif)   RestrictInterGroupVectorOperation (protocols::task_operations)   SymmMinimalistInteractionGraph (core::pack::interaction_graph)   
CentroidRotNum (protocols::make_rot_lib)   GeneralizedKICCreator (protocols::generalized_kinematic_closure)   MyTemplatePointerHash1 (core::pack::guidance_scoreterms::sap)   RestrictInterGroupVectorOperationCreator (protocols::task_operations)   SymmMinimalistNode (core::pack::interaction_graph)   
CentroidScatter (core::scoring::fiber_diffraction)   GeneralizedKICfilter (protocols::generalized_kinematic_closure::filter)   
  N  
RestrictNativeResiduesOperation (protocols::task_operations)   SymmOnTheFlyEdge (core::pack::interaction_graph)   
Chain (protocols::pose_length_moves)   GeneralizedKICperturber (protocols::generalized_kinematic_closure::perturber)   RestrictNativeResiduesOperationCreator (protocols::task_operations)   SymmOnTheFlyInteractionGraph (core::pack::interaction_graph)   
ChainBreak (protocols::simple_filters)   GeneralizedKICselector (protocols::generalized_kinematic_closure::selector)   NamedAngleConstraint (core::scoring::constraints)   RestrictNonSurfaceToRepackingOperation (protocols::task_operations)   SymmOnTheFlyNode (core::pack::interaction_graph)   
ChainbreakDistFunc (protocols::jumping)   GenerateMainchainPotential (protocols::mainchain_potential)   NamedAngleConstraintCreator (core::scoring::constraints)   RestrictNonSurfaceToRepackingOperationCreator (protocols::task_operations)   SymPackRotamersMover (protocols::minimization_packing::symmetry)   
ChainbreakEnergy (core::energy_methods)   GenerateMainchainPotentialOptions (protocols::mainchain_potential)   NamedAtomID (core::id)   RestrictOperationsBase (protocols::task_operations)   SymPackRotamersMoverCreator (protocols::minimization_packing::symmetry)   
ChainbreakEnergyCreator (core::energy_methods)   GenerateStoredRBConfs (protocols::enzdes)   NamedAtomID_Map (core::id)   RestrictResiduesToRepackingOperation (protocols::task_operations)   SymRestrictTaskForDocking (protocols::symmetric_docking)   
ChainBreakFilterCreator (protocols::simple_filters)   GenericBondedEnergy (core::energy_methods)   NamedAtomID_Map_NamedAtomID (core::id)   RestrictResiduesToRepackingOperationCreator (protocols::task_operations)   SymRotamerTrialsMover (protocols::minimization_packing::symmetry)   
ChainbreakUtil (core::util)   GenericBondedEnergyCreator (core::energy_methods)   NamedAtomPairConstraint (core::scoring::constraints)   RestrictResidueToRepacking (core::pack::task::operation)   SymRotamerTrialsMoverCreator (protocols::minimization_packing::symmetry)   
ChainCountFilter (protocols::simple_filters)   GenericBondedPotential (core::scoring)   NamedAtomPairConstraintCreator (protocols::constraints_additional)   RestrictResidueToRepackingCreator (core::pack::task::operation)   SymShakeStructureMover (protocols::symmetry)   
ChainCountFilterCreator (protocols::simple_filters)   GenericJobInputter (protocols::comparative_modeling)   NamedAtomPairConstraintCreator (core::scoring::constraints)   RestrictToAlignedSegmentsOperation (protocols::task_operations)   SymSidechainMinMover (protocols::symmetric_docking)   
ChainExistsFilter (protocols::ligand_docking)   GenericJobInputterCreator (protocols::comparative_modeling)   NamedDihedralConstraint (core::scoring::constraints)   RestrictToAlignedSegmentsOperationCreator (protocols::task_operations)   SymSlideInfo (core::conformation::symmetry)   
ChainExistsFilterCreator (protocols::ligand_docking)   GenericMonteCarloMover (protocols::monte_carlo)   NamedSegmentSelector (protocols::denovo_design::residue_selectors)   RestrictToCDRH3Loop (protocols::task_operations)   SymUnsatHbondFilter (protocols::matdes)   
ChainGroupDiscriminator (protocols::minimization_packing)   GenericMonteCarloMoverCreator (protocols::monte_carlo)   NamedSegmentSelectorCreator (protocols::denovo_design::residue_selectors)   RestrictToCDRH3LoopCreator (protocols::task_operations)   SymUnsatHbondFilterCreator (protocols::matdes)   
ChainIs (core::pack::task::operation)   GenericRemodelConstraintGenerator (protocols::forge::remodel)   NamedSolution (protocols::denovo_design::components)   RestrictToCDRsAndNeighbors (protocols::antibody::task_operations)   
  T  
ChainIsCreator (core::pack::task::operation)   GenericResidueConnectionData (core::scoring::etable::etrie)   NamedSolutions (protocols::denovo_design::components)   RestrictToCDRsAndNeighborsCreator (protocols::antibody::task_operations)   
ChainIsnt (core::pack::task::operation)   GenericSimulatedAnnealer (protocols::monte_carlo)   NamedStubID (core::id)   RestrictToInterface (protocols::simple_task_operations)   TableLookupEtableEnergy (core::scoring::etable)   
ChainIsntCreator (core::pack::task::operation)   GenericSimulatedAnnealerCreator (protocols::monte_carlo)   NATAA (core::pack::task)   RestrictToInterfaceCreator (protocols::simple_task_operations)   TableLookupEvaluator (core::scoring::etable)   
ResiduePDBIndexIs::ChainPos (core::pack::task::operation)   GeneticAlgorithm (protocols::genetic_algorithm)   NatbiasHelicesSheetPotential (protocols::fldsgn::potentials::sspot)   RestrictToInterfaceOperation (protocols::task_operations)   TabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
ChainSelector (core::select::residue_selector)   GeneticAlgorithmBase (protocols::genetic_algorithm)   NatbiasHelixPairPotential (protocols::fldsgn::potentials::sspot)   RestrictToInterfaceOperationCreator (protocols::task_operations)   TagDefinition (protocols::stepwise::screener)   
ChainSelectorCreator (core::select::residue_selector)   GenMeanFieldMover (protocols::mean_field)   NatbiasSecondaryStructureEnergy (protocols::fldsgn::potentials::sspot)   RestrictToInterfaceVectorOperation (protocols::task_operations)   TagManager (protocols::multistage_rosetta_scripts)   
ChainSplitMover (protocols::simple_moves)   GenMeanFieldMoverCreator (protocols::mean_field)   NatbiasSecondaryStructureEnergyCreator (protocols::fldsgn::potentials::sspot)   RestrictToInterfaceVectorOperationCreator (protocols::task_operations)   TagPoseWithRefinementStatsMover (protocols::cryst)   
ChainTerm (protocols::constel)   GenPharmacophore (protocols::pockets)   NatbiasStrandPairPotential (protocols::fldsgn::potentials::sspot)   RestrictToLoops (protocols::simple_task_operations)   TagPoseWithRefinementStatsMoverCreator (protocols::cryst)   
ChangeAncestory (core::chemical)   GenTorsionParams (core::scoring)   NativeAntibodySeq (protocols::antibody::design)   RestrictToLoopsAndNeighbors (protocols::simple_task_operations)   TailSegmentMover (protocols::splice)   
ChangeAndResetFoldTreeMover (protocols::simple_moves)   GeometricFunc (protocols::moves)   NativeEvaluatorCreator (protocols::simple_filters)   RestrictToLoopsAndNeighborsCreator (protocols::simple_task_operations)   TailSegmentMoverCreator (protocols::splice)   
ChangeAndResetFoldTreeMoverCreator (protocols::simple_moves)   GeometricRenameIsomorphismCallback (core::io::pose_from_sfr)   NativeSelector (protocols::residue_selectors)   RestrictToLoopsCreator (protocols::simple_task_operations)   TailsScoreMover (protocols::simple_moves)   
ChangeBondType (core::chemical)   GeometricRenameVerticiesEquivalent (core::io::pose_from_sfr)   NativeSelectorCreator (protocols::residue_selectors)   RestrictToMoveMapChiOperation (protocols::task_operations)   TalosSSSimilarity (protocols::frag_picker::scores)   
ChangeFoldTreeMover (protocols::moves)   GeometricSolEnergyEvaluator (core::scoring::geometric_solvation)   NATRO (core::pack::task)   RestrictToNeighborhoodOperation (protocols::task_operations)   TARGET (core::pack::task)   
ChargeAtom (protocols::qsar::scoring_grid)   GeometricSolvationFeatures (protocols::features)   NCAADefaultPackerPalette (core::pack::palette)   RestrictToNeighborhoodOperationCreator (protocols::task_operations)   TargetClashEnergy (protocols::scoring::methods)   
ChargeCalculator (protocols::pose_metric_calculators)   GeometricSolvationFeaturesCreator (protocols::features)   NCAADefaultPackerPaletteCreator (core::pack::palette)   RestrictToRepacking (core::pack::task::operation)   TargetClashEnergyCreator (protocols::scoring::methods)   
ChargeChargeFeatures (protocols::features)   GeometryFilter (protocols::score_filters)   NCAARotamerLibrarySpecification (core::chemical::rotamers)   RestrictToRepackingCreator (core::pack::task::operation)   TargetPocketGrid (protocols::pockets)   
ChargeChargeFeaturesCreator (protocols::features)   GeometryFilterCreator (protocols::score_filters)   NCAARotamerLibrarySpecificationCreator (core::chemical::rotamers)   RestrictToRepackingRLT (core::pack::task::operation)   TargetRotamerCoords (protocols::match::downstream)   
CHARGED (core::pack::task)   GeometrySecMatchRPE (protocols::match::downstream)   NCAARotLibBBTorsions (core::chemical)   RestrictToRepackingRLTCreator (core::pack::task::operation)   TaskAwareCsts (protocols::protein_interface_design::movers)   
ChargeGrid (protocols::qsar::scoring_grid)   GeomSampleInfo (protocols::toolbox::match_enzdes_util)   NCAARotLibNumRotamerBins (core::chemical)   RestrictToResidueProperties (core::pack::task::operation)   TaskAwareCstsCreator (protocols::protein_interface_design::movers)   
ChargeGridCreator (protocols::qsar::scoring_grid)   GetRBDOFValues (protocols::matdes)   NCAARotLibPath (core::chemical)   RestrictToResiduePropertiesCreator (core::pack::task::operation)   TaskAwareMinMover (protocols::minimization_packing)   
CharmmPeriodicFunc (core::scoring::func)   GetRBDOFValuesCreator (protocols::matdes)   NCaCaC_Dihedral_Func (core::scoring::disulfides)   RestrictToSpecifiedBaseResidueTypes (core::pack::task::operation)   TaskAwareMinMoverCreator (protocols::minimization_packing)   
CharPairHash (core::sequence)   GlobalResidueTypeSet (core::chemical)   NcbbDockDesignProtocol (protocols::ncbb)   RestrictToSpecifiedBaseResidueTypesCreator (core::pack::task::operation)   TaskAwareSASAFilter (protocols::simple_filters)   
CheckPointer (protocols::checkpoint)   GlycanInfoMover (protocols::analysis)   NcbbDockDesignProtocolCreator (protocols::ncbb)   RestrictToTerminiOperation (protocols::task_operations)   TaskAwareSASAFilterCreator (protocols::simple_filters)   
ChemicalManager (core::chemical)   GlycanInfoMoverCreator (protocols::analysis)   NcontactsCalculator (protocols::fldsgn)   RestrictToTerminiOperationCreator (protocols::task_operations)   TaskAwareScoreTypeFilter (protocols::simple_filters)   
ChemicalShiftAnisotropy (core::scoring)   GlycanLayerSelector (core::select::residue_selector)   NcontactsFilter (protocols::fldsgn::filters)   RestrictYSDesign (core::pack::task::operation)   TaskAwareScoreTypeFilterCreator (protocols::simple_filters)   
ChemicalShiftAnisotropyEnergy (core::energy_methods)   GlycanLayerSelectorCreator (core::select::residue_selector)   NcontactsFilterCreator (protocols::fldsgn::filters)   RestrictYSDesignCreator (core::pack::task::operation)   TaskAwareSymMinMover (protocols::minimization_packing::symmetry)   
ChemicalShiftAnisotropyEnergyCreator (core::energy_methods)   GlycanNode (core::conformation::carbohydrates)   NCSResMapping (protocols::symmetry)   RestypeDestructionEvent (core::chemical)   TaskAwareSymMinMoverCreator (protocols::minimization_packing::symmetry)   
ChemicalShiftData (core::scoring::rna::chemical_shift)   GlycanPositionSelector (core::select::residue_selector)   NearNativeLoopCloser (protocols::pose_length_moves)   ResTypeFragmentMover (protocols::simple_moves)   TaskFactory (core::pack::task)   
ChemicalShiftEvaluator (protocols::sparta)   GlycanPositionSelectorCreator (core::select::residue_selector)   NearNativeLoopCloserCreator (protocols::pose_length_moves)   ResTypeSequence_lt (protocols::dna)   TaskOperationFeatures::Taskop_id_name_factory_ (protocols::features)   
ChemicalShiftEvaluatorCreator (protocols::sparta)   GlycanResidueSelector (core::select::residue_selector)   NeighborDependentTabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   RestypeToRDMol (core::chemical::rdkit)   TaskOperation (core::pack::task::operation)   
ChemicalShiftScoringScheme (core::sequence)   GlycanResidueSelectorCreator (core::select::residue_selector)   NeighborDependentTorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   ResultDB (protocols::electron_density)   TaskOperationCreator (core::pack::task::operation)   
ChemicalShiftSequence (core::sequence)   GlycanSampler (protocols::carbohydrates)   Neighborhood (protocols::neighbor)   ResultElements (protocols::jd3::dag_node_managers)   TaskOperationFactory (core::pack::task::operation)   
ChemicalShiftSequenceCreator (core::sequence)   GlycanSamplerCreator (protocols::carbohydrates)   NeighborhoodByDistanceCalculator (protocols::pose_metric_calculators)   ResultOutputter (protocols::jd3::output)   TaskOperationFeatures (protocols::features)   
CheshireCell (protocols::cryst)   GlycanSequonsSelector (core::select::residue_selector)   NeighborhoodResidueSelector (core::select::residue_selector)   RetrieveStoredTaskOperation (protocols::task_operations)   TaskOperationFeaturesCreator (protocols::features)   
ChiAngleNormalization (protocols::qsar::scoring_grid)   GlycanSequonsSelectorCreator (core::select::residue_selector)   NeighborhoodResidueSelectorCreator (core::select::residue_selector)   RetrieveStoredTaskOperationCreator (protocols::task_operations)   TaskOperationLoader (protocols::parser)   
CHIDihedralSamplingData (core::scoring::carbohydrates)   GlycanTree (core::conformation::carbohydrates)   NeighborList (core::scoring)   ReturnResidueSubsetSelector (core::select::residue_selector)   TaskOperationLoaderCreator (protocols::parser)   
CHIEnergyFunction (core::scoring::carbohydrates)   GlycanTreeMinMover (protocols::carbohydrates)   NeighborListData (core::scoring::methods)   ReturnSidechainMover (protocols::simple_moves)   TaskOperationMPM (protocols::match)   
ChiInfo (protocols::ligand_docking::ga_ligand_dock)   GlycanTreeMinMoverCreator (protocols::carbohydrates)   NeighborsByDistanceCalculator (protocols::pose_metric_calculators)   Reversion (protocols::dna)   TaskOperationRegistrator (core::pack::task::operation)   
ChiralFlipAtoms (core::chemical)   GlycanTreeModeler (protocols::carbohydrates)   NeighborTypeFilter (protocols::simple_filters)   Revert (protocols::protein_interface_design)   TaskSelector (protocols::residue_selectors)   
ChiralFlipNaming (core::chemical)   GlycanTreeModelerCreator (protocols::carbohydrates)   NeighborTypeFilterCreator (protocols::simple_filters)   ReweightableRepEnergy (protocols::ligand_docking::ga_ligand_dock)   TaskSelectorCreator (protocols::residue_selectors)   
ChiralMover (protocols::simple_moves::chiral)   GlycanTreeSet (core::conformation::carbohydrates)   NeighTeller (protocols::constel)   ReweightData (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty)   TautomerizeAnomerMover (protocols::carbohydrates)   
ChiSet (core::pack::dunbrack)   GlycanTreeSetObserver (core::conformation::carbohydrates)   NelderMeadSimplex (core::optimization)   RG_Energy_Fast (core::energy_methods)   TautomerizeAnomerMoverCreator (protocols::carbohydrates)   
ChiWellRmsdEvaluator (protocols::simple_filters)   GlycopeptideDockingFlags (protocols::glycopeptide_docking)   NestedEnergyTermDDGMutationOptEData (protocols::optimize_weights)   RG_Energy_FastCreator (core::energy_methods)   TBMB_Helper (protocols::cyclic_peptide::crosslinker)   
ChiWellRmsdEvaluatorCreator (protocols::simple_filters)   GlycopeptideDockingHighResRefinement (protocols::glycopeptide_docking)   NestedEnergyTermPNatAAOptEPositionData (protocols::optimize_weights)   RG_Energy_RNA (core::energy_methods)   TCRmodel (protocols::tcr)   
ChromophoreDataReader (protocols::chromophore)   GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking)   NetChargeConstraint (core::scoring::netcharge_energy)   RG_Energy_RNACreator (core::energy_methods)   TemperatureController (protocols::canonical_sampling)   
Chunk (protocols::nonlocal)   GlycopeptideDockingProtocol (protocols::glycopeptide_docking)   NetChargeEnergy (core::energy_methods)   RG_Local_MinData (core::energy_methods)   TemperedDocking (protocols::docking)   
SliceToMiniProteinMover::Chunk (protocols::pose_creation)   GlycopeptideDockingProtocolCreator (protocols::glycopeptide_docking)   NetChargeEnergyCreator (core::energy_methods)   RG_LocalEnergy (core::energy_methods)   TemperedDockingCreator (protocols::docking)   
ChunkLibraryInnerLarvalJob (protocols::jd3::chunk_library)   GlycosyltransferaseMover (protocols::enzymatic_movers)   NetChargeEnergySetup (core::scoring::netcharge_energy)   RG_LocalEnergyCreator (core::energy_methods)   TemperingBase (protocols::canonical_sampling)   
ChunkLibraryInputSource (protocols::jd3::chunk_library_inputters)   GlycosyltransferaseMoverCreator (protocols::enzymatic_movers)   NetChargeFilter (protocols::simple_filters)   RG_MinData (core::energy_methods)   Template (protocols::abinitio)   
ChunkLibraryInputter (protocols::jd3::chunk_library_inputters)   GoapEnergy (core::energy_methods)   NetChargeFilterCreator (protocols::simple_filters)   RGFilter (protocols::simple_filters)   TemplateFragmentClaimer (protocols::topology_broker)   
ChunkLibraryInputterCreator (protocols::jd3::chunk_library_inputters)   GoapEnergyCreator (core::energy_methods)   NetworkQueue (protocols::network)   RID_FileSource (core::pose)   TemplateHistory (protocols::hybridization)   
ChunkLibraryInputterFactory (protocols::jd3::chunk_library_inputters)   GoapRsdType (core::energy_methods)   NetworkState (protocols::hbnet)   RID_Source (core::pose)   TemplateJumpClaimer (protocols::topology_broker)   
ChunkLibraryInputterRegistrator (protocols::jd3::chunk_library_inputters)   GrabAllCollector (protocols::frag_picker)   NetworkStateScoreComparator (protocols::hbnet)   RigidBodyDeterministicSpinMover (protocols::rigid)   TemplateJumpSetup (protocols::abinitio)   
ChunkLibraryJobQueen (protocols::jd3::chunk_library)   GraftCDRLoopsProtocol (protocols::antibody)   NMerPSSMEnergy (core::scoring::methods)   RigidBodyDofPerturbMover (protocols::rigid)   Templates (protocols::abinitio)   
ChunkLibraryJobResult (protocols::jd3::chunk_library)   GraftedStemOptimizer (protocols::antibody)   NMerPSSMEnergyCreator (core::scoring::methods)   RigidBodyDofRandomizeMover (protocols::rigid)   TenANeighborEdge (core::scoring)   
ChunkLibraryPreliminaryLarvalJob (protocols::jd3::chunk_library)   Grafting_Base_Exception (protocols::antibody::grafting)   NMerPSSMEnergyFilter (protocols::simple_filters)   RigidBodyDofRandomTransMover (protocols::rigid)   TenANeighborGraph (core::scoring)   
ChunkSet (core::import_pose::libraries)   GraftMover (protocols::antibody_legacy)   NMerPSSMEnergyFilterCreator (protocols::simple_filters)   RigidBodyDofSeqPerturbMover (protocols::rigid)   TenANeighborNode (core::scoring)   
ChunkTrialMover (protocols::hybridization)   GraftMoverBase (protocols::grafting)   NMerRefEnergy (core::scoring::methods)   RigidBodyDofSeqRandomizeMover (protocols::rigid)   TensorsOptimizer (protocols::scoring::methods::pcs)   
Circle (core::scoring::packstat)   GraftOneCDRLoop (protocols::antibody)   NMerRefEnergyCreator (core::scoring::methods)   RigidBodyDofSeqTransMover (protocols::rigid)   TensorsOptimizer (protocols::scoring::methods::pcs2)   
CircularGeneral1D_Func (core::scoring::func)   GraftOneMover (protocols::antibody_legacy)   NMerSVMEnergy (core::scoring::methods)   RigidBodyDofTransMover (protocols::rigid)   TensorsOptimizer_Ts1 (protocols::scoring::methods::pcsTs1)   
CircularHarmonicFunc (core::scoring::func)   GraftSwitchMover (protocols::switches)   NMerSVMEnergyCreator (core::scoring::methods)   RigidBodyInfo (protocols::docking)   TensorsOptimizer_Ts2 (protocols::scoring::methods::pcsTs2)   
CircularPermutation (protocols::fldsgn)   GraftSwitchMoverCreator (protocols::switches)   NMerSVMEnergyFilter (protocols::simple_filters)   RigidBodyMotionMover (protocols::rigid)   TensorsOptimizer_Ts3 (protocols::scoring::methods::pcsTs3)   
CircularPermutationCreator (protocols::fldsgn)   GraphicsState (protocols::viewer)   NMerSVMEnergyFilterCreator (protocols::simple_filters)   RigidBodyMoveBaseRSO (protocols::toolbox::rotamer_set_operations)   TensorsOptimizer_Ts4 (protocols::scoring::methods::pcsTs4)   
CircularPermuteFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers)   GraphvizPropertyWriter (core::chemical)   NMRDataFactory (core::scoring::nmr)   RigidBodyMover (protocols::rigid)   TensorsOptimizerFix (protocols::scoring::methods::pcs2)   
CircularPowerFunc (core::scoring::func)   GraphvizPropertyWriter (core::io::pose_from_sfr)   NMRDummySpinlabelAtom (core::scoring::nmr)   RigidBodyMoveRSO (protocols::toolbox::rotamer_set_operations)   TensorsOptimizerSvd (protocols::scoring::methods::pcs2)   
CircularSigmoidalFunc (core::scoring::func)   GreedyKCenter (protocols::toolbox)   NMRDummySpinlabelConformer (core::scoring::nmr)   RigidBodyPerturbMover (protocols::rigid)   TerminiConstraintGenerator (protocols::constraint_generator)   
CircularSplineFunc (core::scoring::func)   GreedyOptMutationMover (protocols::design_opt)   NMRDummySpinlabelEnsemble (core::scoring::nmr)   RigidBodyPerturbNoCenterMover (protocols::rigid)   TerminiConstraintGeneratorCreator (protocols::constraint_generator)   
CisPeptideInformation (core::io)   GreedyOptMutationMoverCreator (protocols::design_opt)   NMRDummySpinlabelVoxelGrid (core::scoring::nmr)   RigidBodyPerturbNoCenterMoverCreator (protocols::rigid)   TerminusDistanceFilter (protocols::simple_filters)   
ClaimerMessage (protocols::topology_broker)   GreenPacker (protocols::minimization_packing)   NMRGridSearch (core::scoring::nmr)   RigidBodyPerturbRandomJumpMover (protocols::rigid)   TerminusDistanceFilterCreator (protocols::simple_filters)   
ClaimStrength (protocols::environment::claims)   GridBase (protocols::qsar::scoring_grid)   NMRSpinlabel (core::scoring::nmr)   RigidBodyRandomizeMover (protocols::rigid)   TerminusMotifScorer (protocols::sewing::scoring)   
ClashBasedRepackShell (core::pack::task::operation)   GridCreator (protocols::qsar::scoring_grid)   NMRTensor (core::scoring::nmr)   RigidBodyRandomTMHMover (protocols::topology_broker)   TerminusMotifScorerCreator (protocols::sewing::scoring)   
ClashBasedRepackShellCreator (core::pack::task::operation)   GriddedAtomTreeMultifunc (protocols::ligand_docking::ga_ligand_dock)   NO_ADDUCTS (core::pack::task)   RigidBodySilentStruct (core::io::silent)   TestCompositeRealMetric (core::simple_metrics)   
ClashBasedShellSelector (core::pack::task::residue_selector)   GridFactory (protocols::qsar::scoring_grid)   Node (protocols::toolbox)   RigidBodySilentStructCreator (core::io::silent)   TestCompositeRealMetricCreator (core::simple_metrics)   
ClashBasedShellSelectorCreator (core::pack::task::residue_selector)   GridHash3D (protocols::ligand_docking::ga_ligand_dock)   Node (core::kinematics)   RigidBodySpinMover (protocols::rigid)   TestCompositeStringMetric (core::simple_metrics)   
ClashCheckFilter (protocols::matdes)   GridInfo (core::energy_methods)   FoldTreeSketch::Node (core::environment)   RigidBodyStepWiseSampler (protocols::stepwise::sampler::rigid_body)   TestCompositeStringMetricCreator (core::simple_metrics)   
ClashCheckFilterCreator (protocols::matdes)   GridManager (protocols::qsar::scoring_grid)   NodeBase (core::pack::interaction_graph)   RigidBodyStepWiseSamplerValueRange (protocols::stepwise::sampler::rigid_body)   TestPattern (protocols::hotspot_hashing)   
ClashCountCalculator (protocols::pose_metric_calculators)   GridRegistrator (protocols::qsar::scoring_grid)   NodeManager (protocols::jd3::dag_node_managers)   RigidBodyStepWiseSamplerWithResidueAlternatives (protocols::stepwise::sampler::rigid_body)   TestPerResidueRealMetric (core::simple_metrics)   
ClashRequirement (protocols::sewing::requirements)   GridScorer (protocols::ligand_docking::ga_ligand_dock)   NodeManagerStorageMatrix (protocols::jd3::dag_node_managers)   RigidBodyStepWiseSamplerWithResidueList (protocols::stepwise::sampler::rigid_body)   TestPerResidueRealMetricCreator (core::simple_metrics)   
ClashRequirementCreator (protocols::sewing::requirements)   GridSearchIterator (protocols::scoring::methods::pcs)   NoDesignPackerPalette (core::pack::palette)   RigidBodyTiltMover (protocols::rigid)   TestPerResidueStringMetric (core::simple_metrics)   
ClashWithTargetFilter (protocols::protein_interface_design::filters)   GridSearchIterator_Ts1 (protocols::scoring::methods::pcsTs1)   NoDesignPackerPaletteCreator (core::pack::palette)   RigidBodyTiltMoverCreator (protocols::rigid)   TestPerResidueStringMetricCreator (core::simple_metrics)   
ClashWithTargetFilterCreator (protocols::protein_interface_design::filters)   GridSearchIterator_Ts2 (protocols::scoring::methods::pcsTs2)   NoesyModule (protocols::noesy_assign)   RigidBodyTransMover (protocols::rigid)   TestRealMetric (core::simple_metrics)   
ClassicAbinitio (protocols::abinitio)   GridSearchIterator_Ts3 (protocols::scoring::methods::pcsTs3)   NoFailDataMap (protocols::multistage_rosetta_scripts)   RigidBodyTransMoverCreator (protocols::rigid)   TestRealMetricCreator (core::simple_metrics)   
ClassicFragmentMover (protocols::simple_moves)   GridSearchIterator_Ts4 (protocols::scoring::methods::pcsTs4)   NomenclatureManager (core::io)   RigidChunkClaimer (protocols::topology_broker)   TestStringMetric (core::simple_metrics)   
ClassicGrid (protocols::qsar::scoring_grid)   GridSearchIteratorCA (protocols::scoring::methods::pcs2)   NonContinuousFrame (core::fragment)   RigidChunkCM (protocols::abinitio::abscript)   TestStringMetricCreator (core::simple_metrics)   
ClassicGridCreator (protocols::qsar::scoring_grid)   GridSet (protocols::qsar::scoring_grid)   NonlocalContactsCalculator (protocols::pose_metric_calculators)   RigidChunkCMCreator (protocols::abinitio::abscript)   TetherLigand (protocols::ligand_docking)   
ClassicMatchAlgorithm (protocols::match::downstream)   GroupDiscriminator (protocols::minimization_packing)   NonlocalFrags (protocols::frag_picker::nonlocal)   RigidDistanceVisitor (core::chemical)   TetrahedralMetal_Helper (protocols::cyclic_peptide::crosslinker)   
ClassicRelax (protocols::relax)   GroupElec (core::scoring::elec)   NonlocalPair (protocols::frag_picker::nonlocal)   RigidLigandBuilder (protocols::match::downstream)   TheozymeInvrotTree (protocols::toolbox::match_enzdes_util)   
ClassicRelaxCreator (protocols::relax)   GrowLeft (protocols::forge::build)   NonPlaidFingerprint (protocols::pockets)   RigidScore (protocols::sic_dock)   ThermalMinimizer (protocols::recces::scratch)   
ClearChiRotamers (core::chemical)   GrowLigand (protocols::ligand_docking)   NonResidueTypeConstraint (core::scoring::constraints)   RigidSearchMover (protocols::ligand_docking)   ThermalMinimizerCreator (protocols::recces::scratch)   
ClearCompositionConstraintsMover (protocols::aa_composition)   GrowLigandCreator (protocols::ligand_docking)   NonSequentialNeighborsFilter (protocols::simple_filters)   RingClosureEnergy (core::energy_methods)   ThermalSamplingMover (protocols::recces::scratch)   
ClearCompositionConstraintsMoverCreator (protocols::aa_composition)   GrowPeptides (protocols::seeded_abinitio)   NonSequentialNeighborsFilterCreator (protocols::simple_filters)   RingClosureEnergyCreator (core::energy_methods)   ThermalSamplingMoverCreator (protocols::recces::scratch)   
ClearConstraintsMover (protocols::constraint_movers)   GrowPeptidesCreator (protocols::seeded_abinitio)   NonTerminalStartingSegmentRequirement (protocols::sewing::requirements)   RingConformationMover (protocols::simple_moves)   ThermodynamicData (protocols::simple_moves)   
ClearConstraintsMoverCreator (protocols::constraint_movers)   GrowPeptidesSegment (protocols::seeded_abinitio)   NonTerminalStartingSegmentRequirementCreator (protocols::sewing::requirements)   RingConformationMoverCreator (protocols::simple_moves)   ThermodynamicMover (protocols::canonical_sampling)   
ClientMover (protocols::environment)   GrowRight (protocols::forge::build)   NoOutputJobOutputter (protocols::jd2)   RingConformer (core::chemical::rings)   ThermodynamicObserver (protocols::canonical_sampling)   
CloseContactResidueSelector (core::select::residue_selector)   GuardedLoopsFromFile (protocols::loops)   NoOutputJobOutputterCreator (protocols::jd2)   RingConformerManager (core::chemical::rings)   Thermostat (protocols::md)   
CloseContactResidueSelectorCreator (core::select::residue_selector)   GunnCost (protocols::simple_moves)   NoPoseXYX_Func (protocols::sic_dock)   RingConformerSet (core::chemical::rings)   ThreadingJob (protocols::comparative_modeling)   
CloseFold (protocols::seeded_abinitio)   GunnCost (protocols::frag_picker::scores)   NoRepackDisulfides (core::pack::task::operation)   RingData (protocols::sparta)   ThreadingJobInputter (protocols::comparative_modeling)   
CloseFoldCreator (protocols::seeded_abinitio)   GunnCostScore (protocols::frag_picker::scores)   NoRepackDisulfidesCreator (core::pack::task::operation)   RingPlaneFlipMover (protocols::carbohydrates)   ThreadingJobInputterCreator (protocols::comparative_modeling)   
CloseOneCDRLoop (protocols::antibody)   GunnTuple (protocols::simple_moves)   NoResFilter (core::pack::task::operation)   RingPlaneFlipMoverCreator (protocols::carbohydrates)   ThreadingMover (protocols::comparative_modeling)   
CloseOneMover (protocols::antibody_legacy)   GunnTuple (protocols::frag_picker::scores)   NoResFilterCreator (core::pack::task::operation)   RMS_Energy (core::energy_methods)   ThreadSequenceOperation (protocols::task_operations)   
CloserToAtom (core::scoring::sc)   
  H  
NormalizedEvaluatedArchive (protocols::jd2::archive)   RMS_EnergyCreator (core::energy_methods)   ThreadSequenceOperationCreator (protocols::task_operations)   
ClosureProblem (protocols::kinematic_closure)   NormalMode (protocols::normalmode)   RMSandEnergyCMP (core::scoring::motif)   TiltMover (protocols::membrane)   
ClosureSolution (protocols::kinematic_closure)   H3CterInsert (protocols::antibody)   NormalModeMinimizer (protocols::normalmode)   RMSComparator (protocols::loop_grower)   TiltMoverCreator (protocols::membrane)   
CloudPDBWriter (protocols::match::output)   H3PerturbCCD (protocols::antibody)   NormalModeMinimizerCreator (protocols::normalmode)   RmsdEvaluator (protocols::simple_filters)   TimeEvaluator (protocols::evaluation)   
Cluster (protocols::cluster)   H3RefineCCD (protocols::antibody)   NormalModeMultifunc (protocols::normalmode)   RmsdEvaluatorCreator (protocols::simple_filters)   TimeFilter (protocols::filters)   
Cluster_Member (protocols::stepwise::legacy::modeler::rna)   HackAroEnergy (core::energy_methods)   NormalModeRelaxMover (protocols::normalmode)   RmsdFilter (protocols::protein_interface_design::filters)   TimeFilterCreator (protocols::filters)   
ClusterBase (protocols::cluster)   HackAroEnergyCreator (core::energy_methods)   NormalModeRelaxMoverCreator (protocols::normalmode)   RmsdFilterCreator (protocols::protein_interface_design::filters)   Timer (protocols::checkpoint)   
ClusterBase (protocols::toolbox)   Hairpin (core::scoring)   NOTAA (core::pack::task)   RmsdFromResidueSelectorFilter (protocols::fold_from_loops::filters)   TimingProfileMetric (core::simple_metrics::metrics)   
ClusterData (protocols::antibody::clusters)   Hairpins (core::scoring)   NotJumpSelector (core::select::jump_selector)   RmsdFromResidueSelectorFilterCreator (protocols::fold_from_loops::filters)   TimingProfileMetricCreator (core::simple_metrics::metrics)   
Clusterer (protocols::mpi_refinement)   HamiltonianExchange (protocols::canonical_sampling)   NotJumpSelectorCreator (core::select::jump_selector)   RMSDMetric (core::simple_metrics::metrics)   TMA_Helper (protocols::cyclic_peptide::crosslinker)   
Clustering (protocols::cluster::calibur)   HamiltonianExchangeCreator (protocols::canonical_sampling)   NotResidueSelector (core::select::residue_selector)   RMSDMetricCreator (core::simple_metrics::metrics)   TMalign (protocols::hybridization)   
ClusterMetric (protocols::multistage_rosetta_scripts::cluster)   Hankel (core::scoring::fiber_diffraction)   NotResidueSelectorCreator (core::select::residue_selector)   RMSDReporter (protocols::pose_reporters)   TMHTopologySamplerClaimer (protocols::topology_broker)   
ClusterMetricCreator (protocols::multistage_rosetta_scripts::cluster)   HarmonicFunc (core::scoring::func)   NPDHBond (core::pack::interaction_graph)   RMSDReporterCreator (protocols::pose_reporters)   TMsAACompFilter (protocols::simple_filters)   
ClusterMetricFactory (protocols::multistage_rosetta_scripts::cluster)   HashEdge (protocols::legacy_sewing)   NPDHBondBackgroundEdge (core::pack::interaction_graph)   RmsdSimpleFilter (protocols::protein_interface_design::filters)   TMsAACompFilterCreator (protocols::simple_filters)   
ClusterMetricRegistrator (protocols::multistage_rosetta_scripts::cluster)   HashedSmartAssembly (protocols::sewing::data_storage)   NPDHBondBackgroundNode (core::pack::interaction_graph)   RmsdSimpleFilterCreator (protocols::protein_interface_design::filters)   TMscore (core::scoring)   
ClusterOptions (protocols::toolbox)   Hasher (protocols::legacy_sewing)   NPDHBondEdge (core::pack::interaction_graph)   RmsdTargetEvaluatorCreator (protocols::simple_filters)   TMscoreStore (core::scoring)   
ClusterPhilStyle (protocols::cluster)   Hasher (protocols::sewing::hashing)   NPDHBondEnergy (core::energy_methods)   RMSVallData (protocols::frags)   TMsSpanMembraneFilter (protocols::simple_filters)   
ClusterPhilStyle (protocols::toolbox)   HasherSettings (protocols::sewing::hashing)   NPDHBondEnergyCreator (core::energy_methods)   RNA_AddDeleteMonteCarlo (protocols::stepwise::monte_carlo::rna)   TMsSpanMembraneFilterCreator (protocols::simple_filters)   
ClusterPhilStyle_Loop (protocols::cluster)   HashResult (protocols::legacy_sewing)   NPDHBondInteractionGraph (core::pack::interaction_graph)   RNA_AnalyticLoopCloser (protocols::stepwise::legacy::modeler::rna)   TNA_SuiteEnergy (core::energy_methods)   
ClusterPhilStyle_PoseReporter (protocols::cluster)   HashValue (protocols::legacy_sewing)   NPDHBondNode (core::pack::interaction_graph)   RNA_AtomVDW (core::scoring::rna)   TNA_SuiteEnergyCreator (core::energy_methods)   
ClusterPoseSelector (protocols::pose_selectors)   HashValue (protocols::sewing::hashing)   NPDHBondSet (core::scoring::hbonds)   RNA_AtrRepChecker (protocols::stepwise::modeler::rna::checker)   TNA_SuitePotential (core::scoring::rna)   
ClusterPoseSelectorCreator (protocols::pose_selectors)   HbaGrid (protocols::qsar::scoring_grid)   NPDHBSimpleEdge (core::pack::interaction_graph)   RNA_AtrRepScreener (protocols::stepwise::legacy::screener)   ToolboxKeys (protocols::loop_modeling)   
RigidChunkClaimer::CM_SuggestFixResidue (protocols::topology_broker)   HbaGridCreator (protocols::qsar::scoring_grid)   NPDHBSimpleInteractionGraph (core::pack::interaction_graph)   RNA_BaseCentroidChecker (protocols::stepwise::modeler::rna::checker)   TopCountOfAllInputs (protocols::features)   
CmdLineData (protocols::topology_broker)   HBAtom (core::scoring::hbonds::hbtrie)   NPDHBSimpleNode (core::pack::interaction_graph)   RNA_BasePairHandler (core::import_pose)   TopCountOfEachInput (protocols::features)   
CoarseRNA_Fragments (protocols::rna::denovo::coarse)   HBCountPairFunction (core::scoring::hbonds::hbtrie)   NPDPropCalculator (protocols::pack_daemon)   RNA_BasicOptions (core::import_pose::options)   TopEntitySet (protocols::pack_daemon)   
CoarseRNA_LoopCloser (protocols::rna::denovo::coarse)   HBCPData (core::scoring::hbonds::hbtrie)   NPDPropCalculatorCreator (protocols::pack_daemon)   RNA_BulgeEnergy (core::energy_methods)   TopNByProperty (protocols::pose_selectors)   
COFilter (protocols::simple_filters)   HBDerivAssigner (core::scoring::hbonds)   NTerminalAcetyltransferaseMover (protocols::enzymatic_movers)   RNA_BulgeEnergyCreator (core::energy_methods)   TopNByPropertyCreator (protocols::pose_selectors)   
ColorGradient (protocols::qsar)   HbdGrid (protocols::qsar::scoring_grid)   NTerminalAcetyltransferaseMoverCreator (protocols::enzymatic_movers)   RNA_CentroidInfo (core::scoring::rna)   TopNMotifScorer (protocols::sewing::scoring)   
Combine_Tags_Info (protocols::stepwise::modeler::rna)   HbdGridCreator (protocols::qsar::scoring_grid)   NtoCConstraintGenerator (protocols::forge::constraints)   RNA_ChainClosableGeometryChecker (protocols::stepwise::modeler::rna::checker)   TopNMotifScorerCreator (protocols::sewing::scoring)   
CombineChainsMover (protocols::domain_assembly)   HBEvalTuple (core::scoring::hbonds)   NtoCConstraintGeneratorCreator (protocols::forge::constraints)   RNA_ChainClosableGeometryResidueBasedScreener (protocols::stepwise::screener)   TopologyBroker (protocols::topology_broker)   
CombinedConstraintEvaluator (protocols::constraints_additional)   HBNet (protocols::hbnet)   Nub (protocols::fold_from_loops::utils)   RNA_ChainClosableGeometryScreener (protocols::stepwise::screener)   TopologyBrokerMover (protocols::protein_interface_design::movers)   
CombinedConstraintEvaluatorCreator (protocols::constraints_additional)   HBNetCreator (protocols::hbnet)   NubInitioLoopClosureMover (protocols::fold_from_loops::movers)   RNA_ChainClosableGeometryStubBasedScreener (protocols::stepwise::screener)   TopologyBrokerMoverCreator (protocols::protein_interface_design::movers)   
CombinedFilter (protocols::filters)   HBNetEnergy (core::pack::guidance_scoreterms::hbnet_energy)   NubInitioLoopClosureMoverCreator (protocols::fold_from_loops::movers)   RNA_ChainClosureChecker (protocols::stepwise::modeler::rna::checker)   TopologyClaimer (protocols::topology_broker)   
CombinedFilterCreator (protocols::filters)   HBNetEnergyCreator (core::pack::guidance_scoreterms::hbnet_energy)   NubInitioMover (protocols::fold_from_loops)   RNA_ChainClosureScreener (protocols::stepwise::screener)   TopologyClaimerFactory (protocols::topology_broker)   
CombinedTaskOperation (protocols::flxbb)   HBNetScore (protocols::hbnet)   NubInitioMoverCreator (protocols::fold_from_loops)   RNA_ChemicalMappingEnergy (core::energy_methods)   TopOutFunc (core::scoring::func)   
CombinePoseMover (protocols::simple_moves)   HBNetScoreFilterCreator (protocols::hbnet)   NubSegment (protocols::fold_from_loops::utils)   RNA_ChemicalMappingEnergyCreator (core::energy_methods)   TopPercentOfAllInputs (protocols::features)   
COMCoordinateConstraint (protocols::constraints_additional)   HBNetStapleInterface (protocols::hbnet)   NucleotideMutation (protocols::evolution)   RNA_ChemicalShiftEnergy (core::energy_methods)   TopPercentOfEachInput (protocols::features)   
Comparator (protocols::environment)   HBNetStapleInterfaceCreator (protocols::hbnet)   NucleotideMutationCreator (protocols::evolution)   RNA_ChemicalShiftEnergyCreator (core::energy_methods)   Torsion (protocols::protein_interface_design::filters)   
CompareByScoreCombination (protocols::frag_picker)   HBond (core::scoring::hbonds)   NullMover (protocols::moves)   RNA_ChemicalShiftPotential (core::scoring::rna::chemical_shift)   Torsion_Info (protocols::stepwise::modeler::rna)   
CompareQueryPosition (protocols::frag_picker)   HBondAcceptorFilter (protocols::ligand_docking)   NullPerturber (protocols::denovo_design::components)   RNA_ChiStepWiseSampler (protocols::stepwise::sampler::rna)   TorsionBinIO (protocols::frag_picker)   
CompareScoreComponent (protocols::frag_picker)   HBondAcceptorFilterCreator (protocols::ligand_docking)   NullPoseFolder (protocols::denovo_design::components)   RNA_ChunkLibrary (core::import_pose::libraries)   TorsionBinSimilarity (protocols::frag_picker::scores)   
CompareTags (protocols::jd2)   HBondBonusOptions (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty)   NumberHBondsCalculator (protocols::simple_pose_metric_calculators)   RNA_CoarseDistEnergy (core::energy_methods)   TorsionClaim (protocols::environment::claims)   
CompareTotalScore (protocols::frag_picker)   HBondCommon (protocols::constel)   NumDerivCheckData (core::optimization)   RNA_CoarseDistEnergyCreator (core::energy_methods)   TorsionCreator (protocols::protein_interface_design::filters)   
ComparisonGrid (protocols::pockets)   HBondDatabase (core::scoring::hbonds)   NumericalDerivCheckResult (core::optimization)   RNA_Coarsify (protocols::rna::movers)   TorsionDistrParams (protocols::ligand_docking::ga_ligand_dock)   
CompassScoringScheme (core::sequence)   HBondDerivs (core::scoring::hbonds)   NumNeighborsMPM (protocols::match)   RNA_CoarsifyCreator (protocols::rna::movers)   TorsionDOFMover (protocols::simple_moves)   
CompleteConnectionsFilter (protocols::ligand_docking)   HBondDonorFilter (protocols::ligand_docking)   NumNeighborsSelector (core::select::residue_selector)   RNA_CS_parameters (core::scoring::rna::chemical_shift)   TorsionFeature (protocols::comparative_modeling::features)   
CompleteConnectionsFilterCreator (protocols::ligand_docking)   HBondDonorFilterCreator (protocols::ligand_docking)   NumNeighborsSelectorCreator (core::select::residue_selector)   RNA_CS_residue_parameters (core::scoring::rna::chemical_shift)   TorsionFourierComponent (core::scoring::dna)   
CompletedJobOutput (protocols::jd3)   HBondEdge (core::scoring::hbonds::graph)   NVlookup (core::scoring::nv)   RNA_CSA_JobDistributor (protocols::rna::setup)   TorsionFragment (protocols::frags)   
MPIArchiveJobDistributor::CompletionMessage (protocols::jd2::archive)   HBondEnergy (core::scoring::hbonds)   NVscore (core::scoring::nv)   RNA_DataBackboneEnergy (core::energy_methods)   TorsionFragmentLibrary (protocols::frags)   
ComposeSearchPatterns (protocols::hotspot_hashing)   HBondEnergyCreator (core::scoring::hbonds)   NVscoreCreator (core::scoring::nv)   RNA_DataBackboneEnergyCreator (core::energy_methods)   TorsionFragmentMover (protocols::frags)   
CompositeEnergyMetric (core::simple_metrics::composite_metrics)   HBondFeatures (protocols::features)   NWAligner (core::sequence)   RNA_DataInfo (core::pose::rna)   TorsionID (core::id)   
CompositeEnergyMetricCreator (core::simple_metrics::composite_metrics)   HBondFeaturesCreator (protocols::features)   
  O  
RNA_DataReader (core::io::rna)   TorsionID_Range (core::id)   
CompositeFragmentSelector (protocols::frag_picker)   HBondGraph (core::scoring::hbonds::graph)   RNA_Datum (core::pose::rna)   TorsionParams (core::scoring)   
CompositeRealMetric (core::simple_metrics)   HBondGraphInitializerIG (core::pack::hbonds)   O2PrimePacker (protocols::stepwise::modeler::rna::o2prime)   RNA_Decoarsify (protocols::rna::movers)   TorsionRange (protocols::make_rot_lib)   
CompositeScoringScheme (core::sequence)   HBondInfo (core::scoring::hbonds::graph)   O2PrimeScreener (protocols::stepwise::screener)   RNA_DecoarsifyCreator (protocols::rna::movers)   TorsionRestrictedKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
CompositeSequence (core::sequence)   HbondMetric (core::simple_metrics::per_residue_metrics)   O_1A (protocols::toolbox::py_inheritance_test)   RNA_DeNovoJobOutputter (protocols::jd2)   TorsionSampler (protocols::ligand_docking::ga_ligand_dock)   
CompositeSequenceCreator (core::sequence)   HbondMetricCreator (core::simple_metrics::per_residue_metrics)   O_1B (protocols::toolbox::py_inheritance_test)   RNA_DeNovoJobOutputterCreator (protocols::jd2)   TorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
CompositeStringMetric (core::simple_metrics)   HBondNetStruct (protocols::hbnet)   O_2A (protocols::toolbox::py_inheritance_test)   RNA_DeNovoMasterMover (protocols::rna::denovo::movers)   TorsionSet (core::fragment::rna)   
CompositionMover (protocols::moves)   HBondNode (core::scoring::hbonds::graph)   O_2A2B (protocols::toolbox::py_inheritance_test)   RNA_DeNovoOptimizer (protocols::rna::movers)   TorsionSetMover (protocols::simple_moves)   
CompoundArchitect (protocols::denovo_design::architects)   HBondOptions (core::scoring::hbonds)   O_2B (protocols::toolbox::py_inheritance_test)   RNA_DeNovoParameters (core::import_pose)   TorsionSpec (protocols::canonical_sampling)   
CompoundArchitectCreator (protocols::denovo_design::architects)   HBondParameterFeatures (protocols::features)   ObserverCache (core::pose::datacache)   RNA_DeNovoPoseInitializer (protocols::rna::denovo)   TorsionSweepingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
CompoundFilter (protocols::filters)   HBondParameterFeaturesCreator (protocols::features)   Obsolet_NamedAtomPairConstraint (core::scoring::constraints)   RNA_DeNovoProtocol (protocols::rna::denovo)   TorsionType (protocols::ligand_docking::ga_ligand_dock)   
CompoundFilterCreator (protocols::filters)   HBondResidueMinData (core::scoring::hbonds)   OccludedHbondSolEnergy (core::energy_methods)   RNA_DeNovoProtocolCreator (protocols::rna::denovo)   TotalEnergyMetric (core::simple_metrics::metrics)   
CompoundPerturber (protocols::denovo_design::components)   HBondResPairMinData (core::scoring::hbonds)   OccludedHbondSolEnergy_onebody (core::energy_methods)   RNA_DeNovoProtocolMover (protocols::rna::denovo::movers)   TotalEnergyMetricCreator (core::simple_metrics::metrics)   
CompoundTranslate (protocols::ligand_docking)   HBondResStruct (protocols::hbnet)   OccludedHbondSolEnergy_onebodyCreator (core::energy_methods)   RNA_DeNovoProtocolMoverCreator (protocols::rna::denovo::movers)   TotalSasaFilter (protocols::simple_filters)   
CompoundTranslateCreator (protocols::ligand_docking)   HBondSelector (protocols::residue_selectors)   OccludedHbondSolEnergyCreator (core::energy_methods)   RNA_DeNovoProtocolOptions (core::import_pose::options)   TotalSasaFilterCreator (protocols::simple_filters)   
ComputeLigandRDF (protocols::ligand_docking)   HBondSelectorCreator (protocols::residue_selectors)   OccupiedSpaceHash (protocols::match)   RNA_DeNovoSetup (core::import_pose)   TotalScoreFeatures (protocols::features)   
ComputeLigandRDFCreator (protocols::ligand_docking)   HBondSet (core::scoring::hbonds)   OctahedralMetal_Helper (protocols::cyclic_peptide::crosslinker)   RNA_DMS_LowResolutionPotential (core::scoring::rna::data)   TotalScoreFeaturesCreator (protocols::features)   
Computes   HbondsToAtomFilter (protocols::protein_interface_design::filters)   Octree2D (core::scoring::packstat)   RNA_DMS_Potential (core::scoring::rna::data)   TrajectoryLogger (protocols::loop_modeling::utilities)   
ComputeTotalDistCst (protocols::abinitio)   HbondsToAtomFilterCreator (protocols::protein_interface_design::filters)   OffsetPeriodicBoundFunc (core::scoring::constraints)   RNA_EnergyMethodOptions (core::scoring::rna)   TrajectoryMapFeatures (protocols::features)   
CoMTrackerCM (protocols::environment)   HbondsToResidueFilter (protocols::protein_interface_design::filters)   OligomericAverageDegreeFilter (protocols::matdes)   RNA_FA_ElecEnergy (core::energy_methods)   TrajectoryMapFeaturesCreator (protocols::features)   
CoMTrackerCMCreator (protocols::environment)   HbondsToResidueFilterCreator (protocols::protein_interface_design::filters)   OligomericAverageDegreeFilterCreator (protocols::matdes)   RNA_FA_ElecEnergyCreator (core::energy_methods)   TrajectoryRecorder (protocols::canonical_sampling)   
ConcatenatePosesMover (protocols::simple_moves)   HBondsTrieVsTrieCachedDataContainer (core::scoring::hbonds::hbtrie)   OmegaBundleParameter (protocols::helical_bundle::parameters)   RNA_FilteredBaseBaseInfo (core::pose::rna)   TrajectoryReportToDB (protocols::features)   
ConcatenatePosesMoverCreator (protocols::simple_moves)   HBondTypeManager (core::scoring::hbonds)   OmegaPerturber (protocols::kinematic_closure::perturbers)   RNA_FittedTorsionInfo (core::chemical::rna)   TrajectoryReportToDBCreator (protocols::features)   
ConcurrencyTest (protocols::features::helixAssembly)   HBP_FinalFullatomRefinementMoveGenerator (protocols::helical_bundle_predict)   OmegaPreferenceSamplingData (core::scoring::carbohydrates)   RNA_FragmentHomologyExclusion (core::fragment::rna)   Transform (protocols::ligand_docking)   
ConcurrencyTestCreator (protocols::features::helixAssembly)   HBP_HelixCoilMoveGenerator (protocols::helical_bundle_predict)   OmegaPreferencesFunction (core::scoring::carbohydrates)   RNA_FragmentMonteCarlo (protocols::rna::denovo)   Transform_info (protocols::ligand_docking)   
Conformation (core::conformation)   HBP_MoveGenerator (protocols::helical_bundle_predict)   OmegaTether (core::scoring)   RNA_FragmentMonteCarloOptions (core::import_pose::options)   Transformation   
ConformationEvent (core::pose::signals)   HBP_SigmoidalTemperatureScheduleGenerator (protocols::helical_bundle_predict)   OmegaTetherEnergy (core::energy_methods)   RNA_FragmentMonteCarloOutputter (protocols::rna::denovo::output)   Transformation (protocols::protein_interface_design)   
ConformationKinWriter (core::conformation)   HBP_TemperatureScheduleGenerator (protocols::helical_bundle_predict)   OmegaTetherEnergyCreator (core::energy_methods)   RNA_FragmentMover (protocols::rna::denovo::movers)   TransformCreator (protocols::ligand_docking)   
ConformationXYZ (core::scoring::func)   HBPHelix (protocols::helical_bundle_predict)   One_Four_BBMB_Helper (protocols::cyclic_peptide::crosslinker)   RNA_Fragments (core::fragment::rna)   TransformEnsemble (protocols::ligand_docking)   
ConformerSwitchMover (protocols::docking)   HBPHelixAssignments (protocols::helical_bundle_predict)   OneBodyEnergy (core::scoring::methods)   RNA_FullAtomStackingEnergy (core::energy_methods)   TransformEnsemble_info (protocols::ligand_docking)   
ConformerSwitchMoverCreator (protocols::docking)   HBPHelixParameters (protocols::helical_bundle_predict)   OneDDistPotential (core::scoring)   RNA_FullAtomStackingEnergyCreator (core::energy_methods)   TransformEnsembleCreator (protocols::ligand_docking)   
ConnectChainsMover (protocols::pose_length_moves)   HbsPatcher (protocols::simple_moves::hbs)   OneGaussianScattering (core::scoring::fiber_diffraction)   RNA_FullAtomVDW_BasePhosphate (core::energy_methods)   TransformIntoMembraneMover (protocols::membrane)   
ConnectChainsMoverCreator (protocols::pose_length_moves)   HeaderInformation (core::io)   OneGaussianScattering (core::scoring::electron_density)   RNA_FullAtomVDW_BasePhosphateCreator (core::energy_methods)   TransformIntoMembraneMoverCreator (protocols::membrane)   
ConnectionArchitect (protocols::denovo_design::connection)   Heat_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   OneToAllEnergyContainer (core::scoring)   RNA_HelixAssembler (core::import_pose)   TransientCutpointHandler (protocols::stepwise::monte_carlo::mover)   
ConnectionEvent (core::conformation::signals)   HeavyAtomFilter (core::chemical)   OneToAllNeighborConstIterator (core::scoring)   RNA_HelixMover (protocols::rna::denovo::movers)   Translate (protocols::ligand_docking)   
ConnectionPerturber (protocols::denovo_design::components)   HeavyAtomFilter (protocols::ligand_docking)   OneToAllNeighborIterator (core::scoring)   RNA_IdealCoord (core::pose::rna)   Translate_info (protocols::ligand_docking)   
ConnectRight (protocols::forge::build)   HeavyAtomFilterCreator (protocols::ligand_docking)   OnTheFlyEdge (core::pack::interaction_graph)   RNA_Info (core::chemical::rna)   TranslateCreator (protocols::ligand_docking)   
ConnectSulfurAndMakeVirtualProton (core::chemical)   HeavyAtomNormalization (protocols::qsar::scoring_grid)   OnTheFlyInteractionGraph (core::pack::interaction_graph)   RNA_JobDistributor (protocols::rna::setup)   TranslationFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers)   
ConsensusDesignMover (protocols::calc_taskop_movers)   HeavyAtomWithHydrogensFilter (core::chemical)   OnTheFlyNode (core::pack::interaction_graph)   RNA_JR_SuiteEnergy (core::energy_methods)   TranslationMover (protocols::membrane)   
ConsensusDesignMoverCreator (protocols::calc_taskop_movers)   HeavyAtomWithPolarHydrogensFilter (core::chemical)   OopCreatorMover (protocols::ncbb::oop)   RNA_JR_SuiteEnergyCreator (core::energy_methods)   TranslationMoverCreator (protocols::membrane)   
ConsensusLoopDatabase (protocols::denovo_design::task_operations)   HedgeArchive (protocols::abinitio)   OopCreatorMoverCreator (protocols::ncbb::oop)   RNA_JumpLibrary (core::import_pose::libraries)   TranslationRotationMover (protocols::membrane)   
ConsensusLoopDesignOperation (protocols::denovo_design::task_operations)   HelicalBundlePredictApplication (protocols::helical_bundle_predict)   OopDockDesignProtocol (protocols::ncbb::oop)   RNA_JumpMover (core::import_pose)   TranslationRotationMoverCreator (protocols::membrane)   
ConsensusLoopDesignOperationCreator (protocols::denovo_design::task_operations)   HelicalBundlePredictApplicationOptions (protocols::helical_bundle_predict)   OopDockDesignProtocolCreator (protocols::ncbb::oop)   RNA_KIC_Sampler (protocols::stepwise::sampler::rna)   TreeBuilder (protocols::nonlocal)   
ConservativeDesignOperation (protocols::task_operations)   HelicalFragment (protocols::features::helixAssembly)   OopDPuckMinusMover (protocols::simple_moves::oop)   RNA_KinematicCloser (protocols::stepwise::sampler::rna)   TreeBuilderFactory (protocols::nonlocal)   
ConservativeDesignOperationCreator (protocols::task_operations)   HelicalGaussianMover (protocols::rbsegment_relax)   OopDPuckPlusMover (protocols::simple_moves::oop)   RNA_LibraryManager (core::import_pose::libraries)   TreeVizBuilder (core::kinematics)   
ConservedPosMutationFilter (protocols::calc_taskop_filters)   Helices (core::scoring)   OopMover (protocols::simple_moves::oop)   RNA_LJ_BaseEnergy (core::energy_methods)   Trial   
ConservedPosMutationFilterCreator (protocols::calc_taskop_filters)   Helix (protocols::fldsgn::topology)   OopPatcher (protocols::simple_moves::oop)   RNA_LJ_BaseEnergyCreator (core::energy_methods)   TrialCounter (protocols::moves)   
ConstAbinitioMoverWeight (protocols::topology_broker::weights)   HelixArchitect (protocols::denovo_design::architects)   OopPuckMinusMover (protocols::simple_moves::oop)   RNA_LoopCloser (protocols::rna::movers)   TrialCounterObserver (protocols::canonical_sampling)   
ConstantConstraint (core::scoring::constraints)   HelixArchitectCreator (protocols::denovo_design::architects)   OopPuckPlusMover (protocols::simple_moves::oop)   RNA_LowResolutionPotential (core::scoring::rna)   TrialCounterObserverCreator (protocols::canonical_sampling)   
ConstantFunc (core::scoring::func)   HelixBendFilter (protocols::fldsgn::filters)   OopRandomPuckMover (protocols::simple_moves::oop)   RNA_LowResolutionPotentialCreator (core::scoring::rna)   TrialMover (protocols::moves)   
ConstantLengthFragSet (core::fragment)   HelixBendFilterCreator (protocols::fldsgn::filters)   OopRandomSmallMover (protocols::simple_moves::oop)   RNA_MgPointEnergy (core::energy_methods)   TriazolamerMover (protocols::simple_moves::triazolamer)   
ConstantLengthFragSetIterator_ (core::fragment)   HelixBundleFeatures (protocols::features::helixAssembly)   OP_const_iterator (protocols::toolbox)   RNA_MgPointEnergyCreator (core::energy_methods)   TriazolamerRandomSmallMover (protocols::simple_moves::triazolamer)   
ConstantScoreBase (protocols::qsar::scoring_grid)   HelixBundleFeaturesCreator (protocols::features::helixAssembly)   OperateOnCertainResidues (core::pack::task::operation)   RNA_Minimizer (protocols::rna::denovo::movers)   TrieCollection (core::scoring::trie)   
ConstFrameIterator (core::fragment)   HelixCapFeatures (protocols::features)   OperateOnCertainResiduesCreator (core::pack::task::operation)   RNA_MinimizerOptions (core::import_pose::options)   TrieCountPair1BC3 (core::scoring::etable::etrie)   
ConstPattern (protocols::hotspot_hashing)   HelixCapFeaturesCreator (protocols::features)   OperateOnResidueSubset (core::pack::task::operation)   RNA_MonteCarloJobDistributor (protocols::rna::setup)   TrieCountPair1BC4 (core::scoring::etable::etrie)   
ConstrainHBondNetwork (protocols::hbnet)   HelixFromSequence (protocols::membrane)   OperateOnResidueSubsetCreator (core::pack::task::operation)   RNA_Motif (core::scoring::rna)   TrieCountPairAll (core::scoring::etable::etrie)   
ConstrainHBondNetworkCreator (protocols::hbnet)   HelixFromSequenceCreator (protocols::membrane)   Operator (protocols::calc_taskop_filters)   RNA_Motifs (core::scoring::rna)   TrieCountPairBase (core::scoring::trie)   
Constraint (protocols::md)   HelixHelixAngleFilter (protocols::simple_filters)   OperatorFilterCreator (protocols::calc_taskop_filters)   RNA_NucleosideStepWiseSampler (protocols::stepwise::sampler::rna)   TrieCountPairGeneric (core::scoring::etable::etrie)   
Constraint (core::scoring::constraints)   HelixHelixAngleFilterCreator (protocols::simple_filters)   OptCysHG (core::pack::task::operation)   RNA_O2PrimeMover (protocols::stepwise::monte_carlo::rna)   TrieCountPairNone (core::scoring::etable::etrie)   
ConstraintClaimer (protocols::topology_broker)   HELIXInformation (core::io)   OptCysHGCreator (core::pack::task::operation)   RNA_PairingTemplate (core::import_pose::libraries)   TrieNode (core::scoring::trie)   
ConstraintConditions (protocols::fold_from_loops::constraint_generator)   HelixKinkFilter (protocols::fldsgn::filters)   OptEData (protocols::optimize_weights)   RNA_PairwiseLowResolutionEnergy (core::energy_methods)   TrieVsTrieCachedDataContainerBase (core::scoring::trie)   
ConstraintCreator (core::scoring::constraints)   HelixKinkFilterCreator (protocols::fldsgn::filters)   OptEMultifunc (protocols::optimize_weights)   RNA_PairwiseLowResolutionEnergyCreator (core::energy_methods)   TrigonalPlanarMetal_Helper (protocols::cyclic_peptide::crosslinker)   
ConstraintEdge (core::scoring::constraints)   HelixNCapperMover (protocols::helix_capper)   OptEPositionData (protocols::optimize_weights)   RNA_PartitionEnergy (core::energy_methods)   TrigonalPyramidalMetal_Helper (protocols::cyclic_peptide::crosslinker)   
ConstraintedOptimizationWeightFunc (protocols::optimize_weights)   HelixPairing (protocols::denovo_design::components)   OptEPositionDataFactory (protocols::optimize_weights)   RNA_PartitionEnergyCreator (core::energy_methods)   TripletID (protocols::fldsgn::topology)   
ConstraintEvaluator (protocols::constraints_additional)   HelixPairing (protocols::fldsgn::topology)   OptEVariableExpression (protocols::optimize_weights)   RNA_RawBaseBaseInfo (core::pose::rna)   TrisBpyScore (protocols::sic_dock::scores)   
ConstraintEvaluatorCreator (protocols::constraints_additional)   HelixPairingFilter (protocols::fldsgn::filters)   OptH (core::pack::task::operation)   RNA_Reactivity (core::pose::rna)   TrueFilter (protocols::filters)   
ConstraintEvaluatorWrapper (protocols::topology_broker)   HelixPairingFilterCreator (protocols::fldsgn::filters)   OptHCreator (core::pack::task::operation)   RNA_Relaxer (protocols::rna::denovo::movers)   TrueFilterCreator (protocols::filters)   
ConstraintEvaluatorWrapperCreator (protocols::topology_broker)   HelixPairingSet (protocols::fldsgn::topology)   OptimizeMembranePositionMover (protocols::membrane)   RNA_ResidueLevelTask (core::pack::task::rna)   TrueResidueSelector (core::select::residue_selector)   
ConstraintFactory (core::scoring::constraints)   HelixPerturber (protocols::denovo_design::components)   OptimizeMembranePositionMoverCreator (protocols::membrane)   RNA_ScoringInfo (core::scoring::rna)   TrueResidueSelectorCreator (core::select::residue_selector)   
ConstraintFragmentSampler (protocols::abinitio)   HelixRotate (protocols::nonlocal)   OptimizeProteinEmbeddingMover (protocols::membrane)   RNA_SecStruct (core::pose::rna)   TruncatedScoreEvaluator (protocols::simple_filters)   
ConstraintFulfilmentFilter (protocols::fold_from_loops::filters)   HelixScore (protocols::sic_dock)   OptimizeProteinEmbeddingMoverCreator (protocols::membrane)   RNA_SecStructLegacyInfo (core::pose::rna::secstruct_legacy)   TryDisulfPermutations (protocols::cyclic_peptide)   
ConstraintFulfilmentFilterCreator (protocols::fold_from_loops::filters)   HelixSheetPairing (protocols::denovo_design::components)   OptimizeThreadingMover (protocols::rbsegment_relax)   RNA_SilentStruct (core::io::silent)   TryDisulfPermutationsCreator (protocols::cyclic_peptide)   
ConstraintGenerator (protocols::constraint_generator)   HierarchicalHybridJD_JobResultsSummary (protocols::cyclic_peptide_predict)   OptimizeThreadingMoverCreator (protocols::rbsegment_relax)   RNA_SilentStructCreator (core::io::silent)   TryRotamers (protocols::protein_interface_design::movers)   
ConstraintGeneratorCreator (protocols::constraint_generator)   HierarchicalHybridJD_PNearToArbitraryStateSummary (protocols::cyclic_peptide_predict)   Orbital (core::chemical)   RNA_StubCoordinateEnergy (core::energy_methods)   TryRotamersCreator (protocols::protein_interface_design::movers)   
ConstraintGeneratorFactory (protocols::constraint_generator)   HierarchicalHybridJD_ResultsSummaryBase (protocols::cyclic_peptide_predict)   OrbitalsFeatures (protocols::features)   RNA_StubCoordinateEnergyCreator (core::energy_methods)   Tumble (protocols::simple_moves)   
ConstraintGeneratorLoader (protocols::parser)   HierarchicalHybridJD_RMSDToBestSummary (protocols::cyclic_peptide_predict)   OrbitalsFeaturesCreator (protocols::features)   RNA_SugarCloseEnergy (core::energy_methods)   TumbleCreator (protocols::simple_moves)   
ConstraintGeneratorLoaderCreator (protocols::parser)   HierarchicalHybridJD_SASASummary (protocols::cyclic_peptide_predict)   OrbitalsLookup (core::scoring::orbitals)   RNA_SugarCloseEnergyCreator (core::energy_methods)   TwelveANeighborEdge (core::scoring)   
ConstraintGeneratorRegistrator (protocols::constraint_generator)   HierarchicalLevel (protocols::canonical_sampling::mc_convergence_checks)   OrbitalsScore (core::scoring::orbitals)   RNA_SugarStepWiseSampler (protocols::stepwise::sampler::rna)   TwelveANeighborGraph (core::scoring)   
ConstraintGraph (core::scoring::constraints)   HighResDocker (protocols::ligand_docking)   OrbitalsScoreCreator (core::scoring::orbitals)   RNA_SuiteAssignment (core::pose::rna)   TwelveANeighborNode (core::scoring)   
ConstraintInfo (protocols::ligand_docking::ga_ligand_dock)   HighResDockerCreator (protocols::ligand_docking)   OrbitalsStatistics (core::scoring::orbitals)   RNA_SuiteEnergy (core::energy_methods)   TwoBodyEnergy (core::scoring::methods)   
ConstraintIO (core::scoring::constraints)   HighResEnsemble (protocols::ligand_docking)   OrbitalType (core::chemical::orbitals)   RNA_SuiteEnergyCreator (core::energy_methods)   
  U  
ConstraintNode (core::scoring::constraints)   HighResEnsembleCreator (protocols::ligand_docking)   OrbitalTypeMapper (core::chemical::orbitals)   RNA_SuiteInfo (core::pose::rna)   
ConstrainToIdealMover (protocols::simple_moves)   BiasEnergy::Histogram (protocols::canonical_sampling)   OrbitalTypeSet (core::chemical::orbitals)   RNA_SuiteName (core::pose::rna)   UBQ_GTPaseMover (protocols::chemically_conjugated_docking)   
ConstraintPreparer (protocols::abinitio::abscript)   Histogram (protocols::recces)   OrbitalXYZCoords (core::conformation::orbitals)   RNA_SuitePotential (core::scoring::rna)   UBQ_GTPaseMoverCreator (protocols::chemically_conjugated_docking)   
ConstraintPreparerCreator (protocols::abinitio::abscript)   Hit (protocols::match)   OrderCavBallOnR (core::scoring::packstat)   RNA_SuiteStepWiseSampler (protocols::stepwise::sampler::rna)   UDPSocketClient (protocols::moves)   
ConstraintRegistrator (core::scoring::constraints)   Hit (protocols::simple_moves)   OrderCavBallOnRmAnb (core::scoring::packstat)   RNA_TorsionEnergy (core::energy_methods)   UIMover (protocols::network)   
ConstraintResidueSelector (protocols::fold_from_loops::selectors)   HitHasher (protocols::match)   OrderCavBallOnRmE (core::scoring::packstat)   RNA_TorsionEnergyCreator (core::energy_methods)   UIObserver (protocols::network)   
ConstraintResidueSelectorCreator (protocols::fold_from_loops::selectors)   HitNeighborFinder (protocols::match)   OrderCavBallOnX (core::scoring::packstat)   RNA_TorsionMover (protocols::stepwise::monte_carlo::rna)   UltraLightResidue (core::conformation)   
Constraints (core::scoring::constraints)   HolesEnergy (core::energy_methods)   OrderCBC (core::scoring::packstat)   RNA_TorsionPotential (core::scoring::rna)   UnboundRotamersOperation (core::pack::rotamer_set)   
ConstraintScoreCutoffFilter (protocols::constraint_filters)   HolesEnergyCreator (core::energy_methods)   OrderedFragSet (core::fragment)   RNA_TorsionScreener (protocols::stepwise::sampler::screener)   UnconstrainedTorsionsMover (protocols::ligand_docking)   
ConstraintScoreCutoffFilterCreator (protocols::constraint_filters)   HolesEnergyRes (core::scoring::packing)   OrderedFragSetIterator_ (core::fragment)   RNA_VDW_BinChecker (protocols::stepwise::modeler::rna::checker)   UnfoldedStateEnergy (core::energy_methods)   
ConstraintScoreFilter (protocols::constraint_filters)   HolesFilter (protocols::simple_filters)   OrderedSequentialSymmetrySlider (protocols::symmetry)   RNA_VDW_Energy (core::energy_methods)   UnfoldedStateEnergyCalculatorJobDistributor (protocols::unfolded_state_energy_calculator)   
ConstraintScoreFilterCreator (protocols::constraint_filters)   HolesFilterCreator (protocols::simple_filters)   OrderSortPredicate (protocols::abinitio)   RNA_VDW_EnergyCreator (core::energy_methods)   UnfoldedStateEnergyCalculatorMover (protocols::unfolded_state_energy_calculator)   
ConstraintsEnergy (core::scoring::constraints)   HolesParams (core::scoring::packing)   OrderSphereOnID (core::scoring::packstat)   RNAIdealizeMover (protocols::rna::movers)   UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (protocols::unfolded_state_energy_calculator)   
ConstraintsEnergyCreator (core::scoring::constraints)   HolesParamsRes (core::scoring::packing)   OrderSphereOnX (core::scoring::packstat)   RNAIdealizeMoverCreator (protocols::rna::movers)   UnfoldedStateEnergyCreator (core::energy_methods)   
ConstraintSet (core::scoring::constraints)   HolesResult (core::scoring::packing)   OrientCommon (protocols::constel)   RNAThreadAndMinimizeMover (protocols::rna::movers)   UnfoldedStatePotential (core::scoring)   
ConstraintSetMover (protocols::constraint_movers)   HotspotDisjointedFoldTreeMover (protocols::protein_interface_design::movers)   OriginalBackboneBuildPoint (protocols::match::upstream)   RNAThreadAndMinimizeMoverCreator (protocols::rna::movers)   UniformPerturber (protocols::kinematic_closure::perturbers)   
ConstraintSetMoverCreator (protocols::constraint_movers)   HotspotDisjointedFoldTreeMoverCreator (protocols::protein_interface_design::movers)   OrJumpSelector (core::select::jump_selector)   RNP_HighResMover (protocols::rna::denovo::movers)   UniformPolicy (protocols::nonlocal)   
ConstraintSetScore (protocols::sic_dock)   HotspotHasherMover (protocols::protein_interface_design::movers)   OrJumpSelectorCreator (core::select::jump_selector)   RNP_LowResEnergy (core::energy_methods)   UniformRigidBodyCM (protocols::rigid)   
ConstraintsManager (protocols::constraint_generator)   HotspotHasherMoverCreator (protocols::protein_interface_design::movers)   OrResidueSelector (core::select::residue_selector)   RNP_LowResEnergyCreator (core::energy_methods)   UniformRigidBodyCMCreator (protocols::rigid)   
ConstraintsMap (protocols::constraint_generator)   HotspotStub (protocols::hotspot_hashing)   OrResidueSelectorCreator (core::select::residue_selector)   RNP_LowResPairDistEnergy (core::energy_methods)   UniformRigidBodyMover (protocols::rigid)   
ConstScore (protocols::frag_picker::scores)   HotspotStubSet (protocols::hotspot_hashing)   OrSelector (protocols::pose_selectors)   RNP_LowResPairDistEnergyCreator (core::energy_methods)   UniformRigidBodyMoverCreator (protocols::rigid)   
Contact (protocols::contact_map)   HPatchBackgroundEdge (core::pack::interaction_graph)   OrSelectorCreator (protocols::pose_selectors)   RNP_LowResPairDistPotential (core::scoring::rna)   UniformRotationMover (protocols::simple_moves)   
Contact (protocols::frag_picker)   HPatchBackgroundNode (core::pack::interaction_graph)   OTFFlexbbEdge (protocols::flexpack::interaction_graph)   RNP_LowResPotential (core::scoring::rna)   UniformSphereTransMover (protocols::rigid)   
ContactCounts (protocols::frag_picker)   HPatchCalculator (protocols::pose_metric_calculators)   OTFFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   RNP_LowResStackData (core::scoring::rna)   UniformTranslationMover (protocols::simple_moves)   
ContactDescription (protocols::sewing::data_storage)   HPatchEdge (core::pack::interaction_graph)   OTFFlexbbNode (protocols::flexpack::interaction_graph)   RNP_LowResStackEnergy (core::energy_methods)   UnionEdge (protocols::pockets)   
ContactMap (protocols::contact_map)   HPatchEnergy (core::pack::interaction_graph)   OtherContextScoreFunction (protocols::flexpack)   RNP_LowResStackEnergyCreator (core::energy_methods)   UnrecognizedAtomFeatures (protocols::features)   
ContactMapCreator (protocols::contact_map)   HPatchEnergyCreator (core::pack::interaction_graph)   OtherPoseEnergy (core::energy_methods)   RollMover (protocols::rigid)   UnrecognizedAtomFeaturesCreator (protocols::features)   
ContactMapEvaluator (protocols::simple_filters)   HPatchInteractionGraph (core::pack::interaction_graph)   OtherPoseEnergyCreator (core::energy_methods)   RollMoverCreator (protocols::rigid)   UnrecognizedAtomRecord (core::pose)   
ContactMapEvaluatorCreator (protocols::simple_filters)   HPatchNode (core::pack::interaction_graph)   OutputSpecification (protocols::jd3::output)   RootData (core::chemical::carbohydrates)   UnsatCorrectionOptions (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty)   
ContactMolecularSurfaceCalculator (core::scoring::sc)   HPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   OutputStructureStore (protocols::ligand_docking::ga_ligand_dock)   Rose (protocols::sic_dock)   UnsatSelector (protocols::hbnet)   
ContactMolecularSurfaceFilter (protocols::simple_filters)   HRF_MSLabelingEnergy (core::energy_methods)   OutputWriter (protocols::match::output)   RosettaScriptsJobQueen (protocols::rosetta_scripts)   UnsatSelectorCreator (protocols::hbnet)   
ContactMolecularSurfaceFilterCreator (protocols::simple_filters)   HRF_MSLabelingEnergyCreator (core::energy_methods)   MergePDBMover::Overlap (protocols::pose_creation)   RosettaScriptsParser (protocols::rosetta_scripts)   UpdateCrystInfo (protocols::cryst)   
ContactOrderEnergy (core::energy_methods)   HRFDynamicsEnergy (core::energy_methods)   OversaturatedHbondAcceptorFilter (protocols::cyclic_peptide)   ROT (protocols::splice)   UpdateCrystInfoCreator (protocols::cryst)   
ContactOrderEnergyCreator (core::energy_methods)   HRFDynamicsEnergyCreator (core::energy_methods)   OversaturatedHbondAcceptorFilterCreator (protocols::cyclic_peptide)   RotamerAssigningAnnealer (core::pack::annealer)   UpdateEnzdesHeaderMover (protocols::enzdes)   
ContactPartner (protocols::contact_map)   HSPairPotential (protocols::fldsgn::potentials::sspot)   
  P  
RotamerBoltzCalculator (protocols::pose_metric_calculators)   UpdateEnzdesHeaderMoverCreator (protocols::enzdes)   
ContactStruct (protocols::normalmode)   HSSTriplet (protocols::fldsgn::topology)   RotamerBoltzmannWeight (protocols::calc_taskop_filters)   UpdateSolventMover (protocols::cryst)   
ContextDependentGeometricSolEnergy (core::energy_methods)   HSSTripletFilter (protocols::fldsgn::filters)   P_AA (core::scoring)   RotamerBoltzmannWeight2 (protocols::calc_taskop_filters)   UpdateSolventMoverCreator (protocols::cryst)   
ContextDependentGeometricSolEnergyCreator (core::energy_methods)   HSSTripletFilterCreator (protocols::fldsgn::filters)   P_AA_ABEGO3 (core::scoring)   RotamerBoltzmannWeight2Creator (protocols::calc_taskop_filters)   UpJumpSRFD (core::fragment)   
ContextDependentLRTwoBodyEnergy (core::scoring::methods)   HSSTripletSet (protocols::fldsgn::topology)   P_AA_Energy (core::energy_methods)   RotamerBoltzmannWeightEvaluator (protocols::toolbox)   UpstreamBuilder (protocols::match::upstream)   
ContextDependentOneBodyEnergy (core::scoring::methods)   HTL_EventX (core::scoring::packstat)   P_AA_EnergyCreator (core::energy_methods)   RotamerBoltzmannWeightFeatures (protocols::features)   UpstreamCollisionFilter (protocols::match::output)   
ContextDependentTwoBodyEnergy (core::scoring::methods)   HybridizeFoldtreeDynamic (protocols::hybridization)   P_AA_pp_Energy (core::energy_methods)   RotamerBoltzmannWeightFeaturesCreator (protocols::features)   UpstreamDownstreamCollisionFilter (protocols::match::output)   
ContextGraph (core::scoring)   HybridizeProtocol (protocols::hybridization)   P_AA_pp_EnergyCreator (core::energy_methods)   RotamerBoltzmannWeightFilterCreator (protocols::calc_taskop_filters)   UpstreamHitCacher (protocols::match::output)   
ContextGraphFactory (core::scoring)   HybridizeProtocolCreator (protocols::hybridization)   P_AA_ss (core::scoring)   RotamerBuildingData (core::pack::dunbrack)   UpstreamResidueProcessor (protocols::match::upstream)   
ContextIndependentGeometricSolEnergy (core::energy_methods)   HybridVDW_Energy (core::energy_methods)   P_AA_ss_Energy (core::energy_methods)   RotamerConstraint (core::pack::dunbrack)   UpstreamResTypeGeometry (protocols::match::upstream)   
ContextIndependentGeometricSolEnergyCreator (core::energy_methods)   HybridVDW_EnergyCreator (core::energy_methods)   P_AA_ss_EnergyCreator (core::energy_methods)   RotamerCouplings (core::pack::rotamer_set)   USE_INPUT_SC (core::pack::task)   
ContextIndependentLRTwoBodyEnergy (core::scoring::methods)   Hydrate (protocols::hydrate)   PackDaemon (protocols::pack_daemon)   RotamerDescriptor (core::scoring::trie)   UseMultiCoolAnnealer (core::pack::task::operation)   
ContextIndependentOneBodyEnergy (core::scoring::methods)   HydrogenAtomFilter (core::chemical)   PackedDunbrackRotamer (core::pack::dunbrack)   RotamerDescriptorAtom (core::scoring::trie)   UseMultiCoolAnnealerCreator (core::pack::task::operation)   
ContextIndependentTwoBodyEnergy (core::scoring::methods)   HydrogenBondConstraintGenerator (protocols::constraint_generator)   PackerNeighborGraphFilter (protocols::simple_filters)   RotamerDNAHBondFilter (protocols::dna)   UserDefinedGroupDiscriminator (protocols::minimization_packing)   
ContingentAcceptMover (protocols::simple_moves)   HydrogenBondConstraintGeneratorCreator (protocols::constraint_generator)   PackerPalette (core::pack::palette)   RotamerDots (core::pack::interaction_graph)   USOGFunc (core::scoring::func)   
ContingentAcceptMoverCreator (protocols::simple_moves)   HydrogenBondInfo (protocols::constraint_generator)   PackerPaletteCreator (core::pack::palette)   RotamerDotsCache (core::pack::interaction_graph)   UDPSocketClient::UUID (protocols::moves)   
ContingentFilter (protocols::filters)   HydrogenBondingAtom (protocols::constraint_generator)   PackerPaletteFactory (core::pack::palette)   RotamerDotsRadiusData (core::pack::interaction_graph)   
  V  
ContingentFilterCreator (protocols::filters)   HydrophobicityProfileSimilarity (protocols::frag_picker::scores)   PackerPaletteLoader (protocols::parser)   RotamerDumpMover (protocols::RotamerDump)   
ContinuousAssembly (protocols::legacy_sewing)   HydrophobicitySimilarity (protocols::frag_picker::scores)   PackerPaletteLoaderCreator (protocols::parser)   RotamerExplosion (core::pack::task::operation)   V   
ContinuousRotamerSet (core::pack::rotamer_set)   HydroxylTorsionEnergy (core::energy_methods)   PackerPaletteRegistrator (core::pack::palette)   RotamerExplosionCreator (core::pack::task::operation)   VallChunk (protocols::frag_picker)   
ContinuousRotamerSets (core::pack::rotamer_set)   HydroxylTorsionEnergyCreator (core::energy_methods)   PackerTask (core::pack::task)   RotamerFeatures (protocols::features)   VallChunkFilter (protocols::frag_picker)   
ConvergenceTest (core::optimization)   HydroxylTorsionPotential (core::scoring)   PackerTask_ (core::pack::task)   RotamerFeaturesCreator (protocols::features)   VallData (protocols::frags)   
ConvertRealToVirtualMover (protocols::simple_moves)   
  I  
PackingScore (core::scoring::packstat)   RotamericData (core::pack::dunbrack)   VallFragmentEval (core::fragment::picking_old::vall::eval)   
ConvertRealToVirtualMoverCreator (protocols::simple_moves)   PackingScoreResData (core::scoring::packstat)   RotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)   VallFragmentGen (core::fragment::picking_old::vall::gen)   
ConvertVirtualToRealMover (protocols::simple_moves)   APBSConfig::I_PARAM (core::scoring)   PackingState (protocols::multistate_design)   RotamericSingleResidueDunbrackLibraryParser (core::pack::dunbrack)   VallFragmentScore (core::fragment::picking_old::vall::scores)   
ConvertVirtualToRealMoverCreator (protocols::simple_moves)   ICoorAtomID (core::chemical)   PackRotamersMover (protocols::minimization_packing)   RotamerInitializer (protocols::features)   VallLibrarian (core::fragment::picking_old::vall)   
CoordConstraintClaimer (protocols::topology_broker)   ICoorOrbitalData (core::chemical::orbitals)   PackRotamersMoverCreator (protocols::minimization_packing)   RotamerizeMover (protocols::minimization_packing)   VallLibrary (core::fragment::picking_old::vall)   
CoordinateConstraint (core::scoring::constraints)   IdealAbegoGenerator (protocols::denovo_design::components)   PackRotamersMoverLazy (protocols::minimization_packing)   RotamerLibrary (core::pack::dunbrack)   VallProvider (protocols::frag_picker)   
CoordinateConstraintCreator (core::scoring::constraints)   IdealBondLengthSet (core::chemical)   PackRotamersMoverLazyCreator (protocols::minimization_packing)   RotamerLibraryScratchSpace (core::pack::dunbrack)   VallResidue (protocols::frag_picker)   
CoordinateConstraintGenerator (protocols::constraint_generator)   IdealContact (protocols::sewing::hashing)   PackRotamersMoverPartGreedy (protocols::enzdes)   RotamerLibrarySpecification (core::chemical::rotamers)   VallResidue (core::fragment::picking_old::vall)   
CoordinateConstraintGeneratorCreator (protocols::constraint_generator)   IdealizeAnomericHydrogens (protocols::carbohydrates)   PackRotamersMoverPartGreedyCreator (protocols::enzdes)   RotamerLibrarySpecificationCreator (core::chemical::rotamers)   VallResidues (core::fragment::picking_old::vall)   
CoordinateConstraintKC (protocols::abinitio)   IdealizeAnomericHydrogensCreator (protocols::carbohydrates)   PackScreener (protocols::stepwise::screener)   RotamerLibrarySpecificationFactory (core::chemical::rotamers)   VallSection (core::fragment::picking_old::vall)   
CoordinateConstraintStack (protocols::protein_interface_design::movers)   IdealizeHelicesMover (protocols::rbsegment_relax)   PackstatCalculator (protocols::pose_metric_calculators)   RotamerLibrarySpecificationRegistrator (core::chemical::rotamers)   VallSections (core::fragment::picking_old::vall)   
CoordinateCst (protocols::seeded_abinitio)   IdealizeHelicesMoverCreator (protocols::rbsegment_relax)   PackStatEnergy (core::energy_methods)   RotamerLinks (core::pack::rotamer_set)   Value (core::pack::annealer)   
CoordinateCstCreator (protocols::seeded_abinitio)   IdealizeMover (protocols::idealize)   PackStatEnergyCreator (core::energy_methods)   RotamerOperation (core::pack::rotamer_set)   ValueEvaluator (protocols::enzdes)   
CopyDofMover (protocols::simple_moves)   IdealizeMoverCreator (protocols::idealize)   PackStatFilter (protocols::simple_filters)   RotamerPairEnergies (protocols::ligand_docking::ga_ligand_dock)   VanillaJobDistributor (protocols::jd3::job_distributors)   
CopyDofs (core::pose::copydofs)   IdealizeNonPhiPsi (protocols::kinematic_closure::perturbers)   PackStatFilterCreator (protocols::simple_filters)   RotamerRecovery (protocols::pose_metric_calculators)   VariableSubstitutionPair (protocols::relax)   
CopyDofsInfo (core::pose::copydofs)   IdealParametersDatabase (core::energy_methods)   PackStatMover (protocols::analysis)   RotamerRecovery (protocols::rotamer_recovery)   VariableVectorExpression (protocols::pack_daemon)   
CopyDofStepWiseSampler (protocols::stepwise::sampler::copy_dofs)   IdentityEval (core::fragment::picking_old::vall::eval)   PairedSheetResidueSelector (protocols::denovo_design::residue_selectors)   RotamerRecoveryFactory (protocols::rotamer_recovery)   VarianceStatisticsArchive (protocols::jd2::archive)   
CopyEdge (core::chemical)   IdentityEvent (core::conformation::signals)   PairedSheetResidueSelectorCreator (protocols::denovo_design::residue_selectors)   RotamerRecoveryFeatures (protocols::features)   VarLengthBuild (protocols::forge::components)   
CopyRotamerMover (protocols::simple_moves)   IdentityFunc (core::scoring::func)   PairEnergy (core::energy_methods)   RotamerRecoveryFeaturesCreator (protocols::features)   VarSolDistSasaCalculator (protocols::vardist_solaccess)   
CopyRotamerMoverCreator (protocols::simple_moves)   IdManager (protocols::calc_taskop_filters)   PairEnergyCreator (core::energy_methods)   RotamerRecoveryMover (protocols::rotamer_recovery)   VarSolDRotamerDots (protocols::vardist_solaccess)   
CopyVertex (core::chemical)   IfMover (protocols::moves)   PairEPotential (core::scoring)   RotamerRecoveryMoverCreator (protocols::rotamer_recovery)   VaryLoopLengthMover (protocols::stepwise::monte_carlo::mover)   
CoreDunbrackFilter (protocols::fldsgn::filters)   IfMoverCreator (protocols::moves)   PairFeatures (protocols::features)   RotamerRecoveryRegistrator (protocols::rotamer_recovery)   VDDistanceMatrix (core::chemical)   
CoreDunbrackFilterCreator (protocols::fldsgn::filters)   IfThenFilter (protocols::filters)   PairFeaturesCreator (protocols::features)   RotamerRotamerHasher (core::pack::guidance_scoreterms::sap)   VDW_BinScreener (protocols::stepwise::screener)   
CorrectionVisitor (protocols::sic_dock)   IfThenFilterCreator (protocols::filters)   PairFuncMap (core::scoring::custom_pair_distance)   RotamerSet (core::pack::rotamer_set)   VDW_CachedRepScreenInfo (protocols::scoring)   
Coulomb (core::scoring::etable::coulomb)   IGEdgeReweightContainer (core::pack::task)   Pairing (core::scoring::dssp)   RotamerSet_ (core::pack::rotamer_set)   VDW_Energy (core::scoring::vdwaals)   
CountFromLeft (protocols::forge::build)   IGEdgeReweighter (core::pack::task)   PairingLibrary (protocols::jumping)   RotamerSetBase (core::conformation)   VDW_EnergyCreator (core::scoring::vdwaals)   
CountPair1B (core::scoring::etable::count_pair)   IGInterfaceEdgeUpweighter (protocols::toolbox)   PairingStatEntry (protocols::abinitio)   RotamerSetFactory (core::pack::rotamer_set)   VDW_Grid (core::pose::rna)   
CountPair2B (core::scoring::etable::count_pair)   IGLigandDesignEdgeUpweighter (protocols::toolbox)   PairingStatistics (protocols::abinitio)   RotamerSetOperation (core::pack::rotamer_set)   VDW_GridEnergy (protocols::scoring)   
CountPairAll (core::scoring::etable::count_pair)   IgnoreSubsetConstraintSet (protocols::comparative_modeling)   PairingTemplate (protocols::jumping)   RotamerSets (core::pack::rotamer_set)   VDW_GridEnergyCreator (protocols::scoring)   
CountPairCrossover3 (core::scoring::etable::count_pair)   Implements   PairQueryExecutor (protocols::indexed_structure_store::search)   RotamerSetsBase (core::pack_basic)   VDW_RepScreenInfo (core::pose::rna)   
CountPairCrossover34 (core::scoring::etable::count_pair)   Implements   PairQuerySummaryStatistics (protocols::indexed_structure_store::search)   RotamerSetsFactory (core::pack::rotamer_set)   VDWAtom (core::scoring::vdwaals)   
CountPairCrossover3full (core::scoring::etable::count_pair)   ImplicitFastClashCheck (protocols::scoring)   PairScoringScheme (core::sequence)   RotamerSetsOperation (core::pack::rotamer_set)   VdwGrid (protocols::qsar::scoring_grid)   
CountPairCrossover4 (core::scoring::etable::count_pair)   ImplicitLipidInfo (core::conformation::membrane)   PalesEvaluator (protocols::simple_filters)   RotamerSubset (core::pack::rotamer_set)   VdwGridCreator (protocols::qsar::scoring_grid)   
CountPairData_1_1 (core::scoring::etable::etrie)   ImportPoseOptions (core::import_pose)   PalesEvaluatorCreator (protocols::simple_filters)   RotamerSubsetRepacker (protocols::pack_daemon)   VdWTinkerEnergy (core::energy_methods)   
CountPairData_1_2 (core::scoring::etable::etrie)   ImportUnboundRotamersOperation (protocols::task_operations)   ParaIon (core::io::nmr)   RotamerSubsets (core::pack::rotamer_set)   VdWTinkerEnergyCreator (core::energy_methods)   
CountPairData_1_3 (core::scoring::etable::etrie)   ImportUnboundRotamersOperationCreator (protocols::task_operations)   ParallelBetaPairingPreferenceFilter (protocols::fldsgn::filters)   RotamerTrialsMinMover (protocols::minimization_packing)   VdWTinkerPoseInfo (core::scoring)   
CountPairDataGeneric (core::scoring::etable::etrie)   IncludeCurrent (core::pack::task::operation)   ParallelBetaPairingPreferenceFilterCreator (protocols::fldsgn::filters)   RotamerTrialsMinMoverCreator (protocols::minimization_packing)   VdWTinkerPotential (core::scoring)   
CountPairFactory (core::scoring::etable::count_pair)   IncludeCurrentCreator (core::pack::task::operation)   ParallelTempering (protocols::canonical_sampling)   RotamerTrialsMover (protocols::minimization_packing)   VdWTinkerResidueInfo (core::scoring)   
CountPairFunction (core::scoring::etable::count_pair)   IncludeCurrentRLT (core::pack::task::operation)   ParallelTemperingCreator (protocols::canonical_sampling)   RotamerTrialsMoverCreator (protocols::minimization_packing)   VdWTinkerResPairMinData (core::energy_methods)   
CountPairGeneric (core::scoring::etable::count_pair)   IncludeCurrentRLTCreator (core::pack::task::operation)   ParamagneticDatabaseHandler (core::io::nmr)   RotamerTrialsRefiner (protocols::loop_modeling::refiners)   VdWTinkerRotamerSetInfo (core::scoring)   
CountPairIntraRes (core::scoring::etable::count_pair)   IndelOptimizationMover (protocols::indel)   Parameter (core::conformation::parametric)   RotamerTrialsRefinerCreator (protocols::loop_modeling::refiners)   VDWTrieCountPair1B (core::scoring::vdwaals)   
CountPairNone (core::scoring::etable::count_pair)   IndependentBBTorsionSRFD (core::fragment)   ParameterizationCalculatorProperties (core::conformation::parametric)   RotamerTrie (core::scoring::trie)   VDWTrieEvaluator (core::scoring::vdwaals)   
CountPairRepMap (core::scoring::elec)   IndependentLoopMover (protocols::loops::loop_mover)   Parameters (core::conformation::parametric)   RotamerTrieBase (core::scoring::trie)   Vec1Hash (protocols::genetic_algorithm)   
CountPairRepresentative (core::scoring::elec)   InitializeByBins (protocols::simple_moves::bin_transitions)   ParametersSet (core::conformation::parametric)   Rotate (protocols::ligand_docking)   Vec3 (protocols::sic_dock)   
CountViolFunc (core::scoring::func)   InitializeByBinsCreator (protocols::simple_moves::bin_transitions)   ParametrizationCalculator (core::conformation::parametric)   Rotate_info (protocols::ligand_docking)   VectorCacheUnit (core::fragment)   
CoupledMover (protocols::simple_moves)   InitializeExtraRotsFromCommandline (core::pack::task::operation)   ParaNMRScoreMover (protocols::nmr)   RotateCreator (protocols::ligand_docking)   VectorExpression (protocols::pack_daemon)   
CoupledMoverCreator (protocols::simple_moves)   InitializeExtraRotsFromCommandlineCreator (core::pack::task::operation)   ParaNMRScoreMoverCreator (protocols::nmr)   RotateJumpAxisMover (protocols::rigid)   VectorExpressionCreator (protocols::pack_daemon)   
CoupledMovesProtocol (protocols::coupled_moves)   InitializeFromCommandline (core::pack::task::operation)   ParatopeEpitopeSiteConstraintMover (protocols::antibody::constraints)   Rotates (protocols::ligand_docking)   VectorFunction (protocols::pack_daemon)   
CoupledMovesProtocolCreator (protocols::coupled_moves)   InitializeFromCommandlineCreator (core::pack::task::operation)   ParatopeEpitopeSiteConstraintMoverCreator (protocols::antibody::constraints)   RotatesCreator (protocols::ligand_docking)   VectorFunction2 (protocols::pack_daemon)   
CovalentCompliance (protocols::noesy_assign)   InitializeFromOptionCollection (core::pack::task::operation)   ParatopeMetric (protocols::antibody)   RotateSegmentMover (protocols::denovo_design::movers)   VectorPair (protocols::hotspot_hashing)   
CovalentConnectionReplaceInfo (protocols::toolbox::match_enzdes_util)   InitializeFromOptionCollectionCreator (core::pack::task::operation)   ParatopeSiteConstraintMover (protocols::antibody::constraints)   RotateSegmentMoverCreator (protocols::denovo_design::movers)   VectorPoseFilter (protocols::filters)   
CovalentLabelingEnergy (core::energy_methods)   InnerJob (protocols::jd2)   ParatopeSiteConstraintMoverCreator (protocols::antibody::constraints)   RotationMover (protocols::membrane)   VectorPoseJobDistributor (protocols::jd2)   
CovalentLabelingEnergyCreator (core::energy_methods)   InnerLarvalJob (protocols::jd3)   ParsedProtocol (protocols::rosetta_scripts)   RotationMoverCreator (protocols::membrane)   VectorPoseMover (protocols::moves)   
CovalentLabelingFAEnergy (core::energy_methods)   InnerMultiThreadingJob (protocols::jd2)   ParsedProtocolCreator (protocols::rosetta_scripts)   RotationRange (protocols::denovo_design::movers)   VectorSelector (protocols::denovo_design::components)   
CovalentLabelingFAEnergyCreator (core::energy_methods)   InputPoseDeallocationMessage (protocols::jd3::deallocation)   ParsedProtocol::ParsedProtocolStep (protocols::rosetta_scripts)   RotationSearchPattern (protocols::hotspot_hashing)   VicinityPerturber (protocols::kinematic_closure::perturbers)   
CovalentResidueNetwork (protocols::toolbox)   InputSource (protocols::jd3)   ParsedTagCache (protocols::multistage_rosetta_scripts)   RotData (protocols::make_rot_lib)   VicinitySamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
CPDataCorrespondence (core::scoring::trie)   InputStreamStepWiseSampler (protocols::stepwise::sampler::input_streams)   ParserJobInputter (protocols::protein_interface_design)   RotLibdb (protocols::splice)   VIP_Mover (protocols::vip)   
CreateAngleConstraint (protocols::cyclic_peptide)   InputStreamWithResidueInfo (protocols::stepwise::modeler::protein)   ParserJobInputterCreator (protocols::protein_interface_design)   RotLibOut (protocols::splice)   VIP_Report (protocols::vip)   
CreateAngleConstraintCreator (protocols::cyclic_peptide)   InsertChunkMover (protocols::hybridization)   PartialAtomID (core::id)   RotLibOutCreator (protocols::splice)   VirtResClaim (protocols::environment::claims)   
CreateDistanceConstraint (protocols::cyclic_peptide)   InsertPoseIntoPoseMover (protocols::grafting::simple_movers)   PartialSecondarySimilarity (protocols::frag_picker::scores)   RotMatrix (protocols::mean_field)   VirtualCoordinate (core::conformation::symmetry)   
CreateDistanceConstraintCreator (protocols::cyclic_peptide)   InsertPoseIntoPoseMoverCreator (protocols::grafting::simple_movers)   PartialThreadingMover (protocols::comparative_modeling)   RotProb (protocols::mean_field)   VirtualizeAll (core::chemical)   
CreateGlycanSequonMover (protocols::carbohydrates)   InsertResMover (protocols::pose_length_moves)   Particle (core::optimization)   RotSub (core::pack::annealer)   VirtualizeSidechain (core::chemical)   
CreateGlycanSequonMoverCreator (protocols::carbohydrates)   InsertResMoverCreator (protocols::pose_length_moves)   ParticleSwarmMinimizer (core::optimization)   RPM_FilterStats (core::scoring::motif)   VirtualRootMover (protocols::simple_moves)   
CreateSequenceMotifMover (protocols::calc_taskop_movers)   InSetExpression (protocols::pack_daemon)   PartitionAggregateFunction (protocols::multistate_design)   RRComparer (protocols::rotamer_recovery)   VirtualRootMoverCreator (protocols::simple_moves)   
CreateSequenceMotifMoverCreator (protocols::calc_taskop_movers)   InstallFarnesylMover (protocols::farnesyl)   PartitionContactScreener (protocols::stepwise::screener)   RRComparerAutomorphicRMSD (protocols::rotamer_recovery)   VirtualSugarJustInTimeInstantiator (protocols::stepwise::modeler::rna::sugar)   
CreateTorsionConstraint (protocols::cyclic_peptide)   InstallFarnesylMoverCreator (protocols::farnesyl)   PartitionedSearchPattern (protocols::hotspot_hashing)   RRComparerAutomorphicRMSDCreator (protocols::rotamer_recovery)   VirtualSugarSampler (protocols::stepwise::modeler::rna::sugar)   
CreateTorsionConstraintCreator (protocols::cyclic_peptide)   IntegrationTestBreaker (protocols::stepwise::screener)   PartnerMotifScorer (protocols::sewing::scoring)   RRComparerChiDiff (protocols::rotamer_recovery)   VirtualSugarSamplerFromStringList (protocols::stepwise::modeler::rna::sugar)   
CrosslinkerMover (protocols::cyclic_peptide)   InteractingRotamerExplosion (protocols::task_operations)   PartnerMotifScorerCreator (protocols::sewing::scoring)   RRComparerChiDiffCreator (protocols::rotamer_recovery)   VisualizeEmbeddingMover (protocols::membrane::visualize)   
CrosslinkerMoverCreator (protocols::cyclic_peptide)   InteractingRotamerExplosionCreator (protocols::task_operations)   Patch (core::chemical)   RRComparerCreator (protocols::rotamer_recovery)   VisualizeEmbeddingMoverCreator (protocols::membrane::visualize)   
CrosslinkerMoverHelper (protocols::cyclic_peptide::crosslinker)   InteractionEnergyMetric (core::simple_metrics::metrics)   PatchCase (core::chemical)   RRComparerElecDensDiff (protocols::rotamer_recovery)   VisualizeMembraneMover (protocols::membrane::visualize)   
CrossoverBehavior   InteractionEnergyMetricCreator (core::simple_metrics::metrics)   PatchdockReader (protocols::protein_interface_design)   RRComparerElecDensDiffCreator (protocols::rotamer_recovery)   VisualizeMembraneMoverCreator (protocols::membrane::visualize)   
CrossPeak (protocols::noesy_assign)   InteractionGraphBase (core::pack::interaction_graph)   PatchdockTransform (protocols::protein_interface_design::movers)   RRComparerRotBins (protocols::rotamer_recovery)   VLB (protocols::protein_interface_design::movers)   
CrossPeak3D (protocols::noesy_assign)   InteractionGraphFactory (core::pack::interaction_graph)   PatchdockTransformCreator (protocols::protein_interface_design::movers)   RRComparerRotBinsCreator (protocols::rotamer_recovery)   VLBCreator (protocols::protein_interface_design::movers)   
CrossPeak4D (protocols::noesy_assign)   InteractionGraphSummaryMetric (protocols::quantum_annealing)   PatchOperation (protocols::canonical_sampling)   RRProtocol (protocols::rotamer_recovery)   VLBInstruction (protocols::protein_interface_design::movers)   
CrossPeakInfo (protocols::noesy_assign)   InteractionGraphSummaryMetricCreator (protocols::quantum_annealing)   PatchOperation (core::chemical)   RRProtocolCreator (protocols::rotamer_recovery)   VLBProtected (protocols::denovo_design::components)   
CrossPeakList (protocols::noesy_assign)   InteratomicVarianceMatrix (protocols::toolbox)   PBLifetimeCache (core::energy_methods)   RRProtocolMinPack (protocols::rotamer_recovery)   VMax (protocols::pack_daemon)   
CrystalContactsOperation (protocols::task_operations)   InterbondAngleScore (protocols::frag_picker::scores)   PCA (protocols::evaluation)   RRProtocolMinPackCreator (protocols::rotamer_recovery)   VMaxBy (protocols::pack_daemon)   
CrystalContactsOperationCreator (protocols::task_operations)   InterchainEnvEnergy (protocols::scoring::methods)   PcaEvaluator (protocols::abinitio)   RRProtocolMover (protocols::rotamer_recovery)   VMin (protocols::pack_daemon)   
CrystInfo (core::io)   InterchainEnvEnergyCreator (protocols::scoring::methods)   PCluster (protocols::pockets)   RRProtocolMoverCreator (protocols::rotamer_recovery)   VMinBy (protocols::pack_daemon)   
CrystRMS (protocols::cryst)   InterchainJumpSelector (core::select::jump_selector)   PClusterSet (protocols::pockets)   RRProtocolPackRotamers (protocols::rotamer_recovery)   VoidsPenaltyEnergy (core::pack::guidance_scoreterms::voids_penalty_energy)   
CrystRMSCreator (protocols::cryst)   InterchainJumpSelectorCreator (core::select::jump_selector)   PCS_data (protocols::scoring::methods::pcs)   RRProtocolPackRotamersCreator (protocols::rotamer_recovery)   VoidsPenaltyEnergyCreator (core::pack::guidance_scoreterms::voids_penalty_energy)   
CS2ndShift (protocols::frag_picker)   InterchainPairEnergy (protocols::scoring::methods)   PCS_data_input (protocols::scoring::methods::pcs)   RRProtocolReferenceStructure (protocols::rotamer_recovery)   VoidsPenaltyVoxelGrid (core::pack::guidance_scoreterms::voids_penalty_energy)   
CSA (core::scoring)   InterchainPairEnergyCreator (protocols::scoring::methods)   PCS_data_input_manager (protocols::scoring::methods::pcs)   RRProtocolReferenceStructureCreator (protocols::rotamer_recovery)   VoxelGridPoint (core::scoring::nmr)   
CSScore (protocols::frag_picker::scores)   InterchainPotential (protocols::scoring)   PCS_data_input_manager_Ts1 (protocols::scoring::methods::pcsTs1)   RRProtocolRelax (protocols::rotamer_recovery)   VoxelGridPoint_AA (core::scoring::nmr)   
CSTalosIO (protocols::frag_picker)   Interface (protocols::ligand_docking::ligand_options)   PCS_data_input_manager_Ts2 (protocols::scoring::methods::pcsTs2)   RRProtocolRelaxCreator (protocols::rotamer_recovery)   VoxelSetIterator (protocols::match)   
CstEnergyContainer (core::scoring::constraints)   Interface (protocols::scoring)   PCS_data_input_manager_Ts3 (protocols::scoring::methods::pcsTs3)   RRProtocolRotamerTrials (protocols::rotamer_recovery)   VoxelSpacingMultifunc (protocols::electron_density)   
CstInfoMover (protocols::constraint_movers)   InterfaceAnalyzerMover (protocols::analysis)   PCS_data_input_manager_Ts4 (protocols::scoring::methods::pcsTs4)   RRProtocolRotamerTrialsCreator (protocols::rotamer_recovery)   VoxelSpacingRefinementMover (protocols::electron_density)   
CstInfoMoverCreator (protocols::constraint_movers)   InterfaceAnalyzerMoverCreator (protocols::analysis)   PCS_data_input_Ts1 (protocols::scoring::methods::pcsTs1)   RRProtocolRTMin (protocols::rotamer_recovery)   VoxelSpacingRefinementMoverCreator (protocols::electron_density)   
CstMinimizationData (core::scoring::constraints)   InterfaceBindingEnergyDensityFilter (protocols::simple_ddg)   PCS_data_input_Ts2 (protocols::scoring::methods::pcsTs2)   RRProtocolRTMinCreator (protocols::rotamer_recovery)   
  W  
CstResInteractions (protocols::toolbox::match_enzdes_util)   InterfaceBindingEnergyDensityFilterCreator (protocols::simple_ddg)   PCS_data_input_Ts3 (protocols::scoring::methods::pcsTs3)   RRReporter (protocols::rotamer_recovery)   
CstResNeighbConstIterator (core::scoring::constraints)   InterfaceBuilder (protocols::ligand_docking)   PCS_data_input_Ts4 (protocols::scoring::methods::pcsTs4)   RRReporterCreator (protocols::rotamer_recovery)   WalkingBondAnglePerturber (protocols::kinematic_closure::perturbers)   
CstResNeighbIterator (core::scoring::constraints)   InterfaceBuilderLoader (protocols::ligand_docking)   PCS_data_per_lanthanides (protocols::scoring::methods::pcs)   RRReporterHuman (protocols::rotamer_recovery)   WalkingPerturber (protocols::kinematic_closure::perturbers)   
CtabParserBase (core::chemical::sdf)   InterfaceBuilderLoaderCreator (protocols::ligand_docking)   PCS_data_per_lanthanides_Ts1 (protocols::scoring::methods::pcsTs1)   RRReporterHumanCreator (protocols::rotamer_recovery)   WallpaperGroup (protocols::cryst)   
CtabV2000Parser (core::chemical::sdf)   InterfaceData (protocols::analysis)   PCS_data_per_lanthanides_Ts2 (protocols::scoring::methods::pcsTs2)   RRReporterSimple (protocols::rotamer_recovery)   WaterAdductHBondEnergy (core::energy_methods)   
CtabV3000Parser (core::chemical::sdf)   InterfaceDdGMover (protocols::features)   PCS_data_per_lanthanides_Ts3 (protocols::scoring::methods::pcsTs3)   RRReporterSimpleCreator (protocols::rotamer_recovery)   WaterAdductHBondEnergyCreator (core::energy_methods)   
CustomAtomPairEnergy (core::energy_methods)   InterfaceDdGMoverCreator (protocols::features)   PCS_data_per_lanthanides_Ts4 (protocols::scoring::methods::pcsTs4)   RRReporterSQLite (protocols::rotamer_recovery)   WaterAdductHBondPotential (core::scoring)   
CustomAtomPairEnergyCreator (core::energy_methods)   InterfaceDefinitionCalculator (core::pose::metrics::simple_calculators)   PCS_data_Ts1 (protocols::scoring::methods::pcsTs1)   RRReporterSQLiteCreator (protocols::rotamer_recovery)   WaterAdductIntraEnergy (core::energy_methods)   
CustomBaseTypePackerPalette (core::pack::palette)   InterfaceDeltaEnergeticsCalculator (core::pose::metrics::simple_calculators)   PCS_data_Ts2 (protocols::scoring::methods::pcsTs2)   RT (core::kinematics)   WaterAdductIntraEnergyCreator (core::energy_methods)   
CustomBaseTypePackerPaletteCreator (core::pack::palette)   InterfaceFeatures (protocols::features)   PCS_data_Ts3 (protocols::scoring::methods::pcsTs3)   RT_helper (core::scoring::disulfides)   WaterAnchorInfo (core::pack::rotamer_set)   
CustomScoreSelector (protocols::frag_picker)   InterfaceFeaturesCreator (protocols::features)   PCS_data_Ts4 (protocols::scoring::methods::pcsTs4)   RTConstraint (core::scoring::constraints)   WaterBuilder (core::scoring::lkball)   
CutAndJump (protocols::denovo_design::movers)   InterfaceHbondsFilter (protocols::simple_filters)   PCS_Energy (protocols::scoring::methods::pcs)   RTMin (core::pack)   WaterBuilderForRestype (core::scoring::lkball)   
CutBiasClaim (protocols::environment::claims)   InterfaceHbondsFilterCreator (protocols::simple_filters)   PCS_Energy_parameters_manager (protocols::scoring::methods::pcs)   RunSimpleMetricsMover (protocols::analysis::simple_metrics)   WaterFeatures (protocols::features)   
CutBiasClaimer (protocols::topology_broker)   InterfaceHolesFilter (protocols::protein_interface_design::filters)   PCS_Energy_parameters_manager_Ts1 (protocols::scoring::methods::pcsTs1)   RunSimpleMetricsMoverCreator (protocols::analysis::simple_metrics)   WaterFeaturesCreator (protocols::features)   
CutBiasElement (protocols::environment::claims)   InterfaceHolesFilterCreator (protocols::protein_interface_design::filters)   PCS_Energy_parameters_manager_Ts2 (protocols::scoring::methods::pcsTs2)   RuntimeFeatures (protocols::features)   WaterMediatedHbondMetric (core::simple_metrics::per_residue_metrics)   
CutChainMover (protocols::simple_moves)   InterfaceHydrophobicResidueContactsFilter (protocols::simple_filters)   PCS_Energy_parameters_manager_Ts3 (protocols::scoring::methods::pcsTs3)   RuntimeFeaturesCreator (protocols::features)   WaterMediatedHbondMetricCreator (core::simple_metrics::per_residue_metrics)   
CutChainMoverCreator (protocols::simple_moves)   InterfaceHydrophobicResidueContactsFilterCreator (protocols::simple_filters)   PCS_Energy_parameters_manager_Ts4 (protocols::scoring::methods::pcsTs4)   
  S  
WaterPackingInfo (core::pack::rotamer_set)   
CutClaim (protocols::topology_broker::claims)   InterfaceInfo (protocols::ligand_docking::ligand_options)   PCS_Energy_Ts1 (protocols::scoring::methods::pcsTs1)   WaterRot (protocols::simple_moves)   
CutElement (protocols::environment::claims)   InterfaceInfo (protocols::scoring)   PCS_Energy_Ts2 (protocols::scoring::methods::pcsTs2)   SA_Energy (core::energy_methods)   WaterRotsDB (protocols::simple_moves)   
CutOutDomain (protocols::cutoutdomain)   InterfaceNeighborDefinitionCalculator (core::pose::metrics::simple_calculators)   PCS_Energy_Ts3 (protocols::scoring::methods::pcsTs3)   SA_EnergyCreator (core::energy_methods)   WaterSpecificEnergy (core::energy_methods)   
CutOutDomainCreator (protocols::cutoutdomain)   InterfacePackingFilter (protocols::matdes)   PCS_Energy_Ts4 (protocols::scoring::methods::pcsTs4)   SaltBridgeCalculator (protocols::pose_metric_calculators)   WaterSpecificEnergyCreator (core::energy_methods)   
CutpointResidueSelector (protocols::fold_from_loops::selectors)   InterfacePackingFilterCreator (protocols::matdes)   PCS_file_data (protocols::scoring::methods::pcs)   SaltBridgeFeatures (protocols::features)   WaterWeightGridSet (core::energy_methods)   
CutpointResidueSelectorCreator (protocols::fold_from_loops::selectors)   InterfaceRecapitulationMover (protocols::protein_interface_design::movers)   PCS_file_data_Ts1 (protocols::scoring::methods::pcsTs1)   SaltBridgeFeaturesCreator (protocols::features)   WatsonCrickResidueMatcher (core::conformation)   
PCluster::Cxyz (protocols::pockets)   InterfaceRecapitulationMoverCreator (protocols::protein_interface_design::movers)   PCS_file_data_Ts2 (protocols::scoring::methods::pcsTs2)   SameChiBinComboGrouper (protocols::match::output)   WatsonCrickRotamerCouplings (protocols::dna)   
CCluster::Cxyz (protocols::pockets)   InterfaceSasaDefinitionCalculator (core::pose::metrics::simple_calculators)   PCS_file_data_Ts3 (protocols::scoring::methods::pcsTs3)   SameRotamerComboGrouper (protocols::match::output)   WatsonCrickRotamerCouplingsCreator (protocols::dna)   
CycleMover (protocols::moves)   InterfaceSasaFilter (protocols::simple_filters)   PCS_file_data_Ts4 (protocols::scoring::methods::pcsTs4)   SameSequenceAndDSPositionGrouper (protocols::match::output)   WeightedFragmentSmoothTrialMover (protocols::hybridization)   
CyclicMover (protocols::moves)   InterfaceSasaFilterCreator (protocols::simple_filters)   PCS_FragDistance (protocols::frag_picker::scores)   SameSequenceGrouper (protocols::match::output)   WeightedFragmentTrialMover (protocols::hybridization)   
CyclizationMover (protocols::simple_moves)   InterfaceScoreCalculator (protocols::ligand_docking)   PCS_line_data (protocols::scoring::methods::pcs)   SameStrand (protocols::jumping)   WeightRangeConstraint (protocols::optimize_weights)   
CyclizedPeptideInfo (protocols::peptide_deriver)   InterfaceScoreCalculatorCreator (protocols::ligand_docking)   PCS_line_data_Ts1 (protocols::scoring::methods::pcsTs1)   SampleApplier (protocols::stepwise::screener)   WhileMover (protocols::moves)   
PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo (protocols::peptide_deriver)   InterfaceSidechainMinMover (protocols::docking)   PCS_line_data_Ts2 (protocols::scoring::methods::pcsTs2)   SampleFarnesylMover (protocols::farnesyl)   WholeBodyRotationMover (protocols::rigid)   
CycpepSymmetryFilter (protocols::cyclic_peptide)   InterfaceTaskOperation (protocols::simple_task_operations)   PCS_line_data_Ts3 (protocols::scoring::methods::pcsTs3)   SampleFarnesylMoverCreator (protocols::farnesyl)   WholeBodyTranslationMover (protocols::rigid)   
CycpepSymmetryFilterCreator (protocols::cyclic_peptide)   InterGroupInterfaceByVectorSelector (core::select::residue_selector)   PCS_line_data_Ts4 (protocols::scoring::methods::pcsTs4)   SampleGrid (protocols::magnesium)   WholeStructureEnergy (core::scoring::methods)   
  D  
InterGroupInterfaceByVectorSelectorCreator (core::select::residue_selector)   PCS_tensor (protocols::scoring::methods::pcs)   SampleRotamersFromPDB (protocols::splice)   WholeWholeEnergyInvoker (core::scoring::etable)   
InterGroupNeighborsCalculator (protocols::pose_metric_calculators)   PCS_tensor_Ts1 (protocols::scoring::methods::pcsTs1)   SampleRotamersFromPDB_RotamerSetOperation (protocols::splice)   WidthFirstSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
D2H_SA_Energy (core::energy_methods)   InterlockAroma (protocols::flxbb)   PCS_tensor_Ts2 (protocols::scoring::methods::pcsTs2)   SampleRotamersFromPDBCreator (protocols::splice)   WobbleMover (protocols::simple_moves)   
D2H_SA_EnergyCreator (core::energy_methods)   InterlockAromaCreator (protocols::flxbb)   PCS_tensor_Ts3 (protocols::scoring::methods::pcsTs3)   SamplerPlusPlus (protocols::toolbox)   NetworkQueue::WorkUnit (protocols::network)   
DaemonSet (protocols::pack_daemon)   InterlockingAromaFilter (protocols::fldsgn::filters)   PCS_tensor_Ts4 (protocols::scoring::methods::pcsTs4)   SampleStrategyData (protocols::match::upstream)   WorkUnit_BatchRelax (protocols::relax)   
DarcParticleSwarmMinimizer (protocols::pockets)   InterlockingAromaFilterCreator (protocols::fldsgn::filters)   PCSData (core::scoring::nmr::pcs)   SampleTiltAngles (protocols::membrane::benchmark)   WorkUnit_BatchRelax_and_PostRescore (protocols::relax)   
DatabaseEntryWorkUnit (protocols::wum)   InterModelMotifScorer (protocols::sewing::scoring)   PcsDataCenter (protocols::scoring::methods::pcs2)   SampleTiltAnglesCreator (protocols::membrane::benchmark)   WorkUnit_bbGauss (protocols::mpi_refinement)   
DatabaseFilter (protocols::features)   InterModelMotifScorerCreator (protocols::sewing::scoring)   PcsDataCenterManager (protocols::scoring::methods::pcs2)   SandwichFeatures (protocols::features::strand_assembly)   WorkUnit_CombinePose (protocols::mpi_refinement)   
DatabaseJobInputter (protocols::features)   IntermolEnergy (core::energy_methods)   PcsDataCenterManagerSingleton (protocols::scoring::methods::pcs2)   SandwichFeaturesCreator (protocols::features::strand_assembly)   WorkUnit_FragInsert (protocols::mpi_refinement)   
DatabaseJobInputterCreator (protocols::features)   IntermolEnergyCreator (core::energy_methods)   PcsDataLanthanide (protocols::scoring::methods::pcs2)   SandwichFragment (protocols::features::strand_assembly)   WorkUnit_KicCloser (protocols::mpi_refinement)   
DatabaseJobOutputter (protocols::features)   InternalWorkingResidueParameter (protocols::stepwise::modeler::rna)   PcsEnergy (protocols::scoring::methods::pcs2)   SaneDockingProtocol (protocols::docking::stateless)   WorkUnit_LoopHash (protocols::loophash)   
DatabaseJobOutputterCreator (protocols::features)   InterRepeatContactFilter (protocols::simple_filters)   PCSEnergy (protocols::nmr::pcs)   SaneMinMover (protocols::minimization_packing)   WorkUnit_LoopHash (protocols::mpi_refinement)   
DatabaseOccSolEne (core::scoring::geometric_solvation)   InterRepeatContactFilterCreator (protocols::simple_filters)   PcsEnergyController (protocols::topology_broker)   SaneMinMoverCreator (protocols::minimization_packing)   WorkUnit_MD (protocols::mpi_refinement)   
DatabaseRelaxScript (protocols::relax)   Interval (protocols::jumping)   PcsEnergyCreator (protocols::scoring::methods::pcs2)   SAnode (core::scoring::power_diagram)   WorkUnit_MoverWrapper (protocols::wum)   
DatabaseSessionLoader (protocols::parser)   Interval (protocols::forge::build)   PCSEnergyCreator (protocols::nmr::pcs)   SAnode (core::scoring)   WorkUnit_NormalMode (protocols::mpi_refinement)   
DatabaseSessionLoaderCreator (protocols::parser)   IntraDesignTerminusMotifScorer (protocols::sewing::scoring)   PcsEnergyParameter (protocols::scoring::methods::pcs2)   SapConstraint (core::pack::guidance_scoreterms::sap)   WorkUnit_PartialAbinitio (protocols::mpi_refinement)   
DatabaseThread (protocols::task_operations)   IntraDesignTerminusMotifScorerCreator (protocols::sewing::scoring)   PcsEnergyParameterManager (protocols::scoring::methods::pcs2)   SapConstraintEnergy (core::pack::guidance_scoreterms::sap)   WorkUnit_RamaPerturber (protocols::mpi_refinement)   
DatabaseThreadCreator (protocols::task_operations)   IntraRepeatContactFilter (protocols::simple_filters)   PcsGridSearchParameter (protocols::scoring::methods::pcs2)   SapConstraintEnergyCreator (core::pack::guidance_scoreterms::sap)   WorkUnit_Relax (protocols::mpi_refinement)   
DataBuffer (protocols::canonical_sampling::mc_convergence_checks)   IntraRepeatContactFilterCreator (protocols::simple_filters)   PcsGridSearchParameterManager (protocols::scoring::methods::pcs2)   SapConstraintHelper (core::pack::guidance_scoreterms::sap)   WorkUnit_Sampler (protocols::mpi_refinement)   
DataLoader (protocols::parser)   InverseRotamersCstGeneratorCreator (protocols::forge::constraints)   PcsInputCenter (protocols::scoring::methods::pcs2)   SapConstraintOptions (core::pack::guidance_scoreterms::sap)   WorkUnit_SilentStructStore (protocols::wum)   
DataLoaderCreator (protocols::parser)   InverseRotamersRCG (protocols::forge::constraints)   PcsInputCenterManager (protocols::scoring::methods::pcs2)   SapDatabase (core::pack::guidance_scoreterms::sap)   WorkUnit_Wait (protocols::wum)   
DataLoaderFactory (protocols::parser)   InvGeometricFunc (protocols::moves)   PcsInputFile (protocols::scoring::methods::pcs2)   SapMathConstraint (core::pack::guidance_scoreterms::sap)   WorkUnitBase (protocols::wum)   
DataLoaderRegistrator (protocols::parser)   Invoker (core::scoring::etable::count_pair)   PcsInputLine (protocols::scoring::methods::pcs2)   SapScoreMetric (core::pack::guidance_scoreterms::sap)   WorkUnitList (protocols::wum)   
DataPoint (protocols::cluster)   InvRotamerDots (core::pack::interaction_graph)   PCSLigandTransformMover (protocols::nmr::pcs)   SapScoreMetricCreator (core::pack::guidance_scoreterms::sap)   WorkUnitManager (protocols::wum)   
DbTrajectoryReader (protocols::trajectory)   InvrotCollector (protocols::toolbox::match_enzdes_util)   PCSLigandTransformMoverCreator (protocols::nmr::pcs)   SasaCalc (core::scoring::sasa)   WorkUnitQueue (protocols::wum)   
DbTrajectoryRecorder (protocols::canonical_sampling)   InvrotTarget (protocols::toolbox::match_enzdes_util)   PCSMultiGrid (protocols::qsar::scoring_grid)   SasaCalculator2 (core::pose::metrics::simple_calculators)   WorkUnitQueue_Swapped (protocols::wum)   
DbTrajectoryRecorderCreator (protocols::canonical_sampling)   InvrotTree (protocols::toolbox::match_enzdes_util)   PCSMultiGridCreator (protocols::qsar::scoring_grid)   SasaCalculatorLegacy (core::pose::metrics::simple_calculators)   WrappedOptEExpressionCreator (protocols::optimize_weights)   
DbTrajectoryWriter (protocols::trajectory)   InvrotTreeCstGeneratorCreator (protocols::forge::constraints)   PCSMultiSet (core::scoring::nmr::pcs)   SASAEnergy (core::energy_methods)   WrapperOptEMultifunc (protocols::optimize_weights)   
DC (core::scoring)   InvrotTreeNode (protocols::toolbox::match_enzdes_util)   PCSSingle (core::scoring::nmr::pcs)   SASAEnergyCreator (core::energy_methods)   WriteFileSFB (protocols::jd2)   
DDGBindOptEData (protocols::optimize_weights)   InvrotTreeNodeBase (protocols::toolbox::match_enzdes_util)   PCSSingleGrid (protocols::qsar::scoring_grid)   SasaMethod (core::scoring::sasa)   WriteFiltersToPose (protocols::simple_moves)   
DdGFeatures (protocols::features)   InvrotTreeRCG (protocols::forge::constraints)   PCSSingleGridCreator (protocols::qsar::scoring_grid)   SasaMetric (core::simple_metrics::metrics)   WriteFiltersToPoseCreator (protocols::simple_moves)   
DdGFeaturesCreator (protocols::features)   IonizableResidue (protocols::simple_moves)   PCSSingleSet (core::scoring::nmr::pcs)   SasaMetricCreator (core::simple_metrics::metrics)   WriteKinemageOutputter (protocols::match::output)   
DdgFilter (protocols::simple_ddg)   IRCollection (protocols::motifs)   PcsTensor (protocols::scoring::methods::pcs2)   SasaOptions (core::scoring::packstat)   WriteLigandMolFile (protocols::ligand_docking)   
DdgFilterCreator (protocols::simple_ddg)   IRmsdFilter (protocols::protein_interface_design::filters)   PCSTensor (core::scoring::nmr::pcs)   SASAPotential (core::scoring)   WriteLigandMolFileCreator (protocols::ligand_docking)   
DDGMutationOptEData (protocols::optimize_weights)   IRmsdFilterCreator (protocols::protein_interface_design::filters)   PCSTensorOptimizer (protocols::nmr::pcs)   SasaResult (core::scoring::packstat)   WriteOut_MpiFileBuffer (protocols::jd2)   
DdGScan (protocols::simple_ddg)   IsMainAtomPredicate (core::scoring)   PDatom (core::scoring)   SaveAndRetrieveSidechains (protocols::protein_interface_design::movers)   WriteSSEMover (protocols::simple_moves)   
DdGScanCreator (protocols::simple_ddg)   IsProteinCAPredicate (core::scoring)   PDB (protocols::sparta)   SaveAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   WriteSSEMoverCreator (protocols::simple_moves)   
DDomainParse (protocols::hybridization)   LoggedFragmentMover::Item (protocols::simple_moves)   PDB_Entry (protocols::sparta)   SavePDBInfoMover (protocols::fold_from_loops::movers)   WriteUpstreamCoordinateKinemage (protocols::match::output)   
DDPlookup (core::scoring::interface_)   IteratedConvergenceMover (protocols::moves)   PDBChunkLibraryInputter (protocols::jd3::chunk_library_inputters)   SavePDBInfoMoverCreator (protocols::fold_from_loops::movers)   WriteUpstreamHitKinemage (protocols::match::output)   
DDPscore (core::scoring::interface_)   IteratedConvergenceMoverCreator (protocols::moves)   PDBChunkLibraryInputterCreator (protocols::jd3::chunk_library_inputters)   SavePoseConstraintToFileFilter (protocols::constraint_filters)   WTEBiasEnergy (protocols::canonical_sampling)   
DDPscoreCreator (core::scoring::interface_)   IterativeAbrelax (protocols::abinitio)   PdbDataFeatures (protocols::features)   SavePoseConstraintToFileFilterCreator (protocols::constraint_filters)   WorkUnitBase::WU_Header (protocols::wum)   
DeallocationMessage (protocols::jd3::deallocation)   IterativeBase (protocols::abinitio)   PdbDataFeaturesCreator (protocols::features)   SavePoseMover (protocols::rosetta_scripts)   
  X  
DebuggingAnnealer (core::pack::annealer)   IterativeCentroid (protocols::abinitio)   PDBDumpMover (protocols::moves)   SavePoseMoverCreator (protocols::rosetta_scripts)   
DebugOut_MpiFileBuffer (protocols::jd2)   IterativeFullatom (protocols::abinitio)   PDBFullModelInputter (protocols::jd3::full_model_inputters)   SaveResfileToDiskFilter (protocols::simple_filters)   XformScore (core::scoring::motif)   
DeclareBond (protocols::cyclic_peptide)   IterativeOptEDriver (protocols::optimize_weights)   PDBFullModelInputterCreator (protocols::jd3::full_model_inputters)   SaveResfileToDiskFilterCreator (protocols::simple_filters)   XformSummary (core::scoring::motif)   
DeclareBondCreator (protocols::cyclic_peptide)   IterativeVectorExpression (protocols::pack_daemon)   PdbIdChunkFilter (protocols::frag_picker)   SaveSequenceToCommentsMover (protocols::simple_moves)   XfoxmScore (protocols::sic_dock)   
DeclareStructureDataCovalentBondMover (protocols::denovo_design::movers)   
  J  
PDBInfo (core::pose)   SaveSequenceToCommentsMoverCreator (protocols::simple_moves)   Xfrag (core::scoring::motif)   
DeclareStructureDataCovalentBondMoverCreator (protocols::denovo_design::movers)   PDBJobInputter (protocols::jd2)   SAXSEnergy (core::energy_methods)   XfragSet (core::scoring::motif)   
DecomposeAndReweightEnergiesCalculator (protocols::pose_metric_calculators)   JacobianStructure (core::kinematics::jacobian)   PDBJobInputterCreator (protocols::jd2)   SAXSEnergyCEN (core::energy_methods)   Xfres (core::scoring::motif)   
DecoratedNetworkState (protocols::hbnet)   JacobiLoopClosureMover (protocols::loops::loop_closure::jacobi)   PDBJobOutputter (protocols::jd2)   SAXSEnergyCreator (core::energy_methods)   XmlObjects (protocols::rosetta_scripts)   
DecoyFileData (core::io::raw_data)   JacobiLoopClosureMoverCreator (protocols::loops::loop_closure::jacobi)   PDBJobOutputterCreator (protocols::jd2)   SAXSEnergyCreatorCEN (core::energy_methods)   XtalMLEnergy (core::energy_methods)   
DecoySetEvaluation (protocols::toolbox)   JCoupling (protocols::frag_picker::scores)   PDBLandmark (protocols::antibody)   SAXSEnergyCreatorFA (core::energy_methods)   XtalMLEnergyCreator (core::energy_methods)   
DecoyStruct (core::io::raw_data)   JCouplingIO (protocols::frag_picker)   PDBNumbering (protocols::antibody::design)   SAXSEnergyFA (core::energy_methods)   XYZ_Func (core::scoring::func)   
DEERChiSqMethod (core::scoring::epr_deer::metrics)   JD2Failure (protocols::jd2)   PDBOutput (protocols::dna)   SAXSScoreFilter (protocols::simple_filters)   XYZClaim (protocols::environment::claims)   
DEERData (core::scoring::epr_deer::metrics)   JGJobNode (protocols::jd3)   PDBPoseInputStream (core::import_pose::pose_stream)   SC_BB_EnergyInvoker (core::scoring::etable)   XYZEvent (core::conformation::signals)   
DEERDataCache (core::scoring::epr_deer)   JobGenealogist::JGJobNodeOP_hash (protocols::jd3)   PDBPoseInputter (protocols::jd3::pose_inputters)   SC_SC_EnergyInvoker (core::scoring::etable)   XYZs (core::scoring::constraints)   
DEERDecayData (core::scoring::epr_deer::metrics)   JGResultNode (protocols::jd3)   PDBPoseInputterCreator (protocols::jd3::pose_inputters)   SC_Whole_EnergyInvoker (core::scoring::etable)   
  Y  
DEERDistanceBounds (core::scoring::epr_deer::metrics)   JobGenealogist::JGResultNodeOP_hash (protocols::jd3)   PDBPoseMap (core::pose)   ScaffoldBuildPoint (protocols::match::upstream)   
DEERDistanceDistribution (core::scoring::epr_deer::metrics)   JJH_Minimizer (core::optimization)   PDBPoseOutputSpecification (protocols::jd3::pose_outputters)   ScalarWeightedFunc (core::scoring::func)   YHHPlanarityEnergy (core::energy_methods)   
DEEREnergy (core::energy_methods)   Job (protocols::jd3)   PDBPoseOutputter (protocols::jd3::pose_outputters)   ScaleAnnealerTemperatureOperation (protocols::optimize_weights)   YHHPlanarityEnergyCreator (core::energy_methods)   
DEEREnergyCreator (core::energy_methods)   Job (protocols::jd2)   PDBPoseOutputterCreator (protocols::jd3::pose_outputters)   ScaleMapIntensities (protocols::electron_density)   
  Z  
DEERIO (core::scoring::epr_deer)   JobDataFeatures (protocols::features)   PDBReloadMover (protocols::simple_moves)   ScaleMapIntensitiesCreator (protocols::electron_density)   
DEERJaccardMethod (core::scoring::epr_deer::metrics)   JobDataFeaturesCreator (protocols::features)   PDBReloadMoverCreator (protocols::simple_moves)   SCAN (core::pack::task)   ZincHeterodimerMover (protocols::metal_interface)   
DEERJSMethod (core::scoring::epr_deer::metrics)   JobDigraph (protocols::jd3)   PDBRotamerLibrarySpecification (core::chemical::rotamers)   Scheduler (protocols::mpi_refinement)   ZincSiteFinder (protocols::metal_interface)   
DEERMiscMethod (core::scoring::epr_deer::metrics)   JobDigraphUpdater (protocols::jd3)   PDBRotamerLibrarySpecificationCreator (core::chemical::rotamers)   SchemePlaceMotifsMover (protocols::matdes)   
  _  
DEEROverlapMethod (core::scoring::epr_deer::metrics)   JobDirectedEdge (protocols::jd3)   PDBSilentStruct (core::import_pose)   SchemePlaceMotifsMoverCreator (protocols::matdes)   
DefaultCubeHash (core::conformation)   JobDirectedNode (protocols::jd3)   PDBSilentStructCreator (core::import_pose)   SCMinMinimizerMap (core::pack::scmin)   _AE_cdr_detection_failed_ (protocols::antibody::grafting)   
DefaultPackerPalette (core::pack::palette)   JobDistributor (protocols::jd3)   PDBTrajectoryRecorder (protocols::canonical_sampling)   SCMinMultifunc (core::pack::scmin)   _AE_cdr_undefined_ (protocols::antibody::grafting)   
DefaultPackerPaletteCreator (core::pack::palette)   JobDistributor (protocols::jd2)   PDBTrajectoryRecorderCreator (protocols::canonical_sampling)   ScoreCache (core::energy_methods)   _AE_grafting_failed_ (protocols::antibody::grafting)   
DefineMovableLoops (protocols::seeded_abinitio)   JobDistributorFactory (protocols::jd3)   PDBWriter (protocols::match::output)   ScoreCutoffFilter (protocols::score_filters)   _AE_invalid_cdr_region_ (protocols::antibody::grafting)   
DefineMovableLoopsCreator (protocols::seeded_abinitio)   JobDistributorFactory (protocols::jd2)   PDDFEnergy (protocols::scoring::methods::saxs)   ScoreCutoffFilterCreator (protocols::score_filters)   _AE_json_cdr_detection_failed_ (protocols::antibody::grafting)   
DeleteActCoordAtom (core::chemical)   JobExtractor (protocols::jd3::job_distributors)   PDDFEnergyCreator (protocols::scoring::methods::saxs)   ScoredBridgingWater (core::scoring::lkball)   _AE_numbering_failed_ (protocols::antibody::grafting)   
DeleteAllRotamerSetOperation (core::pack::rotamer_set)   JobGenealogist (protocols::jd3)   PDDFScoreFilter (protocols::simple_filters)   ScoredPoint (protocols::electron_density)   _AE_scs_failed_ (protocols::antibody::grafting)   
DeleteAtom (core::chemical)   JobInputter (protocols::jd2)   PDEdge (core::pack::interaction_graph)   ScoredPointCmptr (protocols::electron_density)   _AE_unexpected_region_length_ (protocols::antibody::grafting)   
DeleteChainMover (protocols::simple_moves)   JobInputterCreator (protocols::jd2)   PDinter (core::scoring::power_diagram)   ScoreEvaluator (protocols::simple_filters)   _ATOM_RADIUS (core::scoring::sc)   
DeleteChainMoverCreator (protocols::simple_moves)   JobInputterFactory (protocols::jd2)   PDinter (core::scoring)   ScoreEValuator (protocols::frag_picker::scores)   _DOT (core::scoring::sc)   
DeleteChainsMover (protocols::simple_moves)   JobInputterRegistrator (protocols::jd2)   PDInteractionGraph (core::pack::interaction_graph)   ScoreFileData (core::io::raw_data)   _HashEntry (protocols::abinitio)   
DeleteChainsMoverCreator (protocols::simple_moves)   JobOutputIndex (protocols::jd3)   PDNode (core::pack::interaction_graph)   ScoreFileOutputSpecification (protocols::jd3::pose_outputters)   _map_string_vector_Real (protocols::indexed_structure_store)   
DeleteChildProton (core::chemical)   JobOutputter (protocols::jd2)   PDsphere (core::scoring::power_diagram)   ScoreFileOutputter (protocols::jd3::pose_outputters)   _map_string_vector_Size (protocols::indexed_structure_store)   
DeleteMetalbindingAtom (core::chemical)   JobOutputterCreator (protocols::jd2)   PDvertex (core::scoring::power_diagram)   ScoreFileOutputterCreator (protocols::jd3::pose_outputters)   _map_string_vector_vector_Real (protocols::indexed_structure_store)   
DeleteMover (protocols::stepwise::monte_carlo::mover)   JobOutputterFactory (protocols::jd2)   PDvertex (core::scoring)   ScoreFileSilentStruct (core::io::silent)   _MergableEntries (protocols::abinitio)   
DeleteMoverCreator (protocols::stepwise::monte_carlo::mover)   JobOutputterObserver (protocols::jd2)   PeakAssignment (protocols::noesy_assign)   ScoreFileSilentStructCreator (core::io::silent)   _PROBE (core::scoring::sc)   
DeleteProperty (core::chemical)   JobOutputterRegistrator (protocols::jd2)   PeakAssignmentParameters (protocols::noesy_assign)   ScoreFunction (core::scoring)   _RESULTS (core::scoring::sc)   
DeleteRegionMover (protocols::grafting::simple_movers)   JobOutputWriter (protocols::jd3)   PeakAssignmentResidueMap (protocols::noesy_assign)   ScoreFunctionFactory (core::scoring)   
  a  
DeleteRegionMoverCreator (protocols::grafting::simple_movers)   JobQueen (protocols::jd3)   PeakCalibrator (protocols::noesy_assign)   ScoreFunctionFeatures (protocols::features)   
DeleteTerminalChi (core::chemical)   JobResult (protocols::jd3)   PeakCalibratorMap (protocols::noesy_assign)   ScoreFunctionFeaturesCreator (protocols::features)   ai_cmp (core::io::mmtf)   
DeleteVariantType (core::chemical)   JobResultID_hash (protocols::multistage_rosetta_scripts)   PeakFileFormat (protocols::noesy_assign)   ScoreFunctionInfo (core::scoring)   atmInfo (protocols::ligand_docking::ga_ligand_dock)   
DeltaFilter (protocols::simple_filters)   JobsContainer (protocols::jd2)   PeakFileFormat_Base (protocols::noesy_assign)   ScoreFunctionLoader (protocols::parser)   atoms_and_func_struct (core::scoring::custom_pair_distance)   
DeltaFilterCreator (protocols::simple_filters)   JobSummary (protocols::jd3)   PeakFileFormat_Sparky (protocols::noesy_assign)   ScoreFunctionLoaderCreator (protocols::parser)   
  b  
DeNovoArchitect (protocols::denovo_design::architects)   JobTracker (protocols::jd3)   PeakFileFormat_xeasy (protocols::noesy_assign)   ScoreJumpFileSilentStruct (core::io::silent)   
DeNovoArchitectCreator (protocols::denovo_design::architects)   JointScore (protocols::sic_dock)   PeakFileFormat_xpk (protocols::noesy_assign)   ScoreJumpFileSilentStructCreator (core::io::silent)   basis_pair_equal_to (protocols::legacy_sewing)   
DeNovoArchitectFactory (protocols::denovo_design::architects)   JointSequenceOperation (protocols::task_operations)   PeptideBondEnergy (core::energy_methods)   ScoreLessThanComparator (core::import_pose::atom_tree_diffs)   basis_pair_hash (protocols::legacy_sewing)   
DeNovoSilentFilePoseOutputter (protocols::jd3::pose_outputters)   JointSequenceOperationCreator (protocols::task_operations)   PeptideBondEnergyCreator (core::energy_methods)   ScoreMap (core::io::raw_data)   
  c  
DeNovoSilentFilePoseOutputterCreator (protocols::jd3::pose_outputters)   JQKey (protocols::jd3)   PeptideCyclizeMover (protocols::cyclic_peptide)   ScoreMover (protocols::simple_moves)   
DenseEnergyContainer (core::scoring)   JScoreEvaluator (protocols::simple_filters)   PeptideCyclizeMoverCreator (protocols::cyclic_peptide)   ScoreMoverCreator (protocols::simple_moves)   chain_lt (protocols::pose_length_moves)   
DenseIGRepacker (protocols::pack_daemon)   JScoreEvaluatorCreator (protocols::simple_filters)   PeptideDeriverBasicStreamOutputter (protocols::peptide_deriver)   ScoreNormalization (protocols::qsar::scoring_grid)   clique_saver (protocols::features)   
DenseNeighborConstIterator (core::scoring)   JSON_RPC (protocols::rpc)   PeptideDeriverFilter (protocols::peptide_deriver)   ScoreOnlyJobOutputter (protocols::jd2)   compare_base_bin (protocols::stepwise::modeler::rna::rigid_body)   
DenseNeighborIterator (core::scoring)   JSONFormattedLoopsFileReader (protocols::loops)   PeptideDeriverFilterCreator (protocols::peptide_deriver)   ScoreOnlyJobOutputterCreator (protocols::jd2)   compare_by_x (protocols::hbnet)   
DensePDEdge (core::pack::interaction_graph)   JSONStructureStoreBackend (protocols::indexed_structure_store)   PeptideDeriverMarkdownStreamOutputter (protocols::peptide_deriver)   ScorePoseSegmentFromResidueSelectorFilter (protocols::fold_from_loops::filters)   compare_hbond_residues (protocols::hbnet)   
DensePDInteractionGraph (core::pack::interaction_graph)   Jump (core::kinematics)   PeptideDeriverOutputter (protocols::peptide_deriver)   ScorePoseSegmentFromResidueSelectorFilterCreator (protocols::fold_from_loops::filters)   compare_hbond_resnums (protocols::hbnet)   
DensePDNode (core::pack::interaction_graph)   Jump_point (protocols::stepwise::modeler::rna)   PeptideDeriverOutputterContainer (protocols::peptide_deriver)   Scorer (protocols::stepwise::screener)   compare_int_pair (protocols::stepwise::modeler::rna::rigid_body)   
DensityFitResidueSelector (core::select::residue_selector)   JumpAtom (core::kinematics::tree)   PeptideDeriverPoseOutputter (protocols::peptide_deriver)   ScoreRmsPoint (protocols::toolbox)   compare_job_nodes (protocols::jd3)   
DensityFitResidueSelectorCreator (core::select::residue_selector)   RigidChunkClaimer::JumpCalculator (protocols::topology_broker)   PeptideInternalHbondsFilter (protocols::cyclic_peptide)   ScoreRmsPoints (protocols::toolbox)   compare_net_vec (protocols::hbnet)   
DensityScoringClaimer (protocols::topology_broker)   JumpClaim (protocols::topology_broker::claims)   PeptideInternalHbondsFilterCreator (protocols::cyclic_peptide)   ScoreStructJSON (core::io::raw_data)   RawFileData::const_iterator (core::io::raw_data)   
DensitySymmInfo (protocols::electron_density)   JumpClaim (protocols::environment::claims)   PeptideInternalHbondsMetric (protocols::cyclic_peptide)   ScoreStructText (core::io::raw_data)   SilentFileData::const_iterator (core::io::silent)   
DensSkeleton (protocols::loop_grower)   JumpSetup::JumpDef (protocols::jumping)   PeptideInternalHbondsMetricCreator (protocols::cyclic_peptide)   ScoreTermValueBasedSelector (core::select::residue_selector)   coord_equal_to (protocols::legacy_sewing)   
DenyPdbIdFilter (protocols::frag_picker)   ResiduePairJumpSetup::JumpDef (protocols::jumping)   PeptideOrientationMover (protocols::membrane_benchmark)   ScoreTermValueBasedSelectorCreator (core::select::residue_selector)   coord_equal_to (protocols::sewing::hashing)   
DerivCheckDataPoint (core::optimization)   JumpDownstreamSelector (core::select::residue_selector)   PeptideOrientationMoverCreator (protocols::membrane_benchmark)   ScoreTypeFeatures (protocols::features)   coord_hash (protocols::legacy_sewing)   
DerivedPeptideEntry (protocols::peptide_deriver)   JumpDownstreamSelectorCreator (core::select::residue_selector)   PeptideStapleDesignMover (protocols::protein_interface_design::movers)   ScoreTypeFeaturesCreator (protocols::features)   coord_hash (protocols::sewing::hashing)   
DerivedSequenceMapping (core::sequence)   JumpElement (protocols::environment::claims)   PeptideStapleDesignMoverCreator (protocols::protein_interface_design::movers)   ScoreTypeFilter (protocols::score_filters)   cycle_printer (core::scoring::loop_graph)   
DerivVectorPair (core::scoring)   JumpEvaluator (protocols::simple_filters)   PeptideStapleMover (protocols::simple_moves)   ScoreTypeFilterCreator (protocols::score_filters)   
  d  
DescentDirectionAlgorithm (core::optimization)   JumpID (core::id)   PeptideStubMover (protocols::cyclic_peptide)   ScoreTypeManager (core::scoring)   
MakeJunctionsMover::Design (protocols::pose_creation)   JumpIndexSelector (core::select::jump_selector)   PeptideStubMoverCreator (protocols::cyclic_peptide)   ScoringGridLoader (protocols::qsar::scoring_grid)   data_struct (core::scoring)   
DesignableResiduesFilter (protocols::protein_interface_design::filters)   JumpIndexSelectorCreator (core::select::jump_selector)   PeptideTorsionReporter (core::pack::dunbrack)   ScoringGridLoaderCreator (protocols::qsar::scoring_grid)   ddG (protocols::simple_ddg)   
DesignableResiduesFilterCreator (protocols::protein_interface_design::filters)   JumpingFoldConstraintsWrapper (protocols::abinitio)   PeptoidGeneralDOFReporter (core::pack::dunbrack)   ScoringManager (core::scoring)   ddGCreator (protocols::simple_ddg)   
DesignAroundOperation (protocols::task_operations)   JumpingFrame (core::fragment)   PeptoidOmegaReporter (core::pack::dunbrack)   ScoringScheme (core::sequence)   ddGData (protocols::ddG)   
DesignAroundOperationCreator (protocols::task_operations)   JumpMetric (protocols::multistage_rosetta_scripts::cluster::metrics)   PeriodicBoundFunc (core::scoring::constraints)   ScoringSchemeFactory (core::sequence)   ddGMover (protocols::ddg)   
DesignContrast (core::io::sequence_comparation)   JumpMetricCreator (protocols::multistage_rosetta_scripts::cluster::metrics)   PeriodicBoxMover (protocols::simple_moves)   ScoringSecMatchRPE (protocols::match::downstream)   detailedControlsTagSetting (protocols::hybridization)   
DesignInterfacesOperation (protocols::splice)   JumpNrEvaluator (protocols::simple_filters)   PeriodicBoxMoverCreator (protocols::simple_moves)   ScreeningFeatures (protocols::features)   MultiConstraint::dont_copy_constraints (core::scoring::constraints)   
DesignInterfacesOperationCreator (protocols::splice)   JumpNrEvaluatorCreator (protocols::simple_filters)   PeriodicFunc (core::scoring::func)   ScreeningFeaturesCreator (protocols::features)   downstream_hit (protocols::match)   
DesignMeanField (protocols::mean_field)   JumpOutMover (protocols::moves)   PerNativeRRReporterHuman (protocols::rotamer_recovery)   ScreeningJobInputter (protocols::jd2)   
  e  
DesignMinimizeHbonds (protocols::protein_interface_design::movers)   JumpRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   PerResidueClashMetric (core::simple_metrics::per_residue_metrics)   ScreeningJobInputterCreator (protocols::jd2)   
DesignMinimizeHbondsCreator (protocols::protein_interface_design::movers)   JumpRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   PerResidueClashMetricCreator (core::simple_metrics::per_residue_metrics)   ScriptCM (protocols::environment)   exposed_hydrophobic_data (core::pack::interaction_graph)   
DesignProteinBackboneAroundDNA (protocols::dna)   JumpSample (protocols::jumping)   PerResidueDensityFitMetric (core::simple_metrics::per_residue_metrics)   ScriptCMCreator (protocols::environment)   
  f  
DesignProteinBackboneAroundDNACreator (protocols::dna)   JumpSampleData (protocols::abinitio::abscript)   PerResidueDensityFitMetricCreator (core::simple_metrics::per_residue_metrics)   SDFParser (core::chemical::sdf)   
DesignRepackMover (protocols::calc_taskop_movers)   JumpSampleDataCreator (protocols::abinitio::abscript)   PerResidueEnergyMetric (core::simple_metrics::per_residue_metrics)   SealFoldTreeMover (protocols::denovo_design::movers)   find_SilentStructOPs (protocols::wum)   
DesignRestrictions (core::pack::task::operation)   JumpSelector (protocols::jumping)   PerResidueEnergyMetricCreator (core::simple_metrics::per_residue_metrics)   SealFoldTreeMoverCreator (protocols::denovo_design::movers)   container::flat_set (boost)   
DesignRestrictionsCreator (core::pack::task::operation)   JumpSelector (core::select::jump_selector)   PerResidueGlycanLayerMetric (core::simple_metrics::per_residue_metrics)   SearchPattern (protocols::hotspot_hashing)   func_1d (core::optimization)   
DesignTask (protocols::flxbb)   JumpSelectorCreator (core::select::jump_selector)   PerResidueGlycanLayerMetricCreator (core::simple_metrics::per_residue_metrics)   SearchPatternExpansion (protocols::hotspot_hashing)   jagged_array::func_T2 (protocols::mean_field)   
DesignTask_Layer (protocols::flxbb)   JumpSelectorFactory (core::select::jump_selector)   PerResidueInterfaceData (protocols::analysis)   SearchPatternRotSetOp (protocols::hotspot_hashing)   
  h  
DesignTask_Normal (protocols::flxbb)   JumpSelectorLoader (protocols::parser)   PerResidueRealMetric (core::simple_metrics)   SearchPatternTransform (protocols::hotspot_hashing)   
DesignVsNativeComparison (protocols::enzdes)   JumpSelectorLoaderCreator (protocols::parser)   PerResidueRMSDMetric (core::simple_metrics::per_residue_metrics)   SecMatchEvaluatorFactory (protocols::match::downstream)   hash_upstream_hit (protocols::match::downstream)   
DestructionEvent (core::pose::signals)   JumpSelectorRegistrator (core::select::jump_selector)   PerResidueRMSDMetricCreator (core::simple_metrics::per_residue_metrics)   SecMatchResiduePairEvaluator (protocols::match::downstream)   hbAcc (protocols::ligand_docking::ga_ligand_dock)   
DetectProteinLigandInterface (protocols::enzdes)   JumpSetup (protocols::jumping)   PerResidueSapScoreMetric (core::pack::guidance_scoreterms::sap)   SecondaryIdentity (protocols::frag_picker::scores)   hbDon (protocols::ligand_docking::ga_ligand_dock)   
DetectProteinLigandInterfaceOperationCreator (protocols::enzdes)   JumpsFromAllPairings (protocols::jumping)   PerResidueSapScoreMetricCreator (core::pack::guidance_scoreterms::sap)   SecondaryMatcherToDownstreamResidue (protocols::match::downstream)   hConvergenceCheck (protocols::abinitio)   
DetectSymmetry (protocols::symmetry)   JumpStepWiseSampler (protocols::stepwise::sampler::jump)   PerResidueSasaMetric (core::simple_metrics::per_residue_metrics)   SecondaryMatcherToUpstreamResidue (protocols::match::downstream)   hConvergenceCheck (protocols::hybridization)   
DetectSymmetryMoverCreator (protocols::symmetry)   JumpUpstreamSelector (core::select::residue_selector)   PerResidueSasaMetricCreator (core::simple_metrics::per_residue_metrics)   SecondaryMatchProtocol (protocols::enzdes)   history_queue_struct (core::pack::interaction_graph)   
DFIRE_Energy (core::energy_methods::dfire)   JumpUpstreamSelectorCreator (core::select::residue_selector)   PerResidueStringMetric (core::simple_metrics)   SecondaryMatchUpstreamResProcessor (protocols::match::downstream)   
  i  
DFIRE_EnergyCreator (core::energy_methods::dfire)   JumpSelector::JumpWeightDef (protocols::jumping)   PerSphereAccumulator (core::scoring::packstat)   SecondaryPoseOutputter (protocols::jd3::pose_outputters)   
DFIRE_Potential (core::scoring::methods::dfire)   
  K  
PertMinMover (protocols::minimization_packing)   SecondaryPoseOutputterCreator (protocols::jd3::pose_outputters)   RemodelMover::instruction_flags (protocols::forge::remodel)   
DFPMinConvergedAbsolute (core::optimization)   PertMinMoverCreator (protocols::minimization_packing)   SecondaryPoseOutputterRegistrator (protocols::jd3::pose_outputters)   RawFileData::iterator (core::io::raw_data)   
DFPMinConvergedFractional (core::optimization)   KarplusFunc (core::scoring::func)   PerturbBundle (protocols::helical_bundle)   SecondarySimilarity (protocols::frag_picker::scores)   SilentFileData::iterator (core::io::silent)   
DGBindOptEData (protocols::optimize_weights)   KCluster (protocols::toolbox)   PerturbBundleCreator (protocols::helical_bundle)   SecondaryStructure (core::fragment)   
  j  
DiffAtomSasaFilter (protocols::enzdes)   KClusterData (protocols::toolbox)   PerturbBundleHelix (protocols::helical_bundle)   SecondaryStructureCountFilter (protocols::fldsgn::filters)   
DiffAtomSasaFilterCreator (protocols::enzdes)   KClusterElement (protocols::toolbox)   PerturbBundleHelixCreator (protocols::helical_bundle)   SecondaryStructureCountFilterCreator (protocols::fldsgn::filters)   ModuleType1::jacobian_struct (core::kinematics::jacobian)   
DihedralConstraint (core::scoring::constraints)   KeepLigandContactsRequirement (protocols::sewing::requirements)   PerturbByBins (protocols::simple_moves::bin_transitions)   SecondaryStructureEnergy (core::energy_methods)   jagged_array (protocols::mean_field)   
DihedralConstraintCreator (core::scoring::constraints)   KeepLigandContactsRequirementCreator (protocols::sewing::requirements)   PerturbByBinsCreator (protocols::simple_moves::bin_transitions)   SecondaryStructureEnergyCreator (core::energy_methods)   
  l  
DihedralConstraintGenerator (protocols::constraint_generator)   KeepRegionMover (protocols::grafting::simple_movers)   PerturbChiSidechainMover (protocols::simple_moves::sidechain_moves)   SecondaryStructureFilter (protocols::fldsgn::filters)   
DihedralConstraintGeneratorCreator (protocols::constraint_generator)   KeepRegionMoverCreator (protocols::grafting::simple_movers)   PerturbChiSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   SecondaryStructureFilterCreator (protocols::fldsgn::filters)   lbfgs_iteration_data (core::optimization)   
DihedralConstraintsScore (protocols::frag_picker::scores)   KeepSequenceSymmetry (core::pack::task::operation)   Perturber (protocols::kinematic_closure::perturbers)   SecondaryStructureHasResidueFilter (protocols::fldsgn::filters)   less_then_match_rmsd (protocols::simple_moves)   
DihedralDistanceMetric (core::simple_metrics::metrics)   KeepSequenceSymmetryCreator (core::pack::task::operation)   PerturberSet (protocols::kinematic_closure::perturbers)   SecondaryStructureHasResidueFilterCreator (protocols::fldsgn::filters)   
  m  
DihedralDistanceMetricCreator (core::simple_metrics::metrics)   Key (core::pack::annealer)   PerturbRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   SecondaryStructureMetric (core::simple_metrics::metrics)   
DihedralPairConstraint (core::scoring::constraints)   KeyHasher (core::pack::annealer)   PerturbRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   SecondaryStructureMetricCreator (core::simple_metrics::metrics)   match_dspos1 (protocols::match)   
DihedralPairConstraintCreator (core::scoring::constraints)   KicMover (protocols::kinematic_closure)   Pharmacophore (protocols::ligand_docking::ga_ligand_dock)   SecondaryStructureMPM (protocols::match)   match_lite_equals (protocols::match)   
DimerPairing (core::scoring)   KicMoverCreator (protocols::kinematic_closure)   PhenixInterface (core::scoring::cryst)   SecondaryStructurePool (protocols::frag_picker::quota)   match_lite_hasher (protocols::match)   
DimerPairing (protocols::fldsgn::topology)   KinaseMover (protocols::enzymatic_movers)   Phi (protocols::frag_picker::scores)   SecondaryStructurePotential (core::scoring)   missing_fraction_sorter_biggest_first (protocols::frag_picker::quota)   
DimerPairings (protocols::fldsgn::topology)   KinaseMoverCreator (protocols::enzymatic_movers)   PhiPsiRmsd (protocols::frag_picker::scores)   SecondaryStructureSegment (protocols::features)   mmCIFJobOutputter (protocols::jd2)   
DipolarCoupling (core::scoring)   KinematicAbinitio (protocols::abinitio)   PhiPsiSquareWell (protocols::frag_picker::scores)   SecondaryStructureSegmentFeatures (protocols::features)   mmCIFJobOutputterCreator (protocols::jd2)   
DipolarCouplingEnergy (core::energy_methods)   KinematicControl (protocols::abinitio)   PhiPsiTalosIO (protocols::frag_picker)   SecondaryStructureSegmentFeaturesCreator (protocols::features)   mmCIFParser (core::chemical::mmCIF)   
DipolarCouplingEnergyCreator (core::energy_methods)   KinematicMover (protocols::loops::loop_closure::kinematic_closure)   PhiSelector (core::select::residue_selector)   SecondaryStructureSelector (core::select::residue_selector)   mmtfJobOutputter (protocols::jd2)   
DirectReadoutEnergy (core::energy_methods)   KinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   PhiSelectorCreator (core::select::residue_selector)   SecondaryStructureSelectorCreator (core::select::residue_selector)   mmtfJobOutputterCreator (protocols::jd2)   
DirectReadoutEnergyCreator (core::energy_methods)   KinematicTaskControl (protocols::abinitio)   PhosphateMove (protocols::stepwise::modeler::rna::phosphate)   SecondaryStructureWeights (core::scoring)   mmTFPoseOutputSpecification (protocols::jd3::pose_outputters)   
DirectReadoutPotential (core::scoring::dna)   KinematicWrapper (protocols::loops::loop_closure::kinematic_closure)   PhosphateMover (protocols::stepwise::modeler::rna::phosphate)   SecretionPredictionFilter (protocols::simple_filters)   mmTFPoseOutputter (protocols::jd3::pose_outputters)   
DirectSegmentLookup (protocols::indexed_structure_store)   KinFunGroupTK (protocols::kinmatch)   PhosphateScreener (protocols::stepwise::screener)   SecretionPredictionFilterCreator (protocols::simple_filters)   mmTFPoseOutputterCreator (protocols::jd3::pose_outputters)   
DirectSegmentLookupConfig (protocols::indexed_structure_store)   KMedoid (protocols::toolbox)   Picker (protocols::denovo_design::components)   SecStructFinder (protocols::ncbb)   motif2scaffold_data (protocols::motif_grafting::movers)   
DirectSegmentLookupMover (protocols::indexed_structure_store::movers)   KofNConstraint (core::scoring::constraints)   PIKAA (core::pack::task)   SecStructFinderCreator (protocols::ncbb)   motif2scaffold_indexes (protocols::motif_grafting::movers)   
DirectSegmentLookupMoverCreator (protocols::indexed_structure_store::movers)   KofNConstraintCreator (core::scoring::constraints)   PIKNA (core::pack::task)   SecStructGen (core::fragment::picking_old::vall::gen)   mover_or_filter (protocols::multistage_rosetta_scripts)   
DirectSegmentLookupResult (protocols::indexed_structure_store)   KromerMann (core::scoring::fiber_diffraction)   PiPiCalculator (protocols::pose_metric_calculators)   SecStructInfo (protocols::denovo_design::architects)   SecretionPredictionFilter::mutt (protocols::simple_filters)   
DirStructureStoreBackend (protocols::indexed_structure_store)   KromerMann (core::scoring::electron_density)   PivotPicker (protocols::kinematic_closure::pivot_pickers)   SecStructMinimizeMover (protocols::ncbb)   
  n  
DisableAntibodyRegionOperation (protocols::antibody::task_operations)   KRSQuery (protocols::kinmatch)   PlaceableRotamer (protocols::ligand_docking::ga_ligand_dock)   SecStructMinimizeMoverCreator (protocols::ncbb)   
DisableAntibodyRegionOperationCreator (protocols::antibody::task_operations)   
  L  
PlacementAuctionMover (protocols::protein_interface_design::movers)   SecStructMinimizeMultiFunc (protocols::ncbb)   nmer_svm_res_data (protocols::simple_filters)   
DisableCDRsOperation (protocols::antibody::task_operations)   PlacementAuctionMoverCreator (protocols::protein_interface_design::movers)   SecstructSRFD (core::fragment)   PDBPoseMap::no_segID_comp (core::pose)   
DisableCDRsOperationCreator (protocols::antibody::task_operations)   L1ScoringScheme (core::sequence)   PlacementMinimizationMover (protocols::protein_interface_design::movers)   SeedFoldTree (protocols::seeded_abinitio)   
  o  
DisallowIfNonnative (core::pack::task::operation)   LabelPoseFromResidueSelectorMover (protocols::fold_from_loops::movers)   PlacementMinimizationMoverCreator (protocols::protein_interface_design::movers)   SeedFoldTreeCreator (protocols::seeded_abinitio)   
DisallowIfNonnativeCreator (core::pack::task::operation)   LabelPoseFromResidueSelectorMoverCreator (protocols::fold_from_loops::movers)   PlaceOnLoop (protocols::protein_interface_design::movers)   SeedSetupMover (protocols::seeded_abinitio)   output_data_struct (protocols::stepwise::modeler::rna)   
DisallowIfNonnativeRLT (core::pack::task::operation)   LabelResonance (protocols::noesy_assign)   PlaceOnLoopCreator (protocols::protein_interface_design::movers)   SeedSetupMoverCreator (protocols::seeded_abinitio)   
  p  
DisallowIfNonnativeRLTCreator (core::pack::task::operation)   LAMBEGO_IO (protocols::frag_picker)   PlaceProbeMover (protocols::hotspot_hashing::movers)   Segment (protocols::features)   
DiscreteRandomizer (protocols::genetic_algorithm)   LAMBEGO_Similarity (protocols::frag_picker::scores)   PlaceSimultaneouslyMover (protocols::protein_interface_design::movers)   Segment (protocols::denovo_design::components)   CentroidRelax::parameters (protocols::relax)   
DisembodiedAssembly (protocols::legacy_sewing)   LargeFragWeight (protocols::topology_broker::weights)   PlaceSimultaneouslyMoverCreator (protocols::protein_interface_design::movers)   Segment (protocols::forge::remodel)   pHEnergy (core::energy_methods)   
DisplayPoseLabelsMover (protocols::fold_from_loops::movers)   LargeNstructJobInputter (protocols::jd2)   PlaceStubMover (protocols::protein_interface_design::movers)   SegmentContactOrderScorer (protocols::sewing::scoring)   pHEnergyCreator (core::energy_methods)   
DisplayPoseLabelsMoverCreator (protocols::fold_from_loops::movers)   LargeNstructJobInputterCreator (protocols::jd2)   PlaceStubMoverCreator (protocols::protein_interface_design::movers)   SegmentContactOrderScorerCreator (protocols::sewing::scoring)   pHVariantTaskOperation (protocols::task_operations)   
DistanceChainbreakEnergy (core::energy_methods)   LarvalJob (protocols::jd3)   PlaceSurfaceProbe (protocols::hotspot_hashing::movers)   SegmentCounts (protocols::denovo_design::components)   pHVariantTaskOperationCreator (protocols::task_operations)   
DistanceChainbreakEnergyCreator (core::energy_methods)   LayerDesignOperation (protocols::flxbb)   PlaceSurfaceProbeCreator (protocols::hotspot_hashing::movers)   SegmentedAtomPairConstraintGenerator (protocols::fold_from_loops::constraint_generator)   point3d (core::scoring::atomic_depth)   
DistanceConstraintGenerator (protocols::constraint_generator)   LayerDesignOperationCreator (protocols::flxbb)   PlaidFingerprint (protocols::pockets)   SegmentedAtomPairConstraintGeneratorCreator (protocols::fold_from_loops::constraint_generator)   poseCoord (core::scoring::electron_density)   
DistanceConstraintGeneratorCreator (protocols::constraint_generator)   LayerSelector (core::select::residue_selector)   PlainPdbJobDistributor (protocols::jobdist)   SegmentGraph (protocols::legacy_sewing)   pre_talaris_2013_behavior_settings (core::init)   
DistanceFunc (core::scoring::custom_pair_distance)   LayerSelectorCreator (core::select::residue_selector)   PlainRawJobDistributor (protocols::jobdist)   SegmentHybridizer (protocols::seeded_abinitio)   principal_angle_degrees (core::pose::rna)   
DistanceHistogram (core::scoring::saxs)   LazyEdge (core::pack::interaction_graph)   PlainSilentFileJobDistributor (protocols::jobdist)   SegmentHybridizerCreator (protocols::seeded_abinitio)   
  q  
DistancePairConstraint (core::scoring::constraints)   LazyInteractionGraph (core::pack::interaction_graph)   PNatAAOptEPositionData (protocols::optimize_weights)   SegmentInsert (protocols::forge::build)   
FragsToAtomDist::DistanceRecord (protocols::noesy_assign)   LazyNode (core::pack::interaction_graph)   PNatAAOptERotamerData (protocols::optimize_weights)   SegmentPairing (protocols::denovo_design::components)   qsarCreator (protocols::qsar)   
DistanceResidueNetwork (protocols::toolbox)   LazySilentFileJobInputter (protocols::jd2)   PNatLigPoseOptEData (protocols::optimize_weights)   SegmentPairSet (protocols::denovo_design::components)   qsarMap (protocols::qsar)   
DistanceScoreMover (protocols::noesy_assign)   LazySilentFileJobInputterCreator (protocols::jd2)   PNatRotOptEPositionData (protocols::optimize_weights)   SegmentRebuild (protocols::forge::build)   qsarMover (protocols::qsar)   
DistributionMap (protocols::ligand_docking)   LazySilentFilePoseInputStream (core::import_pose::pose_stream)   PNatRotOptERotamerData (protocols::optimize_weights)   SegmentSequenceProfile (protocols::indexed_structure_store)   qsarOptData (protocols::qsar)   
DisulfideAtomIndices (core::scoring::disulfides)   LazySortedVector1 (protocols::frag_picker)   PNatStructureOptEData (protocols::optimize_weights)   SegmentSequenceProfileConfig (protocols::indexed_structure_store)   qsarOptFunc (protocols::qsar)   
DisulfideDistance (protocols::frag_picker::scores)   LeapIndex (protocols::loophash)   PNearCalculator (protocols::cyclic_peptide_predict)   SegmentSequenceProfileMover (protocols::indexed_structure_store::movers)   qsarPoint (protocols::qsar)   
DisulfideEntropyFilter (protocols::simple_filters)   LeastNativeLike9merFilter (protocols::simple_filters)   PocketConstraint (protocols::pockets)   SegmentSequenceProfileMoverCreator (protocols::indexed_structure_store::movers)   quota_limits_sorter_biggest_first (protocols::frag_picker::quota)   
DisulfideEntropyFilterCreator (protocols::simple_filters)   LeastNativeLike9merFilterCreator (protocols::simple_filters)   PocketConstraintCreator (protocols::pockets)   SegmentSequenceProfileResult (protocols::indexed_structure_store)   quota_limits_sorter_smallest_first (protocols::frag_picker::quota)   
DisulfideFile (core::io::raw_data)   LeeRichards (core::scoring::packstat)   PocketExemplarMultifunc (protocols::pockets)   SegmentSpec (protocols::seeded_abinitio)   
  r  
DisulfideFilter (protocols::protein_interface_design::filters)   LegacyAddStartnodeFragments (protocols::legacy_sewing)   PocketGrid (protocols::pockets)   SegmentSwap (protocols::forge::build)   
DisulfideFilterCreator (protocols::protein_interface_design::filters)   LegacyAddStartnodeFragmentsCreator (protocols::legacy_sewing)   Point (core::scoring::packstat)   SegmentVector (protocols::sewing::hashing)   ray_distance_derivs (protocols::pockets)   
DisulfideIdentity (protocols::frag_picker::scores)   LegacyAppendAssemblyMover (protocols::legacy_sewing)   PointDwell (core::pack::annealer)   SelectByDeltaScoreOperation (protocols::task_operations)   resatom_and_func_struct (core::scoring::custom_pair_distance)   
DisulfideInsertionMover (protocols::simple_moves)   LegacyAppendAssemblyMoverCreator (protocols::legacy_sewing)   PointGraphEdgeData (core::conformation)   SelectByDeltaScoreOperationCreator (protocols::task_operations)   running_average_pair (protocols::make_rot_lib)   
DisulfideInsertionMoverCreator (protocols::simple_moves)   LegacyAssemblyConstraintsMover (protocols::legacy_sewing)   PointGraphVertexData (core::conformation)   SelectByDensityFitOperation (protocols::task_operations)   
  s  
DisulfideMatchingDatabase (core::scoring::disulfides)   LegacyAssemblyConstraintsMoverCreator (protocols::legacy_sewing)   PointMutationCalculator (protocols::design_opt)   SelectByDensityFitOperationCreator (protocols::task_operations)   
DisulfideMatchingEnergy (core::energy_methods)   LegacyAssemblyMover (protocols::legacy_sewing)   PointMutScanDriver (protocols::pmut_scan)   SelectBySASAOperation (protocols::task_operations)   ModuleType1::screw_construct_struct (core::kinematics::jacobian)   
DisulfideMatchingEnergyComponents (core::scoring::disulfides)   LegacyAssemblyScoreFunction (protocols::legacy_sewing::scoring)   PointPair (core::scoring::packstat)   SelectBySASAOperationCreator (protocols::task_operations)   sd_index (core::io::mmtf)   
DisulfideMatchingEnergyContainer (core::scoring::disulfides)   LegacyAssemblyScorer (protocols::legacy_sewing::scoring)   PointScoreComparator (protocols::electron_density)   SelectedResidueCountMetric (core::simple_metrics::metrics)   segment (protocols::legacy_sewing)   
DisulfideMatchingEnergyCreator (core::energy_methods)   LegacyBlosumScorer (protocols::legacy_sewing::scoring)   PointWaterEnergy (core::energy_methods)   SelectedResidueCountMetricCreator (core::simple_metrics::metrics)   sort_pred (core::optimization)   
DisulfideMatchingNeighborConstIterator (core::scoring::disulfides)   LegacyCalciumMotifScorer (protocols::legacy_sewing::scoring)   PointWaterEnergyCreator (core::energy_methods)   SelectedResiduesMetric (core::simple_metrics::metrics)   sort_SilentStructOPs (protocols::wum)   
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