Rosetta Protocols  2014.16.56682
Class Index
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  A  
DockMCMCycle (protocols::docking)   LinearFunc (protocols::moves)   PlaceStubMover (protocols::protein_interface_design::movers)   SecondaryStructureSegmentFeatures (protocols::features)   
DockMCMProtocol (protocols::docking)   LineObject (protocols::forge::remodel)   PlaceStubMoverCreator (protocols::protein_interface_design::movers)   SecondaryStructureSegmentFeaturesCreator (protocols::features)   
AACompositionEnergy (protocols::fldsgn::potentials)   DockMinMover (protocols::docking)   LinkerScore (protocols::sic_dock)   PlaceSurfaceProbe (protocols::hotspot_hashing::movers)   SeedFoldTree (protocols::seeded_abinitio)   
AACompositionEnergyCreator (protocols::fldsgn::potentials)   DockSetupMover (protocols::docking)   LinkResidues (protocols::toolbox::task_operations)   PlaceSurfaceProbeCreator (protocols::hotspot_hashing::movers)   SeedFoldTreeCreator (protocols::seeded_abinitio)   
Ab_TemplateInfo (protocols::antibody)   DockSetupMoverCreator (protocols::docking)   LinkResiduesCreator (protocols::toolbox::task_operations)   PlaidFingerprint (protocols::pockets)   SeedSetupMover (protocols::seeded_abinitio)   
ABEGO_SS_Config (protocols::frag_picker::quota)   DockTaskFactory (protocols::docking)   LnExpression (protocols::pack_daemon)   PlainPdbJobDistributor (protocols::jobdist)   SeedSetupMoverCreator (protocols::seeded_abinitio)   
ABEGO_SS_Map (protocols::frag_picker::quota)   DockWithHotspotMover (protocols::protein_interface_design::movers)   LoadDensityMapMover (protocols::cryst)   PlainRawJobDistributor (protocols::jobdist)   Segment (protocols::forge::remodel)   
ABEGO_SS_Pool (protocols::frag_picker::quota)   DockWithHotspotMoverCreator (protocols::protein_interface_design::movers)   LoadDensityMapMoverCreator (protocols::cryst)   PlainSilentFileJobDistributor (protocols::jobdist)   SegmentHybridizer (protocols::seeded_abinitio)   
ABEGO_SS_Score (protocols::frag_picker::scores)   DofClaim (protocols::topology_broker::claims)   LoadPDBMover (protocols::simple_moves)   PNatAAOptEPositionData (protocols::optimize_weights)   SegmentHybridizerCreator (protocols::seeded_abinitio)   
AbinitioBaseFilter (protocols::simple_filters)   DOFHistogramRecorder (protocols::simple_moves)   LoadPDBMoverCreator (protocols::simple_moves)   PNatAAOptERotamerData (protocols::optimize_weights)   SegmentInsert (protocols::forge::build)   
AbinitioMoverWeight (protocols::topology_broker::weights)   DofUnlock (protocols::environment)   LoadUnboundRotMover (protocols::simple_moves)   PNatLigPoseOptEData (protocols::optimize_weights)   SegmentRebuild (protocols::forge::build)   
AbrelaxApplication (protocols::abinitio)   DomainAssembly (protocols::abinitio)   LoadUnboundRotMoverCreator (protocols::simple_moves)   PNatRotOptEPositionData (protocols::optimize_weights)   SegmentSwap (protocols::forge::build)   
AbrelaxMover (protocols::abinitio)   DomainAssembly (protocols::hybridization)   LocalInserter (protocols::loophash)   PNatRotOptERotamerData (protocols::optimize_weights)   SelectByDensityFitOperation (protocols::toolbox::task_operations)   
AbscriptLoopCloserCM (protocols::abinitio::abscript)   DomainAssemblyCreator (protocols::abinitio)   LocalInserter_SimpleMin (protocols::loophash)   PNatStructureOptEData (protocols::optimize_weights)   SelectByDensityFitOperationCreator (protocols::toolbox::task_operations)   
AbscriptMover (protocols::abinitio::abscript)   DomainInterfaceFilter (protocols::simple_filters)   LocalMinimizationRefiner (protocols::loop_modeling::refiners)   PocketConstraint (protocols::pockets)   SelectBySASAOperation (protocols::toolbox::task_operations)   
AbscriptMoverCreator (protocols::abinitio::abscript)   DoubleDenseIGRepacker (protocols::pack_daemon)   LoggedFragmentMover (protocols::simple_moves)   PocketConstraintCreator (protocols::pockets)   SelectBySASAOperationCreator (protocols::toolbox::task_operations)   
AbscriptStageMover (protocols::abinitio::abscript)   DoubleLayerKinematicAbinitio (protocols::abinitio)   Logger (protocols::loop_modeling::loggers)   PocketExemplarMultifunc (protocols::pockets)   SelectGdtEvaluator (protocols::simple_filters)   
AbstractArchiveBase (protocols::jd2::archive)   DownstreamAlgorithm (protocols::match::downstream)   LogicalSelector (protocols::pose_selectors)   PocketGrid (protocols::pockets)   SelectMaxsubEvaluator (protocols::simple_filters)   
AcceptanceCheck (protocols::loop_modeling::utilities)   DownstreamBuilder (protocols::match::downstream)   Loop (protocols::fldsgn::topology)   PointMutationCalculator (protocols::design_opt)   SelectRDC_Evaluator (protocols::simple_filters)   
ActiveSiteGrid (protocols::match::downstream)   DownstreamCoordinateKinemageWriter (protocols::match::output)   Loop (protocols::loops)   PointMutScanDriver (protocols::pmut_scan)   SelectResiduesByLayer (protocols::toolbox)   
AdaptiveScoreHistogram (protocols::frag_picker::scores)   DownstreamRMSEvaluator (protocols::match::output)   Loop_lt (protocols::loops)   Policy (protocols::nonlocal)   SelectResiduesWithinChainOperation (protocols::toolbox::task_operations)   
AddAllPositionsMPM (protocols::match)   DsspMover (protocols::moves)   LoopAnalyzerMover (protocols::analysis)   PolicyFactory (protocols::nonlocal)   SelectResiduesWithinChainOperationCreator (protocols::toolbox::task_operations)   
AddAssemblyConstraints (protocols::domain_assembly)   DsspMoverCreator (protocols::moves)   LoopAnchorFeatures (protocols::features)   Poly (protocols::sasa_scores)   SelectRmsdEvaluator (protocols::simple_filters)   
AddCavitiesMover (protocols::simple_moves)   DualMonteCarlo (protocols::moves)   LoopAnchorFeaturesCreator (protocols::features)   Pool_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   SemiExplicitWaterUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   
AddChainBreak (protocols::protein_interface_design::movers)   DummyClass (protocols::toolbox)   LoopBuilder (protocols::loop_modeling)   Pool_Evaluator (protocols::canonical_sampling::mc_convergence_checks)   SeparateDnaFromNonDna (protocols::dna)   
AddChainBreakCreator (protocols::protein_interface_design::movers)   DumpPdb (protocols::simple_moves)   LoopBuildMover (protocols::loop_build)   Pool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   SeparateDnaFromNonDnaCreator (protocols::dna)   
AddChainMover (protocols::simple_moves)   DumpPdbCreator (protocols::simple_moves)   LoopClosure (protocols::loops::loop_closure::ccd)   PoolData (protocols::canonical_sampling::mc_convergence_checks)   SeqprofConsensusOperation (protocols::toolbox::task_operations)   
AddChainMoverCreator (protocols::simple_moves)   DunbrackSCSampler (protocols::match::upstream)   LoopFilter (protocols::loop_modeling::utilities)   PoolEvaluatorCreator (protocols::simple_filters)   SeqprofConsensusOperationCreator (protocols::toolbox::task_operations)   
AddConstraintsToCurrentConformationMover (protocols::simple_moves)   DynamicAggregateFunction (protocols::pack_daemon)   LoopFinder (protocols::protein_interface_design::movers)   PoseComment (protocols::simple_filters)   SequenceClaim (protocols::topology_broker::claims)   
AddConstraintsToCurrentConformationMoverCreator (protocols::simple_moves)   DynamicAggregateFunctionDriver (protocols::pack_daemon)   LoopFinderCreator (protocols::protein_interface_design::movers)   PoseCommentFilterCreator (protocols::simple_filters)   SequenceClaimer (protocols::topology_broker)   
AddHydrogen (protocols::ligand_docking)   
  E  
LoopFragmentClaimer (protocols::topology_broker)   PoseCommentsFeatures (protocols::features)   SequenceComparison (protocols::toolbox::pose_metric_calculators)   
AddHydrogens (protocols::ligand_docking)   LoopFromFileData (protocols::loops)   PoseCommentsFeaturesCreator (protocols::features)   SequenceCoupling1BDConstraint (protocols::constraints_additional)   
AddHydrogensCreator (protocols::ligand_docking)   EdgeStandScore (protocols::sic_dock)   LoopHashDiversifier (protocols::loophash)   PoseCondition (protocols::moves)   SequenceCoupling1BDConstraintCreator (protocols::constraints_additional)   
AddJobPairData (protocols::simple_moves)   EggshellGrid (protocols::pockets)   LoopHashDiversifierCreator (protocols::loophash)   PoseConformationFeatures (protocols::features)   SequenceCouplingConstraint (protocols::constraints_additional)   
AddJobPairDataCreator (protocols::simple_moves)   EllipsoidalRandomizationMover (protocols::docking)   LoopHashLibrary (protocols::loophash)   PoseConformationFeaturesCreator (protocols::features)   SequenceCouplingConstraintCreator (protocols::constraints_additional)   
AddLigandMotifRotamers (protocols::enzdes)   EmptyVertexData (protocols::toolbox::pose_metric_calculators)   LoopHashLibraryLoader (protocols::loophash)   PoseEvaluator (protocols::evaluation)   SequenceIdentity (protocols::frag_picker::scores)   
AddLigandMotifRotamersOperationCreator (protocols::enzdes)   EndPoint (protocols::wum2)   LoopHashLibraryLoaderCreator (protocols::loophash)   PoseFoundResiduesCombination (protocols::enzdes)   SequenceMover (protocols::moves)   
AddMover (protocols::stepwise::monte_carlo::rna)   EndToEndPivots (protocols::kinematic_closure::pivot_pickers)   LoopHashLibraryOptions (protocols::loophash)   PoseInfoFilter (protocols::simple_filters)   SequenceNumberResolver (protocols::topology_broker)   
AddOrDeleteMover (protocols::stepwise::monte_carlo::rna)   EnergiesData (protocols::toolbox::pose_metric_calculators)   LoopHashLibraryOptionsCreator (protocols::loophash)   PoseInfoFilterCreator (protocols::simple_filters)   SequenceProfileMover (protocols::simple_moves)   
AddOrRemoveMatchCsts (protocols::enzdes)   EnergyCutRotamerTrialsMinMover (protocols::simple_moves)   LoopHashMap (protocols::loophash)   PoseInputStreamJobInputter (protocols::jd2)   SequenceProfileMoverCreator (protocols::simple_moves)   
AddOrRemoveMatchCstsCreator (protocols::enzdes)   EnergyCutRotamerTrialsMover (protocols::simple_moves)   LoopHashMoverWrapper (protocols::loophash)   PoseInputStreamJobInputterCreator (protocols::jd2)   SequenceRecoveryFilter (protocols::protein_interface_design::filters)   
AddRigidBodyLigandConfs (protocols::enzdes)   EnergyPerResidueFilter (protocols::simple_filters)   LoopHashMoverWrapperCreator (protocols::loophash)   PoseInserter (protocols::match::output)   SequenceRecoveryFilterCreator (protocols::protein_interface_design::filters)   
AddRigidBodyLigandConfsCreator (protocols::enzdes)   EnergyPerResidueFilterCreator (protocols::simple_filters)   LoopHashRelaxProtocol (protocols::loophash)   PoseMatchOutputWriter (protocols::match::output)   SequenceShiftMover (protocols::rbsegment_relax)   
AddSearchPatternRotSetOp (protocols::hotspot_hashing)   EnergyReporter (protocols::pose_reporters)   LoopHashSampler (protocols::loophash)   PoseMetricEvaluator (protocols::simple_filters)   SequentialSymmetrySlider (protocols::simple_moves::symmetry)   
AddSidechainConstraintsToHotspots (protocols::protein_interface_design::movers)   EnergyReporterCreator (protocols::pose_reporters)   LoopJumpFoldCst (protocols::abinitio)   PoseNumberedLoopFileReader (protocols::loops)   SerializedLoop (protocols::loops)   
AddSidechainConstraintsToHotspotsCreator (protocols::protein_interface_design::movers)   EnsembleConstraints (protocols::cluster)   LoopLengthChange (protocols::protein_interface_design::movers)   PosePropertyReporter (protocols::rosetta_scripts)   SetAACompositionPotential (protocols::fldsgn::potentials)   
AddZincSiteConstraints (protocols::metal_interface)   EnsembleConstraints_Simple (protocols::cluster)   LoopLengthChangeCreator (protocols::protein_interface_design::movers)   PosePropertyReporterCreator (protocols::rosetta_scripts)   SetAACompositionPotentialCreator (protocols::fldsgn::potentials)   
AlaScan (protocols::simple_filters)   EnsembleEnergy (protocols::scoring::methods)   LoopMover (protocols::loop_modeling)   PosePropertyReporterFactory (protocols::rosetta_scripts)   SetAtomTree (protocols::protein_interface_design::movers)   
AlaScanFilterCreator (protocols::simple_filters)   EnsembleEnergyCreator (protocols::scoring::methods)   LoopMover (protocols::loops::loop_mover)   PosePropertyReporterRegistrator (protocols::rosetta_scripts)   SetAtomTreeCreator (protocols::protein_interface_design::movers)   
Align_RmsdEvaluator (protocols::comparative_modeling)   Entity (protocols::genetic_algorithm)   LoopMover_Perturb_CCD (protocols::loops::loop_mover::perturb)   PoseSelectionScreener (protocols::stepwise::screener)   SetCatalyticResPackBehavior (protocols::enzdes)   
Align_RotamerEvaluator (protocols::comparative_modeling)   EntityCorrespondence (protocols::pack_daemon)   LoopMover_Perturb_CCDCreator (protocols::loops::loop_mover::perturb)   PoseSelector (protocols::rosetta_scripts)   SetCatalyticResPackBehaviorCreator (protocols::enzdes)   
AlignChainMover (protocols::simple_moves)   EntityElement (protocols::genetic_algorithm)   LoopMover_Perturb_KIC (protocols::loops::loop_mover::perturb)   PoseSelectorCreator (protocols::rosetta_scripts)   SetChiMover (protocols::simple_moves::sidechain_moves)   
AlignChainMoverCreator (protocols::simple_moves)   EntityElementCreator (protocols::genetic_algorithm)   LoopMover_Perturb_KICCreator (protocols::loops::loop_mover::perturb)   PoseSelectorFactory (protocols::rosetta_scripts)   SetChiMoverCreator (protocols::simple_moves::sidechain_moves)   
AlignEvaluator (protocols::evaluation)   EntityElementFactory (protocols::genetic_algorithm)   LoopMover_Perturb_QuickCCD (protocols::loops::loop_mover::perturb)   PoseSelectorRegistrator (protocols::rosetta_scripts)   SetCrystWeightMover (protocols::cryst)   
AlignmentCluster (protocols::comparative_modeling)   EntityElementRegistrator (protocols::genetic_algorithm)   LoopMover_Perturb_QuickCCD_Moves (protocols::loops::loop_mover::perturb)   PositionSpecificRandomizer (protocols::genetic_algorithm)   SetCrystWeightMoverCreator (protocols::cryst)   
AlignmentClustering (protocols::comparative_modeling)   EntityElementsEqual (protocols::genetic_algorithm)   LoopMover_Perturb_QuickCCD_MovesCreator (protocols::loops::loop_mover::perturb)   PositionType (protocols::dna)   SetIGTypeOperation (protocols::toolbox::task_operations)   
AlignmentID (protocols::id)   EntityFunc (protocols::pack_daemon)   LoopMover_Perturb_QuickCCDCreator (protocols::loops::loop_mover::perturb)   PostDockAssemblyScorer (protocols::domain_assembly)   SetIGTypeOperationCreator (protocols::toolbox::task_operations)   
AlignmentSet (protocols::comparative_modeling)   EntityFuncExpressionCreator (protocols::pack_daemon)   LoopMover_Refine_Backrub (protocols::loops::loop_mover::refine)   PosType (protocols::multistate_design)   SetRefinementOptionsMover (protocols::cryst)   
AlignPoseToInvrotTreeMover (protocols::toolbox::match_enzdes_util)   EntityHistoryLT (protocols::pack_daemon)   LoopMover_Refine_BackrubCreator (protocols::loops::loop_mover::refine)   PosTypeCreator (protocols::multistate_design)   SetRefinementOptionsMoverCreator (protocols::cryst)   
AlignRmsdTargetEvaluatorCreator (protocols::comparative_modeling)   EntityRandomizer (protocols::genetic_algorithm)   LoopMover_Refine_CCD (protocols::loops::loop_mover::refine)   PowExpression (protocols::pack_daemon)   SetReturningPackRotamersMover (protocols::simple_moves)   
AllAtomNormalization (protocols::qsar::scoring_grid)   EnvBeginMover (protocols::environment)   LoopMover_Refine_CCDCreator (protocols::loops::loop_mover::refine)   PPoly (protocols::sasa_scores)   SetSecStructEnergies (protocols::fldsgn::potentials)   
AllowedSeqposForGeomCst (protocols::toolbox::match_enzdes_util)   EnvClaim (protocols::environment::claims)   LoopMover_Refine_KIC (protocols::loops::loop_mover::refine)   PrecomputedFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   SetSecStructEnergiesCreator (protocols::fldsgn::potentials)   
AllowInsert (protocols::toolbox)   EnvClaimBroker (protocols::environment)   LoopMover_Refine_KICCreator (protocols::loops::loop_mover::refine)   PredesignPerturbMover (protocols::enzdes)   SetTemperatureFactor (protocols::protein_interface_design::movers)   
AllowPdbIdFilter (protocols::frag_picker)   EnvEndMover (protocols::environment)   LoopMover_SlidingWindow (protocols::loop_build)   PredesignPerturbMoverCreator (protocols::enzdes)   SetTemperatureFactorCreator (protocols::protein_interface_design::movers)   
AllResiduesChanged (protocols::abinitio)   Environment (protocols::environment)   LoopMover_SlidingWindowCreator (protocols::loop_build)   PredictedBurialEvaluator (protocols::simple_filters)   SetTorsion (protocols::simple_moves)   
AllResiduesChanged (protocols::hybridization)   EnzConstraintIO (protocols::toolbox::match_enzdes_util)   LoopMoverFactory (protocols::loops)   PredictedBurialFnEvaluatorCreator (protocols::simple_filters)   SetTorsionCreator (protocols::simple_moves)   
Alternating   EnzConstraintParameters (protocols::toolbox::match_enzdes_util)   LoopMoverFromCommandLine (protocols::protein_interface_design::movers)   PrepackMover (protocols::protein_interface_design::movers)   SetupForDensityScoringMover (protocols::electron_density)   
AlternativePairings (protocols::abinitio)   EnzCstTemplateRes (protocols::toolbox::match_enzdes_util)   LoopMoverFromCommandLineCreator (protocols::protein_interface_design::movers)   PrepackMoverCreator (protocols::protein_interface_design::movers)   SetupForDensityScoringMoverCreator (protocols::electron_density)   
AlterSpecDisruptionDriver (protocols::pmut_scan)   EnzCstTemplateResAtoms (protocols::toolbox::match_enzdes_util)   LoopMoverGroup (protocols::loop_modeling::utilities)   PreventChainFromRepackingOperation (protocols::toolbox::task_operations)   SetupForFibrilMover (protocols::fibril)   
AmbigCSScore (protocols::frag_picker::scores)   EnzCstTemplateResCache (protocols::toolbox::match_enzdes_util)   LoopOpener (protocols::loop_modeling::openers)   PreventChainFromRepackingOperationCreator (protocols::toolbox::task_operations)   SetupForSymmetryMover (protocols::simple_moves::symmetry)   
AmbiguousMultiConstraint (protocols::constraints_additional)   EnzdesBaseProtocol (protocols::enzdes)   LoopOver (protocols::protein_interface_design::movers)   PreventResiduesFromRepackingOperation (protocols::toolbox::task_operations)   SetupForSymmetryMoverCreator (protocols::simple_moves::symmetry)   
An   EnzdesCacheableObserver (protocols::toolbox::match_enzdes_util)   LoopOverCreator (protocols::protein_interface_design::movers)   PreventResiduesFromRepackingOperationCreator (protocols::toolbox::task_operations)   SetupHotspotConstraintsLoopsMover (protocols::protein_interface_design::movers)   
An   EnzdesConstraintReporter (protocols::enzdes)   LoopPivots (protocols::kinematic_closure::pivot_pickers)   ProcessorFactory (protocols::match::output)   SetupHotspotConstraintsLoopsMoverCreator (protocols::protein_interface_design::movers)   
Anchor (protocols::anchored_design)   EnzdesCstCache (protocols::toolbox::match_enzdes_util)   LoopProtocol (protocols::loop_modeling)   ProfilerMover (protocols::moves)   SetupHotspotConstraintsMover (protocols::protein_interface_design::movers)   
AnchoredDesignMover (protocols::anchored_design)   EnzdesCstParamCache (protocols::toolbox::match_enzdes_util)   LoopRebuild (protocols)   ProfileScore (protocols::frag_picker::scores)   SetupHotspotConstraintsMoverCreator (protocols::protein_interface_design::movers)   
AnchoredGraftMover (protocols::grafting)   EnzdesFixBBProtocol (protocols::enzdes)   LoopRefine (protocols)   ProfileScoreBlosum62 (protocols::frag_picker::scores)   SetupNCSMover (protocols::simple_moves::symmetry)   
AnchoredPerturbMover (protocols::anchored_design)   EnzdesFlexBBProtocol (protocols::enzdes)   LoopRefineInnerCycle (protocols::loops::loop_mover::refine)   ProfileScoreDistWeight (protocols::frag_picker::scores)   SetupNCSMoverCreator (protocols::simple_moves::symmetry)   
AnchoredRefineMover (protocols::anchored_design)   EnzdesFlexibleRegion (protocols::enzdes)   LoopRefineInnerCycleContainer (protocols::loops::loop_mover::refine)   ProfileScoreL1 (protocols::frag_picker::scores)   SetupPoissonBoltzmannPotential (protocols::pb_potential)   
AnchorMoversData (protocols::anchored_design)   EnzdesJobInputter (protocols::enzdes)   LoopRefineInnerCycleContainerCreator (protocols::loops::loop_mover::refine)   ProfileScoreStructL1 (protocols::frag_picker::scores)   SetupPoissonBoltzmannPotentialCreator (protocols::pb_potential)   
AnchorSugarScreener (protocols::stepwise::screener)   EnzdesJobInputterCreator (protocols::enzdes)   LoopRefineInnerCycleFactory (protocols::loops::loop_mover::refine)   ProfileScoreSubMatrix (protocols::frag_picker::scores)   SF_Replica (protocols::toolbox)   
AndSelector (protocols::pose_selectors)   EnzdesJobOutputter (protocols::enzdes)   LoopRelaxMover (protocols::comparative_modeling)   ProgressBar (protocols::loop_modeling::loggers)   ShakeStructureMover (protocols::simple_moves)   
AndSelectorCreator (protocols::pose_selectors)   EnzdesJobOutputterCreator (protocols::enzdes)   LoopRelaxMoverCreator (protocols::comparative_modeling)   ProgressBarObserver (protocols::canonical_sampling)   ShapeComplementarityFilter (protocols::simple_filters)   
ANN (protocols::sparta)   EnzdesLoopInfo (protocols::toolbox::match_enzdes_util)   LoopRelaxThreadingMover (protocols::comparative_modeling)   ProgressBarObserverCreator (protocols::canonical_sampling)   ShapeComplementarityFilterCreator (protocols::simple_filters)   
Antibody (protocols::antibody_legacy)   EnzdesLoopsFile (protocols::toolbox::match_enzdes_util)   LoopRemodel (protocols::protein_interface_design::movers)   ProlineFixMover (protocols::simple_moves)   ShapeGrid (protocols::qsar::scoring_grid)   
AntibodyCDRDesigner (protocols::antibody::design)   EnzdesScorefileFilter (protocols::enzdes)   LoopRemodelCreator (protocols::protein_interface_design::movers)   ProlinePhiScore (protocols::frag_picker::scores)   ShapeGridCreator (protocols::qsar::scoring_grid)   
AntibodyDatabaseManager (protocols::antibody::design)   EnzdesScorefileFilterCreator (protocols::enzdes)   LoopRlxMover (protocols::antibody_legacy)   ProtectedConformation (protocols::environment)   ShearMinCCDTrial (protocols::loops::loop_mover::refine)   
AntibodyDesignModeler (protocols::antibody::design)   EnzdesSeqRecoveryCache (protocols::toolbox::match_enzdes_util)   LoopRmsdEvaluator (protocols::simple_filters)   ProteinAtrRepChecker (protocols::stepwise::sampling::protein::checker)   ShearMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
AntibodyDesignMover (protocols::antibody::design)   EnzRepackMinimize (protocols::enzdes)   Loops (protocols::loops)   ProteinAtrRepScreener (protocols::stepwise::screener)   ShearMover (protocols::simple_moves)   
AntibodyEnumManager (protocols::antibody)   EnzRepackMinimizeCreator (protocols::enzdes)   LoopsDatabaseDefiner (protocols::loops::loops_definers)   ProteinBackboneAtomAtomPairFeatures (protocols::features)   ShearMoverCreator (protocols::simple_moves)   
AntibodyGraftDesigner (protocols::antibody::design)   EnzScoreFilter (protocols::enzdes)   LoopsDatabaseDefinerCreator (protocols::loops::loops_definers)   ProteinBackboneAtomAtomPairFeaturesCreator (protocols::features)   Sheet (protocols::fldsgn::topology)   
AntibodyInfo (protocols::antibody)   EnzScoreFilterCreator (protocols::enzdes)   LoopsDefiner (protocols::loops::loops_definers)   ProteinBackboneBuildPoint (protocols::match::upstream)   SheetBuilder (protocols::jumping)   
AntibodyModeler (protocols::antibody_legacy)   EulerAngles (protocols::rotamer_sampler::rigid_body)   LoopsDefinerCreator (protocols::loops::loops_definers)   ProteinBackboneTorsionAngleFeatures (protocols::features)   SheetConstraintsRCG (protocols::fldsgn)   
AntibodyModelerProtocol (protocols::antibody)   EvaluatedArchive (protocols::jd2::archive)   LoopsDefinerFactory (protocols::loops::loops_definers)   ProteinBackboneTorsionAngleFeaturesCreator (protocols::features)   SheetCstGeneratorCreator (protocols::fldsgn)   
AntibodyNumbering (protocols::antibody)   EvaluatedTrialMover (protocols::simple_filters)   LoopsDefinerLoader (protocols::loops::loops_definers)   ProteinBetaAntiParallelRotamer (protocols::rotamer_sampler::protein)   SheetFilter (protocols::simple_filters)   
AntibodyNumberingParser (protocols::antibody)   EvaluatorCreator (protocols::evaluation)   LoopsDefinerLoaderCreator (protocols::loops::loops_definers)   ProteinBondGeometryFeatures (protocols::features)   SheetFoldTypeManager (protocols::fldsgn::topology)   
APCluster (protocols::cluster)   EvaluatorFactory (protocols::evaluation)   LoopsDefinerRegistrator (protocols::loops::loops_definers)   ProteinBondGeometryFeaturesCreator (protocols::features)   SheetSet (protocols::fldsgn::topology)   
ApplyRandomStoredRBConf (protocols::enzdes)   EvaluatorRegistrator (protocols::evaluation)   LoopsExplicitDefiner (protocols::loops::loops_definers)   ProteinCore (protocols::toolbox::task_operations)   SheetTopologyFilter (protocols::fldsgn::filters)   
ArchiveBase (protocols::jd2::archive)   EXCN_Archive (protocols::jd2::archive)   LoopsExplicitDefinerCreator (protocols::loops::loops_definers)   ProteinCoreFilterCreator (protocols::toolbox::task_operations)   SheetTopologyFilterCreator (protocols::fldsgn::filters)   
ArchiveManager (protocols::jd2::archive)   EXCN_AssignmentNotFound (protocols::noesy_assign)   LoopsFileData (protocols::loops)   ProteinFragmentRotamer (protocols::rotamer_sampler::protein)   SheetTranslate (protocols::nonlocal)   
ArchiveMasterBase (protocols::mpi)   EXCN_bbdb_Merge_Failed (protocols::loophash)   LoopsFileDefiner (protocols::loops::loops_definers)   ProteinInterfaceDesignOperation (protocols::toolbox::task_operations)   ShortLoopClosure (protocols::loops::loop_closure::ccd)   
AssembleLinkerMover (protocols::domain_assembly)   EXCN_Converged (protocols::moves::mc_convergence_checks)   LoopsFileDefinerCreator (protocols::loops::loops_definers)   ProteinInterfaceDesignOperationCreator (protocols::toolbox::task_operations)   ShoveResidueMover (protocols::protein_interface_design::movers)   
AssignToClustersMover (protocols::cluster)   EXCN_Converged (protocols::moves)   LoopsFileFallbackConfiguration (protocols::loops)   ProteinInterfaceMultiStateDesignMover (protocols::protein_interface_design::movers)   ShoveResidueMoverCreator (protocols::protein_interface_design::movers)   
AsymFoldandDockClaimer (protocols::topology_broker)   EXCN_DB_IO_Failed (protocols::loophash)   LoopsFileFallbackConfigurationCreator (protocols::loops)   ProteinInterfaceMultiStateDesignMoverCreator (protocols::protein_interface_design::movers)   ShowViolation (protocols::abinitio)   
AsymFoldandDockMoveRbJumpMover (protocols::simple_moves::asym_fold_and_dock)   EXCN_Env_Passport (protocols::environment)   LoopsFileIO (protocols::loops)   ProteinLigandInterfaceUpweighter (protocols::enzdes)   ShuffleFileSystemJobDistributor (protocols::jd2)   
AsymFoldandDockRbTrialMover (protocols::simple_moves::asym_fold_and_dock)   EXCN_Env_Security_Exception (protocols::environment)   LoopsFileLoader (protocols::loops)   ProteinLigandInterfaceUpweighterOperationCreator (protocols::enzdes)   SICFast (protocols::sic_dock)   
Atom_Bin (protocols::stepwise::sampling::rna::checker)   EXCN_FailedBroking (protocols::topology_broker)   LoopsFileLoaderCreator (protocols::loops)   ProteinMainChainRotamer (protocols::rotamer_sampler::protein)   SICPatternAtTransform (protocols::hotspot_hashing)   
AtomAngleSecMatchRPE (protocols::match::downstream)   EXCN_FileFormat (protocols::noesy_assign)   LoopsFileOptions (protocols::loops)   ProteinPackScreener (protocols::stepwise::screener)   SidechainContactDistCutoff (protocols::frag_picker)   
AtomAtomPairFeatures (protocols::features)   EXCN_FilterFailed (protocols::topology_broker)   LoopsFileOptionsCreator (protocols::loops)   ProteinResidueConformationFeatures (protocols::features)   SidechainMCMover (protocols::simple_moves::sidechain_moves)   
AtomAtomPairFeaturesCreator (protocols::features)   EXCN_Heat_Converged (protocols::canonical_sampling::mc_convergence_checks)   LRmsdFilter (protocols::protein_interface_design::filters)   ProteinResidueConformationFeaturesCreator (protocols::features)   SidechainMCMoverCreator (protocols::simple_moves::sidechain_moves)   
AtomBasedConstraintsScore (protocols::frag_picker::scores)   EXCN_Input (protocols::topology_broker)   LRmsdFilterCreator (protocols::protein_interface_design::filters)   ProteinRMSDFeatures (protocols::features)   SidechainMetropolisHastingsMover (protocols::canonical_sampling)   
AtomCoordinateCstMover (protocols::relax)   EXCN_Invalid_Hashmap (protocols::loophash)   LSMSearchPattern (protocols::hotspot_hashing)   ProteinRMSDFeaturesCreator (protocols::features)   SidechainMetropolisHastingsMoverCreator (protocols::canonical_sampling)   
AtomCoordinateCstMoverCreator (protocols::relax)   EXCN_Loop_not_closed (protocols::loops)   
  M  
ProteinRMSDNoSuperpositionFeatures (protocols::features)   SidechainMinMover (protocols::docking)   
AtomCountFilter (protocols::ligand_docking)   EXCN_No_Extra_Data_To_Write (protocols::loophash)   ProteinRMSDNoSuperpositionFeaturesCreator (protocols::features)   SidechainMover (protocols::simple_moves::sidechain_moves)   
AtomCountFilterCreator (protocols::ligand_docking)   EXCN_NoesyAssign (protocols::noesy_assign)   MainChainTorsionSet (protocols::stepwise::sampling::protein)   ProteinSCSampler (protocols::match::upstream)   SidechainMoverBase (protocols::simple_moves::sidechain_moves)   
AtomDihedralSecMatchRPE (protocols::match::downstream)   EXCN_Pool_Converged (protocols::canonical_sampling::mc_convergence_checks)   MakeABEGO_SS_Score (protocols::frag_picker::scores)   ProteinSilentReport (protocols::features)   SidechainMoverCreator (protocols::simple_moves::sidechain_moves)   
AtomDistanceSecMatchRPE (protocols::match::downstream)   EXCN_TopologyBroker (protocols::topology_broker)   MakeAmbigCSScore (protocols::frag_picker::scores)   ProteinUpstreamBuilder (protocols::match::upstream)   SidechainRmsdFilter (protocols::simple_filters)   
AtomGeometrySecMatchRPE (protocols::match::downstream)   EXCN_Unknown (protocols::topology_broker)   MakeAtomPairConstraintsScore (protocols::frag_picker::scores)   Protocol (protocols::abinitio)   SidechainRmsdFilterCreator (protocols::simple_filters)   
AtomicContactCountFilter (protocols::protein_interface_design::filters)   EXCN_UnknownAtomname (protocols::noesy_assign)   MakeBFactor (protocols::frag_picker::scores)   ProtocolFeatures (protocols::features)   Sigmoid (protocols::simple_filters)   
AtomicContactCountFilterCreator (protocols::protein_interface_design::filters)   EXCN_UnknownResonance (protocols::noesy_assign)   MakeConstScore (protocols::frag_picker::scores)   ProtocolFeaturesCreator (protocols::features)   SigmoidFilterCreator (protocols::simple_filters)   
AtomicContactFilter (protocols::simple_filters)   EXCN_Wrong_DB_Format (protocols::loophash)   MakeCSScore (protocols::frag_picker::scores)   PseudocontactShiftEnergyController (protocols::topology_broker)   SilentFileInputter (protocols::inputter)   
AtomicContactFilterCreator (protocols::simple_filters)   Exemplar (protocols::cluster)   MakeDihedralConstraintsScore (protocols::frag_picker::scores)   PseudocontactShiftEnergyController_Ts1 (protocols::topology_broker)   SilentFileJobInputter (protocols::jd2)   
AtomicDistanceFilter (protocols::simple_filters)   ExpExpression (protocols::pack_daemon)   MakeDisulfideDistance (protocols::frag_picker::scores)   PseudocontactShiftEnergyController_Ts2 (protocols::topology_broker)   SilentFileJobInputterCreator (protocols::jd2)   
AtomicDistanceFilterCreator (protocols::simple_filters)   ExpiryFilter (protocols::simple_filters)   MakeDisulfideIdentity (protocols::frag_picker::scores)   PseudocontactShiftEnergyController_Ts3 (protocols::topology_broker)   SilentFileJobOutputter (protocols::jd2)   
AtomIDHashFunction (protocols::sic_dock)   ExpiryFilterCreator (protocols::simple_filters)   MakeFragmentAllAtomCrmsd (protocols::frag_picker::scores)   PseudocontactShiftEnergyController_Ts4 (protocols::topology_broker)   SilentFileJobOutputterCreator (protocols::jd2)   
AtomInResidueAtomInResiduePairFeatures (protocols::features)   ExplicitWaterUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   MakeFragmentChunkCrms (protocols::frag_picker::scores)   PseudocontactShiftEnergyCreator (protocols::scoring::methods::pcs)   SilentFileOutputter (protocols::outputter)   
AtomInResidueAtomInResiduePairFeaturesCreator (protocols::features)   ExposedHydrophobicsFilter (protocols::denovo_design::filters)   MakeFragmentCrmsd (protocols::frag_picker::scores)   PseudocontactShiftEnergyCreator_Ts1 (protocols::scoring::methods::pcsTs1)   SilentObserver (protocols::viewer)   
AtomPairConstraintsData (protocols::frag_picker::scores)   ExposedHydrophobicsFilterCreator (protocols::denovo_design::filters)   MakeFragmentCrmsdResDepth (protocols::frag_picker::scores)   PseudocontactShiftEnergyCreator_Ts2 (protocols::scoring::methods::pcsTs2)   SilentStructStore (protocols::wum)   
AtomPairConstraintsScore (protocols::frag_picker::scores)   ExtendedPoseMover (protocols::simple_moves)   MakeFragmentDME (protocols::frag_picker::scores)   PseudocontactShiftEnergyCreator_Ts3 (protocols::scoring::methods::pcsTs3)   SilentTrajectoryRecorder (protocols::canonical_sampling)   
AtomPairData (protocols::ligand_docking::rdf)   ExtendedPoseMoverCreator (protocols::simple_moves)   MakeFragmentScoringMethod (protocols::frag_picker::scores)   PseudocontactShiftEnergyCreator_Ts4 (protocols::scoring::methods::pcsTs4)   SilentTrajectoryRecorderCreator (protocols::canonical_sampling)   
AtomTreeDiffJobDistributor (protocols::jobdist)   Extender (protocols::star)   MakeGunnCostScore (protocols::frag_picker::scores)   Psi (protocols::frag_picker::scores)   Simple   
AtomTreeDiffJobInputter (protocols::jd2)   ExternalEvaluator (protocols::simple_filters)   MakeHydrophobicityProfileSimilarity (protocols::frag_picker::scores)   PSSM2BfactorMover (protocols::simple_moves)   SimplePoseSelection (protocols::stepwise::screener)   
AtomTreeDiffJobInputterCreator (protocols::jd2)   ExternalGeomSampler (protocols::toolbox::match_enzdes_util)   MakeHydrophobicitySimilarity (protocols::frag_picker::scores)   PSSM2BfactorMoverCreator (protocols::simple_moves)   SimpleRMSD_Screener (protocols::stepwise::screener)   
AtomTreeDiffJobOutputter (protocols::jd2)   ExtractAsymmetricPoseMover (protocols::simple_moves::symmetry)   MakeInterbondAngleScore (protocols::frag_picker::scores)   PSSMOptEPositionData (protocols::optimize_weights)   SimpleTreeBuilder (protocols::nonlocal)   
AtomTreeDiffJobOutputterCreator (protocols::jd2)   ExtractAsymmetricPoseMoverCreator (protocols::simple_moves::symmetry)   MakeJCoupling (protocols::frag_picker::scores)   PValuedFragmentScoreManager (protocols::frag_picker::scores)   SimulatedTempering (protocols::canonical_sampling)   
AtomTypesFeatures (protocols::features)   ExtractAsymmetricUnitMover (protocols::simple_moves::symmetry)   MakeLAMBEGO_Similarity (protocols::frag_picker::scores)   PyMolMover (protocols::moves)   SimulatedTempering (protocols::moves)   
AtomTypesFeaturesCreator (protocols::features)   ExtractAsymmetricUnitMoverCreator (protocols::simple_moves::symmetry)   MakeMidPhiOut (protocols::frag_picker::scores)   PyMolMoverCreator (protocols::moves)   SimulatedTemperingCreator (protocols::canonical_sampling)   
AtrGrid (protocols::qsar::scoring_grid)   ExtraScoreEvaluatorCreator (protocols::simple_filters)   MakeMidPsiOut (protocols::frag_picker::scores)   PyMolObserver (protocols::moves)   SingleDownstreamResidueWriter (protocols::match::output)   
AtrGridCreator (protocols::qsar::scoring_grid)   ExtraThreadingMover (protocols::comparative_modeling)   MakePartialSecondarySimilarity (protocols::frag_picker::scores)   
  Q  
SingleFileBuffer (protocols::jd2)   
AtrRepChecker (protocols::stepwise::sampling::rna::checker)   
  F  
MakePCS_FragDistance (protocols::frag_picker::scores)   SingleFragmentMover (protocols::nonlocal)   
AtrRepScreener (protocols::stepwise::screener)   MakePhi (protocols::frag_picker::scores)   Quat (protocols::simple_filters)   SingleFragmentMoverCreator (protocols::nonlocal)   
Attachment (protocols::stepwise::monte_carlo)   FaDockingSlideIntoContact (protocols::docking)   MakePhiPsiRmsd (protocols::frag_picker::scores)   QuickRepacker (protocols::pack_daemon)   SingleGrid (protocols::qsar::scoring_grid)   
AutoCutData (protocols::environment)   FalseFilter (protocols::filters)   MakePhiPsiSquareWell (protocols::frag_picker::scores)   QuotaCollector (protocols::frag_picker::quota)   SingleMotif (protocols::motifs)   
AutoCutDataCreator (protocols::environment)   FalseFilterCreator (protocols::filters)   MakePolyXMover (protocols::simple_moves)   QuotaConfig (protocols::frag_picker::quota)   SingleResidueInvrotTarget (protocols::toolbox::match_enzdes_util)   
AutoRBMover (protocols::rbsegment_relax)   FASelectSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   MakePolyXMoverCreator (protocols::simple_moves)   QuotaDebug (protocols::frag_picker)   SingleResidueTorsionFragmentLibrary (protocols::frags)   
AverageDegreeFilter (protocols::protein_interface_design::filters)   FastaInputter (protocols::inputter)   MakeProfileScore (protocols::frag_picker::scores)   QuotaPool (protocols::frag_picker::quota)   SingleState (protocols::multistate_design)   
AverageDegreeFilterCreator (protocols::protein_interface_design::filters)   FASTER_IG_Repacker (protocols::pack_daemon)   MakeProfileScoreBlosum62 (protocols::frag_picker::scores)   QuotaSelector (protocols::frag_picker::quota)   SingleStateEntityData (protocols::multistate_design)   
AveragePathLengthFilter (protocols::simple_filters)   FastForwardToNextResidueAlternative (protocols::stepwise::screener)   MakeProfileScoreDistWeight (protocols::frag_picker::scores)   
  R  
SingleStateFitnessFunction (protocols::multistate_design)   
AveragePathLengthFilterCreator (protocols::simple_filters)   FastForwardToNextRigidBody (protocols::stepwise::screener)   MakeProfileScoreL1 (protocols::frag_picker::scores)   SingleStructureData (protocols::optimize_weights)   
  B  
FastGapMover (protocols::loophash)   MakeProfileScoreStructL1 (protocols::frag_picker::scores)   RadiusOfGyrationFeatures (protocols::features)   SingleValuePoseEvaluator (protocols::evaluation)   
FastLinearFunc (protocols::moves)   MakeProfileScoreSubMatrix (protocols::frag_picker::scores)   RadiusOfGyrationFeaturesCreator (protocols::features)   SlicedPoseJobParameters (protocols::stepwise::sampling::rna)   
BackboneDB (protocols::loophash)   FastRelax (protocols::relax)   MakeProlinePhiScore (protocols::frag_picker::scores)   RamachandranOpener (protocols::loop_modeling::openers)   SlideTogether (protocols::ligand_docking)   
BackboneMover (protocols::simple_moves)   FastRelaxCreator (protocols::relax)   MakePsi (protocols::frag_picker::scores)   RamaPerturber (protocols::kinematic_closure::perturbers)   SlideTogetherCreator (protocols::ligand_docking)   
BackboneSampler (protocols::enzdes)   FaSymDockingSlideTogether (protocols::simple_moves::symmetry)   MakeRamaScore (protocols::frag_picker::scores)   RamaScore (protocols::frag_picker::scores)   SlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
BackboneSamplerCreator (protocols::enzdes)   FavorNativeResidue (protocols::protein_interface_design)   MakeRDCScore (protocols::frag_picker::scores)   RampingFunc (protocols::moves)   SmallFragWeight (protocols::topology_broker::weights)   
BackboneSegment (protocols::loophash)   FavorNativeResiduePreCycle (protocols::protein_interface_design::movers)   MakeScoreEValuator (protocols::frag_picker::scores)   RampingMover (protocols::moves)   SmallMinCCDTrial (protocols::loops::loop_mover::refine)   
BackrubDDMover (protocols::protein_interface_design::movers)   FavorNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MakeSecondaryIdentity (protocols::frag_picker::scores)   RampingMoverCreator (protocols::moves)   SmallMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
BackrubDDMoverCreator (protocols::protein_interface_design::movers)   FavorNonNativeResidue (protocols::protein_interface_design)   MakeSecondarySimilarity (protocols::frag_picker::scores)   RandomConformerMover (protocols::ligand_docking)   SmallMover (protocols::simple_moves)   
BackrubMover (protocols::backrub)   FavorNonNativeResiduePreCycle (protocols::protein_interface_design::movers)   MakeSequenceIdentity (protocols::frag_picker::scores)   RandomConformers (protocols::ligand_docking)   SmallMoverCreator (protocols::simple_moves)   
BackrubMoverCreator (protocols::backrub)   FavorNonNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MakeSolventAccessibility (protocols::frag_picker::scores)   RandomConformersCreator (protocols::ligand_docking)   SmoothFragmentMover (protocols::simple_moves)   
BackrubSegment (protocols::backrub)   FavorSequenceProfile (protocols::simple_moves)   MakeStarTopologyMover (protocols::rbsegment_relax)   RandomMover (protocols::moves)   SmoothFragWeight (protocols::topology_broker::weights)   
BackrubSidechainMover (protocols::backrub)   FavorSequenceProfileCreator (protocols::simple_moves)   MakeStarTopologyMoverCreator (protocols::rbsegment_relax)   RandomMoverCreator (protocols::moves)   SmoothPolicy (protocols::nonlocal)   
BackrubSidechainMoverCreator (protocols::backrub)   FavorSymmetricSequence (protocols::simple_moves)   MakeTalosSSSimilarity (protocols::frag_picker::scores)   RandomMutation (protocols::protein_interface_design::movers)   SmoothSymmetricFragmentMover (protocols::simple_moves)   
BalancedKicMover (protocols::kinematic_closure)   FavorSymmetricSequenceCreator (protocols::simple_moves)   MakeTorsionBinSimilarity (protocols::frag_picker::scores)   RandomMutationCreator (protocols::protein_interface_design::movers)   SmotifFeatures (protocols::features)   
BaseBin (protocols::stepwise::sampling::rna::rigid_body)   FeaturesReporter (protocols::features)   MapHotspot (protocols::protein_interface_design::movers)   RandomSheetBuilder (protocols::jumping)   SmotifFeaturesCreator (protocols::features)   
BaseBinMapUpdater (protocols::stepwise::screener)   FeaturesReporterCreator (protocols::features)   MapHotspotCreator (protocols::protein_interface_design::movers)   RandomSolutions (protocols::kinematic_closure::solution_pickers)   SnugDock (protocols::antibody)   
BaseCentroidScreener (protocols::stepwise::screener)   FeaturesReporterFactory (protocols::features)   MatchCollisionFilter (protocols::match::output)   RandomSymmetrySlider (protocols::simple_moves::symmetry)   SnugDockProtocol (protocols::antibody)   
BaseDisulfPairingLibrary (protocols::jumping)   FeaturesReporterRegistrator (protocols::features)   MatchConsolidator (protocols::match::output)   RangeFilter (protocols::simple_filters)   SolutionPicker (protocols::kinematic_closure::solution_pickers)   
BaseJobDistributor (protocols::jobdist)   FibrilModelingClaimer (protocols::topology_broker)   MatchConstraintFileInfo (protocols::toolbox::match_enzdes_util)   RangeFilterCreator (protocols::simple_filters)   SolvationGrid (protocols::qsar::scoring_grid)   
BaseJumpSetup (protocols::jumping)   FileBuffer (protocols::checkpoint)   MatchConstraintFileInfoList (protocols::toolbox::match_enzdes_util)   RationalLoopComparator (protocols::loops)   SolvationGridCreator (protocols::qsar::scoring_grid)   
BasePairingLibrary (protocols::jumping)   FileExistFilter (protocols::simple_filters)   MatchCounter (protocols::match)   RationalMonteCarlo (protocols::simple_moves::rational_mc)   SolvationMetaGrid (protocols::qsar::scoring_grid)   
BasePairStep (protocols::farna)   FileExistFilterCreator (protocols::simple_filters)   Matcher (protocols::match)   Rattle (protocols::md)   SolvationMetaGridCreator (protocols::qsar::scoring_grid)   
BasePairStepLibrary (protocols::farna)   FileJobOutputter (protocols::jd2)   MatcherMover (protocols::match)   RawType (protocols::jd2::utility)   SolventAccessibility (protocols::frag_picker::scores)   
BasePairStepSequence (protocols::farna)   FileRemoveFilter (protocols::simple_filters)   MatcherMoverCreator (protocols::match)   RawType< T & > (protocols::jd2::utility)   SortPredicate (protocols::jd2::archive)   
BasePairType (protocols::farna)   FileRemoveFilterCreator (protocols::simple_filters)   MatcherOutputStats (protocols::match)   RawType< T * > (protocols::jd2::utility)   SourcePositions (protocols::coarse_rna)   
BasicCmdLineInit (protocols::rpc)   FileSystemJobDistributor (protocols::jd2)   MatcherTask (protocols::match)   RB_lt (protocols::rbsegment_relax)   Sparta (protocols::sparta)   
BasicInit (protocols::rpc)   Filter (protocols::filters)   MatchEvaluator (protocols::match::output)   RBResidueRange (protocols::rbsegment_relax)   Sparta::SpartaLib (protocols::sparta)   
BasicJob (protocols::jobdist)   FilterBucket (protocols::loophash)   MatchFilter (protocols::match::output)   RBSegment (protocols::rbsegment_relax)   SpecialRotamerEnergy (protocols::scoring::methods)   
BasicJumpClaimer (protocols::topology_broker)   FilterCollection (protocols::filters)   MatchGrafter (protocols::metal_interface)   RBSegmentMover (protocols::rbsegment_relax)   SpecialRotamerEnergyCreator (protocols::scoring::methods)   
BasicSimAnnealerRepacker (protocols::pack_daemon)   FilterCreator (protocols::filters)   MatchGrouper (protocols::match::output)   RBSegmentRelax (protocols::rbsegment_relax)   SpecialRotamerRSO (protocols::toolbox::rotamer_set_operations)   
Batch (protocols::jd2::archive)   FilteredSolutions (protocols::kinematic_closure::solution_pickers)   MatchOutputter (protocols::match::output)   RBSegmentRelaxImpl (protocols)   SpecificGeometryLibrary (protocols::jumping)   
BatchEvaluator (protocols::simple_filters)   Filterer_Count (protocols::stepwise::sampling::rna)   MatchOutputTracker (protocols::match)   RDC_Evaluator (protocols::simple_filters)   SpecificResiduesNearInterfaceFilter (protocols::protein_interface_design::filters)   
BatchFeatures (protocols::features)   FilterFactory (protocols::filters)   MatchPositionModifier (protocols::match)   RdcEvaluatorCreator (protocols::simple_filters)   SpecificResiduesNearInterfaceFilterCreator (protocols::protein_interface_design::filters)   
BatchFeaturesCreator (protocols::features)   FilterMover (protocols::moves)   MatchProcessor (protocols::match::output)   RDCScore (protocols::frag_picker::scores)   SphericalRotationSearchPattern (protocols::hotspot_hashing)   
BatchJobInputter (protocols::jd2)   FilterRegistrator (protocols::filters)   MatchResidues (protocols::fldsgn)   RdcSelectEvaluatorCreator (protocols::simple_filters)   CrossPeak::Spin (protocols::noesy_assign)   
BatchNrEvaluator (protocols::simple_filters)   FilterReporter (protocols::pose_reporters)   MatchResiduesMover (protocols::fldsgn)   RdcTargetEvaluatorCreator (protocols::simple_filters)   SpinMover (protocols::protein_interface_design::movers)   
BB_Pos (protocols::fldsgn::topology)   FilterReporterCreator (protocols::pose_reporters)   MatchResiduesMoverCreator (protocols::fldsgn)   RDFBase (protocols::ligand_docking::rdf)   SpinMoverCreator (protocols::protein_interface_design::movers)   
BBClaim (protocols::topology_broker::claims)   FilterScanFilter (protocols::protein_interface_design::filters)   MatchScoreWriter (protocols::match::output)   RDFBinaryHbondCreator (protocols::ligand_docking::rdf)   SRelaxPose (protocols::relax)   
BBConRotMover (protocols::simple_moves)   FilterScanFilterCreator (protocols::protein_interface_design::filters)   MaxSeqSepConstraintSet (protocols::constraints_additional)   RDFBinaryHbondFunction (protocols::ligand_docking::rdf)   SS_Base (protocols::fldsgn::topology)   
BBData (protocols::loophash)   FilterStructs (protocols::flxbb)   McComb (protocols::rotamer_sampler)   RDFBinaryOrbitalFunction (protocols::ligand_docking::rdf)   SS_Info2 (protocols::fldsgn::topology)   
BBExtraData (protocols::loophash)   FilterStructs_Packstat (protocols::flxbb)   McOneTorsion (protocols::rotamer_sampler)   RDFBinaryOrbitalFunctionCreator (protocols::ligand_docking::rdf)   SS_predictor (protocols::ss_prediction)   
BBG8T3AMover (protocols::simple_moves)   FilterStructs_TotalCharge (protocols::flxbb)   McRotamer (protocols::rotamer_sampler)   RDFChargeCreator (protocols::ligand_docking::rdf)   SSFeature (protocols::comparative_modeling::features)   
BBGaussianMover (protocols::simple_moves)   FinalMinimizer (protocols::ligand_docking)   MCShowMover (protocols::moves)   RDFChargeFunction (protocols::ligand_docking::rdf)   SSPairPotential (protocols::fldsgn::potentials::sspot)   
BBGaussianMoverCreator (protocols::simple_moves)   FinalMinimizerCreator (protocols::ligand_docking)   MD_Angle (protocols::cartesian)   RDFElecCreator (protocols::ligand_docking::rdf)   Stage1Sampler (protocols::abinitio)   
BDR (protocols::forge::components)   FingerprintBase (protocols::pockets)   MD_Bond (protocols::cartesian)   RDFElecFunction (protocols::ligand_docking::rdf)   StagePreparer (protocols::abinitio::abscript)   
BDRSegmentInfo (protocols::forge::components)   FingerprintMultifunc (protocols::pockets)   MD_HarmonicDihedral (protocols::cartesian)   RDFEtableCreator (protocols::ligand_docking::rdf)   AbscriptMover::StageTracker (protocols::abinitio::abscript)   
BestHotspotCstMover (protocols::protein_interface_design::movers)   FitBfactorsMover (protocols::cryst)   MDBase (protocols::md)   RDFEtableFunction (protocols::ligand_docking::rdf)   StandardDisulfPairingLibrary (protocols::jumping)   
BestHotspotCstMoverCreator (protocols::protein_interface_design::movers)   FitBfactorsMoverCreator (protocols::cryst)   MDscheduleData (protocols::md)   RDFFunctionCreator (protocols::ligand_docking::rdf)   StandardPairingLibrary (protocols::jumping)   
BestMatchesCollection (protocols::match::output)   FitnessFunction (protocols::genetic_algorithm)   MedalExchangeMover (protocols::medal)   RDFFunctionFactory (protocols::ligand_docking::rdf)   StandardPivots (protocols::kinematic_closure::pivot_pickers)   
BestTotalScoreSelector (protocols::frag_picker)   FixedOffsetPivots (protocols::kinematic_closure::pivot_pickers)   MedalMover (protocols::medal)   RDFFunctionRegistrator (protocols::ligand_docking::rdf)   StarAbinitio (protocols::star)   
BetaAlphaBetaMotif (protocols::fldsgn::topology)   FixedPivots (protocols::kinematic_closure::pivot_pickers)   MembraneAbinitio (protocols::abinitio)   RDFHbondCreator (protocols::ligand_docking::rdf)   StartFrom (protocols::ligand_docking)   
BetaAlphaBetaMotifSet (protocols::fldsgn::topology)   FixedTemperatureController (protocols::canonical_sampling)   MembraneCenterPerturbationMover (protocols::rigid)   RDFHbondFunction (protocols::ligand_docking::rdf)   StartFromCreator (protocols::ligand_docking)   
BetaTurnDetectionFeatures (protocols::features)   FixTemplateJumpSetup (protocols::abinitio)   MembraneJump (protocols::jumping)   RDFOrbitalFunction (protocols::ligand_docking::rdf)   StarTreeBuilder (protocols::nonlocal)   
BetaTurnDetectionFeaturesCreator (protocols::features)   FlexbbEdge (protocols::flexpack::interaction_graph)   MembraneNormalPerturbationMover (protocols::rigid)   RDFOrbitalFunctionCreator (protocols::ligand_docking::rdf)   StartStructClaimer (protocols::topology_broker)   
BFactor (protocols::frag_picker::scores)   FlexbbIGFactory (protocols::flexpack::interaction_graph)   MembraneTopology (protocols::simple_moves)   ReadResfileFromDB (protocols::toolbox::task_operations)   StateAccumulatingMatchFilter (protocols::match::output)   
BfactorFittingMover (protocols::electron_density)   FlexbbInteractionGraph (protocols::flexpack::interaction_graph)   MembraneTopologyClaimer (protocols::topology_broker)   ReadResfileFromDBCreator (protocols::toolbox::task_operations)   StatusRequest (protocols::wum2)   
BfactorFittingMoverCreator (protocols::electron_density)   FlexbbNode (protocols::flexpack::interaction_graph)   MembraneTopologyCreator (protocols::simple_moves)   RecomputeDensityMapMover (protocols::cryst)   StatusResponse (protocols::wum2)   
BfactorMPM (protocols::match)   FlexbbRotamerSet (protocols::flexpack::rotamer_set)   MembraneUnitTestMover (protocols::membrane)   RecomputeDensityMapMoverCreator (protocols::cryst)   StealLigandMover (protocols::comparative_modeling)   
BfactorMultifunc (protocols::electron_density)   FlexbbRotamerSets (protocols::flexpack::rotamer_set)   ClosureProblem::Memento (protocols::kinematic_closure)   RecoverSideChainsMover (protocols::comparative_modeling)   StealSideChainsMover (protocols::comparative_modeling)   
BiasedFragmentMover (protocols::nonlocal)   FlexbbSimAnnealer (protocols::flexpack::annealer)   MetalloClaimer (protocols::topology_broker)   RefineBetaBarrel (protocols::antibody)   StepWiseBetaAntiParallelJumpSampleGenerator (protocols::stepwise::sampling::protein)   
BindingSiteConstraint (protocols::constraints_additional)   FlexbbSparseMatrixIndex (protocols::flexpack::interaction_graph)   MetalSiteResidue (protocols::metal_interface)   RefineOneCDRLoop (protocols::antibody)   StepWiseClusterer (protocols::stepwise::sampling::general)   
BindingSiteConstraintCreator (protocols::constraints_additional)   FlexPacker (protocols::flexpack)   MetaPoseEvaluator (protocols::evaluation)   RefineOneCDRLoopCentroid (protocols::antibody)   StepWiseClustererSilentBased (protocols::stepwise::sampling::general)   
BindingStrainFilter (protocols::protein_interface_design::filters)   FlexPepDockingAbInitio (protocols::flexpep_docking)   MethylNameLibrary (protocols::noesy_assign)   Region (protocols::nonlocal)   StepWiseModeler (protocols::stepwise::sampling)   
BindingStrainFilterCreator (protocols::protein_interface_design::filters)   FlexPepDockingFlags (protocols::flexpep_docking)   MethylNames (protocols::noesy_assign)   RegionalConnections (protocols::simple_filters)   StepWiseMonteCarlo (protocols::stepwise::monte_carlo::rna)   
BluePrint (protocols::jd2::parser)   FlexPepDockingLowRes (protocols::flexpep_docking)   MetricCalculatorFitnessFunction (protocols::multistate_design)   RelativeConnectRight (protocols::forge::build)   StepWiseMonteCarloOptions (protocols::stepwise::monte_carlo::rna)   
BluePrintBDR (protocols::fldsgn)   FlexPepDockingPoseMetrics (protocols::flexpep_docking)   MetricRecorder (protocols::canonical_sampling)   RelativePoseFilter (protocols::simple_filters)   StepWisePoseAligner (protocols::stepwise::sampling::general)   
BluePrintBDRCreator (protocols::fldsgn)   FlexPepDockingProtocol (protocols::flexpep_docking)   MetricRecorderCreator (protocols::canonical_sampling)   RelativePoseFilterCreator (protocols::simple_filters)   StepWisePoseSetup (protocols::stepwise::sampling::protein)   
Boinc (protocols::boinc)   FlexPepDockingProtocolCreator (protocols::flexpep_docking)   MetricValueGetter (protocols::toolbox::pose_metric_calculators)   RelativeSegmentFilter (protocols::protein_interface_design::filters)   StepWiseProteinBackboneSampler (protocols::stepwise::sampling::protein)   
BoincCurrentPoseObserver (protocols::boinc)   FloatingResonance (protocols::noesy_assign)   MetropolisHastingsMover (protocols::canonical_sampling)   RelativeSegmentFilterCreator (protocols::protein_interface_design::filters)   StepWiseProteinCCD_Closer (protocols::stepwise::sampling::protein)   
BOINCJobDistributor (protocols::jd2)   FloppyTailMover (protocols::floppy_tail)   MetropolisHastingsMoverCreator (protocols::canonical_sampling)   RelativeSequencePosition (protocols::forge::build)   StepWiseProteinJobParameters (protocols::stepwise::sampling::protein)   
BoincSharedMemory (protocols::boinc)   FlxbbDesign (protocols::flxbb)   MidPhiOut (protocols::frag_picker::scores)   RelaxProtocolBase (protocols::relax)   StepWiseProteinJumpSampleGenerator   
BoltzmannFilter (protocols::protein_interface_design::filters)   FlxbbDesignCreator (protocols::flxbb)   MidPsiOut (protocols::frag_picker::scores)   RelaxScriptCommand (protocols::relax)   StepWiseProteinLoopBridger (protocols::stepwise::sampling::protein)   
BoltzmannFilterCreator (protocols::protein_interface_design::filters)   FlxbbDesignPack (protocols::flxbb)   MinimalistFlexbbEdge (protocols::flexpack::interaction_graph)   RemodelAccumulator (protocols::forge::remodel)   StepWiseProteinModeler (protocols::stepwise::sampling::protein)   
BondAngleOpener (protocols::loop_modeling::openers)   FNatFilter (protocols::protein_interface_design::filters)   MinimalistFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   RemodelConstraintGenerator (protocols::forge::remodel)   StepWiseProteinModelerOptions (protocols::stepwise::sampling::protein)   
BondAnglePerturber (protocols::kinematic_closure::perturbers)   FNatFilterCreator (protocols::protein_interface_design::filters)   MinimalistFlexbbNode (protocols::flexpack::interaction_graph)   RemodelData (protocols::forge::remodel)   StepWiseProteinMultiPosePacker (protocols::stepwise::sampling::protein)   
Bool3DGrid (protocols::match)   FoldandDockClaimer (protocols::topology_broker)   MinimalRotamer (protocols::simple_moves)   RemodelDesignMover (protocols::forge::remodel)   StepWiseProteinPacker (protocols::stepwise::sampling::protein)   
Bool3DGridKinemageWriter (protocols::match)   FoldConstraints (protocols::abinitio)   MinimizeBackbone (protocols::ligand_docking)   RemodelEnzdesCstModule (protocols::forge::remodel)   StepWiseProteinPoseMinimizer (protocols::stepwise::sampling::protein)   
BoundedCollector (protocols::frag_picker)   FoldResonance (protocols::noesy_assign)   MinimizeBackboneCreator (protocols::ligand_docking)   RemodelGlobalFrame (protocols::forge::remodel)   StepWiseProteinResidueSampler (protocols::stepwise::sampling::protein)   
BoundedCollector_CompareTotalScore (protocols::frag_picker)   FoldTreeFromLoops (protocols::loops)   MinimizeLigand (protocols::ligand_docking)   RemodelLoopMover (protocols::forge::remodel)   StepWiseResiduePairScreener (protocols::stepwise::screener)   
BoundedPriorityQueue (protocols::frag_picker)   FoldTreeFromLoopsCreator (protocols::loops)   MinimizeStoredRBConfs (protocols::enzdes)   RemodelLoopMoverCreator (protocols::forge::remodel)   StepWiseRNA_ClassicResidueSampler (protocols::stepwise::sampling::rna::legacy::suite)   
BranchAngleOptimizer (protocols::branch_angle)   FoldTreeHybridize (protocols::hybridization)   MiniRelax (protocols::relax)   RemodelMover (protocols::forge::remodel)   StepWiseRNA_Clusterer (protocols::stepwise::sampling::rna)   
BranchCoef1 (protocols::branch_angle)   FoldTreeHybridizeCreator (protocols::hybridization)   MinMover (protocols::simple_moves)   RemodelMoverCreator (protocols::forge::remodel)   StepWiseRNA_CombineLongLoopFilterer (protocols::stepwise::sampling::rna)   
BranchCoef2 (protocols::branch_angle)   ForceDisulfidesMover (protocols::simple_moves)   MinMoverCreator (protocols::simple_moves)   RemodelRotamerLinks (protocols::forge::remodel)   StepWiseRNA_ConnectionSampler (protocols::stepwise::sampling::rna::connection)   
BranchParam1 (protocols::branch_angle)   ForceDisulfidesMoverCreator (protocols::simple_moves)   MinPackMover (protocols::simple_moves)   RemodelRotamerLinksCreator (protocols::forge::remodel)   StepWiseRNA_CountStruct (protocols::stepwise::sampling::rna)   
BranchParam2 (protocols::branch_angle)   FormatStringOutputter (protocols::outputter)   MinPackMoverCreator (protocols::simple_moves)   RemodelWorkingSet (protocols::forge::remodel)   StepWiseRNA_FloatingBaseSampler (protocols::stepwise::sampling::rna::legacy::rigid_body)   
Bridge (protocols::forge::build)   FourAtomsConstraintData (protocols::frag_picker::scores)   MinValueEvaluator (protocols::simple_filters)   RemoveCsts (protocols::forge::constraints)   StepWiseRNA_JobParameters (protocols::stepwise::sampling::rna)   
EnvClaimBroker::BrokerResult (protocols::environment)   FragInsertAndAlignMover (protocols::rbsegment_relax)   MissingDensityToJumpMover (protocols::simple_moves)   RemoveCstsCreator (protocols::forge::constraints)   StepWiseRNA_JobParametersSetup (protocols::stepwise::sampling::rna::legacy)   
BruteFunGroupTK (protocols::kinmatch)   FragLib (protocols::frags)   ModelCDRH3 (protocols::antibody)   RemoveLigandFilter (protocols::enzdes)   StepWiseRNA_Minimizer (protocols::stepwise::sampling::rna)   
BuildAlaPose (protocols::protein_interface_design::movers)   FragmentAllAtomCrmsd (protocols::frag_picker::scores)   ModifyAnnealer (protocols::toolbox::task_operations)   RemoveLigandFilterCreator (protocols::enzdes)   StepWiseRNA_Modeler (protocols::stepwise::sampling::rna)   
BuildAlaPoseCreator (protocols::protein_interface_design::movers)   FragmentCandidate (protocols::frag_picker)   ModifyAnnealerCreator (protocols::toolbox::task_operations)   RemoveNorCTermMPM (protocols::match)   StepWiseRNA_ModelerOptions (protocols::stepwise::sampling::rna)   
BuildInstruction (protocols::forge::build)   FragmentChunkCrms (protocols::frag_picker::scores)   ModifyStoredRBConfs (protocols::enzdes)   RenderGridsToKinemage (protocols::qsar)   StepWiseRNA_PoseSelection (protocols::stepwise::sampling::rna)   
BuildManager (protocols::forge::build)   FragmentClaimer (protocols::topology_broker)   ModifyVariantTypeMover (protocols::simple_moves)   RenderGridsToKinemageCreator (protocols::qsar)   StepWiseRNA_PoseSetup (protocols::stepwise::sampling::rna::legacy)   
BuildPosition (protocols::motifs)   FragmentCM (protocols::abinitio::abscript)   ModifyVariantTypeMoverCreator (protocols::simple_moves)   RepackingRefiner (protocols::loop_modeling::refiners)   StepWiseRNA_ResidueSampler (protocols::stepwise::sampling::rna)   
BuildSet (protocols::match::upstream)   FragmentComparatorBase (protocols::frag_picker)   MolarMassFilter (protocols::ligand_docking)   RepackLigandSiteWithoutLigandMover (protocols::enzdes)   StepWiseRNA_RigidBodyConnectionSampler (protocols::stepwise::sampling::rna::legacy::rigid_body)   
BulgeApplier (protocols::stepwise::screener)   FragmentContainer (protocols::topology_broker)   MolarMassFilterCreator (protocols::ligand_docking)   RepackMinimize (protocols::protein_interface_design::movers)   StepWiseRNA_RigidBodySampler (protocols::stepwise::sampling::rna::legacy::rigid_body)   
BulgeApplyMover (protocols::stepwise::sampling::rna::bulge)   FragmentCost (protocols::simple_moves)   MolecularDynamics (protocols::cartesian)   RepackMinimizeCreator (protocols::protein_interface_design::movers)   StepWiseRNA_VirtualSugarJustInTimeInstantiator (protocols::stepwise::sampling::rna::sugar)   
BulgeUnApplyMover (protocols::stepwise::sampling::rna::bulge)   FragmentCrmsd (protocols::frag_picker::scores)   MolecularMassFilter (protocols::ligand_docking)   RepackSidechainsMover (protocols::simple_moves)   StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD (protocols::stepwise::sampling::rna::sugar::legacy)   
BumpGrid (protocols::match)   FragmentCrmsdResDepth (protocols::frag_picker::scores)   MolecularMassFilterCreator (protocols::ligand_docking)   RepackSidechainsMoverCreator (protocols::simple_moves)   StepWiseRNA_VirtualSugarSampler (protocols::stepwise::sampling::rna::sugar)   
BuriedPolarScore (protocols::sic_dock)   FragmentDME (protocols::frag_picker::scores)   MolecularWeightNormalization (protocols::qsar::scoring_grid)   RepackTrial (protocols::loops::loop_mover::refine)   StepWiseRNA_VirtualSugarSamplerFromStringList (protocols::stepwise::sampling::rna::sugar)   
BuriedRegionsFilter (protocols::simple_filters)   FragmentJumpClaimer (protocols::topology_broker)   MonteCarlo (protocols::moves)   RepackTrialCreator (protocols::loops::loop_mover::refine)   StepWiseSampleAndScreen (protocols::stepwise)   
BuriedUnsatHbondFilter (protocols::simple_filters)   FragmentJumpCM (protocols::abinitio::abscript)   MonteCarloExceptionConverge (protocols::moves)   RepackWithoutLigandFilter (protocols::enzdes)   StepWiseScreener (protocols::stepwise::screener)   
BuriedUnsatHbondFilterCreator (protocols::simple_filters)   FragmentJumpCMCreator (protocols::abinitio::abscript)   MonteCarloLoader (protocols::jd2::parser)   RepackWithoutLigandFilterCreator (protocols::enzdes)   StochasticFilter (protocols::filters)   
BuriedUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   FragmentLibrary (protocols::farna)   MonteCarloLoaderCreator (protocols::jd2::parser)   RepeatedMover (protocols::loop_modeling::utilities)   StochasticFilterCreator (protocols::filters)   
  C  
FragmentMover (protocols::simple_moves)   MonteCarloRecover (protocols::simple_moves)   RepeatMover (protocols::moves)   Strand (protocols::fldsgn::topology)   
FragmentPair (protocols::features::helixAssembly)   MonteCarloRecoverCreator (protocols::simple_moves)   RepGrid (protocols::qsar::scoring_grid)   StrandBundleFeatures (protocols::features::strand_assembly)   
CachingScoringMethod (protocols::frag_picker::scores)   FragmentPicker (protocols::frag_picker)   MonteCarloReset (protocols::simple_moves)   RepGridCreator (protocols::qsar::scoring_grid)   StrandBundleFeaturesCreator (protocols::features::strand_assembly)   
CAcstGenerator (protocols::seeded_abinitio)   FragmentReader (protocols::jd2::parser)   MonteCarloResetCreator (protocols::simple_moves)   ReplicaExchangeMC (protocols::moves)   StrandConstraints (protocols::abinitio)   
CAcstGeneratorCreator (protocols::seeded_abinitio)   FragmentSampler (protocols::abinitio)   MonteCarloTest (protocols::simple_moves)   ReplicateFilter (protocols::filters)   StrandFragment (protocols::features::strand_assembly)   
CalculatorFilter (protocols::filters)   FragmentScoreManager (protocols::frag_picker::scores)   MonteCarloTestCreator (protocols::simple_moves)   ReplicateFilterCreator (protocols::filters)   StrandPairing (protocols::fldsgn::topology)   
CalculatorFilterCreator (protocols::filters)   FragmentScoreMap (protocols::frag_picker::scores)   MonteCarloUtil (protocols::moves)   Report (protocols::features)   StrandPairingSet (protocols::fldsgn::topology)   
CamShiftEvaluator (protocols::simple_filters)   FragmentScoringMethod (protocols::frag_picker::scores)   Motif (protocols::motifs)   ReportFilter (protocols::simple_filters)   StrandTwistingMover (protocols::rbsegment_relax)   
CamShiftEvaluatorCreator (protocols::simple_filters)   FragmentSelectingRule (protocols::frag_picker)   MotifDnaPacker (protocols::motifs)   ReportFilterCreator (protocols::simple_filters)   StructuralSimilarityEvaluator (protocols::simple_filters)   
SmoothPolicy::Candidate (protocols::nonlocal)   FragQualCalculator (protocols::toolbox::pose_metric_calculators)   MotifDnaPackerCreator (protocols::motifs)   ReportFSC (protocols::electron_density)   StructureDependentPeakCalibrator (protocols::noesy_assign)   
CandidatesCollector (protocols::frag_picker)   FragQualFilter (protocols::fldsgn::filters)   MotifGraftCreator (protocols::motif_grafting::movers)   ReportFSCCreator (protocols::electron_density)   StructureFeatures (protocols::features)   
CanonicalSamplingMover (protocols::canonical_sampling)   FragQualFilterCreator (protocols::fldsgn::filters)   MotifGraftMover (protocols::motif_grafting::movers)   ReportPSSMDifferences (protocols::protein_interface_design)   StructureFeaturesCreator (protocols::features)   
CanonicalSamplingMover (protocols::moves)   FragSetLoader (protocols::jd2::parser)   MotifHash (protocols::motif_hash)   ReportSequenceDifferences (protocols::protein_interface_design)   StructureFileNames (protocols::pack_daemon)   
CartesianAtom (protocols::cartesian)   FragSetLoaderCreator (protocols::jd2::parser)   MotifHashManager (protocols::motif_hash)   ReportToDB (protocols::features)   StructureIndependentPeakCalibrator (protocols::noesy_assign)   
CartesianHybridize (protocols::hybridization)   FragsToAtomDist (protocols::noesy_assign)   MotifHashRigidScore (protocols::sic_dock::scores)   ReportToDBCreator (protocols::features)   StructureRestrictor (protocols::moves)   
CartesianHybridizeCreator (protocols::hybridization)   DbTrajectoryRecorder::Frame (protocols::canonical_sampling)   MotifHit (protocols::motif_hash)   RepulsiveOnlyMover (protocols::simple_moves)   StructureScoresFeatures (protocols::features)   
CartesianMD (protocols::md)   DbTrajectoryWriter::Frame (protocols::trajectory)   MotifHit (protocols::motifs)   ResampleMover (protocols::stepwise::monte_carlo::rna)   StructureScoresFeaturesCreator (protocols::features)   
CartesianMDCreator (protocols::md)   FrameWork (protocols::antibody)   MotifHits (protocols::motif_hash)   ResFileOutputter (protocols::outputter)   StructureSimilarityEvaluatorCreator (protocols::simple_filters)   
CartesianNormalModeMover (protocols::normalmode)   FromScratchMover (protocols::stepwise::monte_carlo::rna)   MotifLibrary (protocols::motifs)   ResId (protocols::moves)   StructureStore (protocols::abinitio)   
CartesianSampler (protocols::hybridization)   FullatomRelaxMover (protocols::surface_docking)   MotifMatch (protocols::motif_grafting::movers)   ResidualDipolarCouplingEnergyRigidSegments (protocols::scoring::methods)   StubApplier (protocols::stepwise::screener)   
CartesianSamplerCreator (protocols::hybridization)   FullAtomRNA_Fragments (protocols::farna)   MotifRotamerSetOperation (protocols::motif_hash)   ResidualDipolarCouplingEnergyRigidSegmentsCreator (protocols::scoring::methods)   StubDistanceScreener (protocols::stepwise::screener)   
CartesianSearchPattern (protocols::hotspot_hashing)   FullChiSampleSet (protocols::match::upstream)   MotifSearch (protocols::motifs)   ResidualDipolarCouplingRigidSegments (protocols::scoring)   StubGenerator (protocols::hotspot_hashing)   
CatPiCalculator (protocols::toolbox::pose_metric_calculators)   FunGroupTK (protocols::kinmatch)   MoveBeforeFilter (protocols::filters)   Residue_info (protocols::stepwise::sampling::rna)   StubScoreFilter (protocols::protein_interface_design::filters)   
CBScore (protocols::sic_dock)   
  G  
MoveBeforeFilterCreator (protocols::filters)   ResidueAlternativeRotamer (protocols::rotamer_sampler::copy_dofs)   StubScoreFilterCreator (protocols::protein_interface_design::filters)   
CBScoreVisitor (protocols::sic_dock)   MoveMapBuilder (protocols::ligand_docking)   ResidueAlternativeRotamerComb (protocols::rotamer_sampler::copy_dofs)   StubScoreLoopsFilter (protocols::protein_interface_design::filters)   
CcdLoopClosureMover (protocols::loops::loop_closure::ccd)   GatherPosesMover (protocols::cluster)   MoveMapBuilderLoader (protocols::ligand_docking)   ResidueAlternativeSet (protocols::rotamer_sampler::copy_dofs)   StubScoreLoopsFilterCreator (protocols::protein_interface_design::filters)   
CcdMover (protocols::loops::loop_closure::ccd)   GaussianRBSegmentMover (protocols::rbsegment_relax)   MoveMapBuilderLoaderCreator (protocols::ligand_docking)   ResidueBurialFeatures (protocols::features)   SubroutineMover (protocols::protein_interface_design::movers)   
CCDMoveWrapper (protocols::rbsegment_relax)   GDB (protocols::sparta)   MovePoseToMembraneCenterMover (protocols::rigid)   ResidueBurialFeaturesCreator (protocols::features)   SubroutineMoverCreator (protocols::protein_interface_design::movers)   
CCluster (protocols::pockets)   GenerateStoredRBConfs (protocols::enzdes)   Mover (protocols::moves)   ResidueBurialFilter (protocols::simple_filters)   SugarInstantiateMover (protocols::stepwise::sampling::rna::sugar)   
CClusterSet (protocols::pockets)   GenericJobInputter (protocols::comparative_modeling)   Mover_LoopHashRefine (protocols::loophash)   ResidueBurialFilterCreator (protocols::simple_filters)   SugarInstantiator (protocols::stepwise::screener)   
CDRCluster (protocols::antibody::clusters)   GenericJobInputterCreator (protocols::comparative_modeling)   MoverContainer (protocols::moves)   ResidueConformationFeatures (protocols::features)   SugarModeling (protocols::stepwise::sampling::rna::sugar)   
CDRClusterEnumManager (protocols::antibody::clusters)   GenericMonteCarloMover (protocols::simple_moves)   MoverCreator (protocols::moves)   ResidueConformationFeaturesCreator (protocols::features)   SugarVirtualizeMover (protocols::stepwise::sampling::rna::sugar)   
CDRClusterFeatures (protocols::antibody::clusters)   GenericMonteCarloMoverCreator (protocols::simple_moves)   MoverFactory (protocols::moves)   ResidueConformerFilter (protocols::enzdes)   SuggestValueMessage (protocols::topology_broker)   
CDRClusterFeaturesCreator (protocols::antibody::clusters)   GeneticAlgorithm (protocols::genetic_algorithm)   MoverForPoseList (protocols::moves)   ResidueConformerFilterCreator (protocols::enzdes)   SuperimposeMover (protocols::simple_moves)   
CDRClusterMatcher (protocols::antibody::clusters)   GeneticAlgorithmBase (protocols::genetic_algorithm)   MoverList (protocols::wum)   ResidueContactScreener (protocols::stepwise::screener)   SuperimposeMoverCreator (protocols::simple_moves)   
CDRClusterSet (protocols::antibody::clusters)   GeometricFunc (protocols::moves)   MoverRegistrator (protocols::moves)   ResidueCountFilter (protocols::simple_filters)   SurfaceCalculator (protocols::toolbox::pose_metric_calculators)   
CDRDesignInstructions (protocols::antibody::design)   GeometricSolvationFeatures (protocols::features)   MoverStatistics (protocols::moves)   ResidueCountFilterCreator (protocols::simple_filters)   SurfaceDockingProtocol (protocols::surface_docking)   
CDRGraftInstructions (protocols::antibody::design)   GeometricSolvationFeaturesCreator (protocols::features)   MPI_LoopHashRefine (protocols::loophash)   ResidueDecompositionByChainCalculator (protocols::toolbox::pose_metric_calculators)   SurfaceOrientMover (protocols::surface_docking)   
CDRH3Modeler (protocols::antibody_legacy)   GeometryFilter (protocols::simple_filters)   MPI_LoopHashRefine_Emperor (protocols::loophash)   ResidueDecompositionCalculator (protocols::toolbox::pose_metric_calculators)   SurfaceParameters (protocols::surface_docking)   
CDRsMinPackMin (protocols::antibody)   GeometryFilterCreator (protocols::simple_filters)   MPI_LoopHashRefine_Master (protocols::loophash)   ResidueDistanceFilter (protocols::simple_filters)   SurfaceSearchPattern (protocols::hotspot_hashing)   
CentroidDistanceScreener (protocols::stepwise::screener)   GeometrySecMatchRPE (protocols::match::downstream)   MPI_Relax (protocols::wum)   ResidueDistanceFilterCreator (protocols::simple_filters)   SurfaceVectorFallbackConfiguration (protocols::surface_docking)   
CentroidRelax (protocols::relax)   GeomSampleInfo (protocols::toolbox::match_enzdes_util)   MPI_WorkUnitManager (protocols::wum)   ResidueElement (protocols::environment::claims)   SurfaceVectorFallbackConfigurationCreator (protocols::surface_docking)   
CentroidRelaxMover (protocols::surface_docking)   GrabAllCollector (protocols::frag_picker)   MPI_WorkUnitManager_Slave (protocols::wum)   ResidueFeature (protocols::comparative_modeling::features)   SurfaceVectorLoader (protocols::surface_docking)   
ChainbreakDistFunc (core::scoring::constraints)   GraftCDRLoopsProtocol (protocols::antibody)   MPIArchiveJobDistributor (protocols::jd2::archive)   ResidueFeatureFactory (protocols::comparative_modeling::features)   SurfaceVectorLoaderCreator (protocols::surface_docking)   
ChainClosableGeometryChecker (protocols::stepwise::sampling::rna::checker)   GraftedStemOptimizer (protocols::antibody)   MPIBPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   ResidueFeatures (protocols::features)   SurfaceVectorOptions (protocols::surface_docking)   
ChainClosableGeometryResidueBasedScreener (protocols::stepwise::screener)   GraftMover (protocols::antibody_legacy)   MpiFileBuffer (protocols::jd2)   ResidueFeaturesCreator (protocols::features)   SurfaceVectorOptionsCreator (protocols::surface_docking)   
ChainClosableGeometryScreener (protocols::stepwise::screener)   GraftMoverBase (protocols::grafting)   MPIFileBufJobDistributor (protocols::jd2)   ResidueGridScoresFeatures (protocols::features)   SurrogateVariableExpression (protocols::pack_daemon)   
ChainClosableGeometryStubBasedScreener (protocols::stepwise::screener)   GraftOneCDRLoop (protocols::antibody)   MpiHamiltonianExchange (protocols::canonical_sampling)   ResidueGridScoresFeaturesCreator (protocols::features)   SWA_Move (protocols::stepwise::monte_carlo)   
ChainClosureChecker (protocols::stepwise::sampling::rna::checker)   GraftOneMover (protocols::antibody_legacy)   MpiHamiltonianExchangeCreator (protocols::canonical_sampling)   ResidueGroupIGEdgeUpweighter (protocols::toolbox)   SWA_MoveSelector (protocols::stepwise::monte_carlo)   
ChainClosureScreener (protocols::stepwise::screener)   GraphicsState (protocols::viewer)   MPIHPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   ResidueIEFilter (protocols::simple_filters)   SwapSegment (protocols::seeded_abinitio)   
ChainExistsFilter (protocols::ligand_docking)   GreedyKCenter (protocols::toolbox)   MPIMultiCommJobDistributor (protocols::jd2)   ResidueIEFilterCreator (protocols::simple_filters)   SwapSegmentCreator (protocols::seeded_abinitio)   
ChainExistsFilterCreator (protocols::ligand_docking)   GreedyOptMutationMover (protocols::design_opt)   MPIMultistateFitnessFunction (protocols::pack_daemon)   ResidueIndexDescription (protocols::loops)   SwitchChainOrderMover (protocols::simple_moves)   
ChainGroupDiscriminator (protocols::simple_moves)   GreedyOptMutationMoverCreator (protocols::design_opt)   MpiParallelTempering (protocols::canonical_sampling)   ResidueIndexDescriptionFromFile (protocols::loops)   SwitchChainOrderMoverCreator (protocols::simple_moves)   
ChainSplitMover (protocols::simple_moves)   GreenPacker (protocols::simple_moves)   MpiParallelTemperingCreator (protocols::canonical_sampling)   ResidueKinemageWriter (protocols::match::output)   SwitchResidueTypeSetMover (protocols::simple_moves)   
ChangeFoldTreeMover (protocols::moves)   GridBase (protocols::qsar::scoring_grid)   MPIPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   ResidueListRotamer (protocols::rotamer_sampler::copy_dofs)   SwitchResidueTypeSetMoverCreator (protocols::simple_moves)   
ChargeAtom (protocols::qsar::scoring_grid)   GridCreator (protocols::qsar::scoring_grid)   MPIWorkPartitionJobDistributor (protocols::jd2)   ResidueNetwork (protocols::toolbox)   SymDockBaseProtocol (protocols::symmetric_docking)   
ChargeCalculator (protocols::toolbox::pose_metric_calculators)   GridFactory (protocols::qsar::scoring_grid)   MPIWorkPoolJobDistributor (protocols::jd2)   ResiduePairJump (protocols::jumping)   SymDockingHiRes (protocols::symmetric_docking)   
ChargeChargeFeatures (protocols::features)   GridInitMover (protocols::qsar::scoring_grid)   MRMover (protocols::hybridization)   ResiduePairJumpSetup (protocols::jumping)   SymDockingInitialPerturbation (protocols::simple_moves::symmetry)   
ChargeChargeFeaturesCreator (protocols::features)   GridInitMoverCreator (protocols::qsar::scoring_grid)   MultiPhosphateSampler (protocols::stepwise::sampling::rna::phosphate)   ResiduePairJumpSingle (protocols::jumping)   SymDockingLowRes (protocols::symmetric_docking)   
ChargeGrid (protocols::qsar::scoring_grid)   GridManager (protocols::qsar::scoring_grid)   MultipleDomainMover (protocols::farna)   ResidueProbDesignOperation (protocols::antibody::design)   SymDockingSlideIntoContact (protocols::simple_moves::symmetry)   
ChargeGridCreator (protocols::qsar::scoring_grid)   GridRegistrator (protocols::qsar::scoring_grid)   MultipleOutputWrapper (protocols::rosetta_scripts)   ResidueScoresFeatures (protocols::features)   SymDockProtocol (protocols::symmetric_docking)   
CheckPointer (protocols::checkpoint)   GridSearchIterator (protocols::scoring::methods::pcs)   MultipleOutputWrapperCreator (protocols::rosetta_scripts)   ResidueScoresFeaturesCreator (protocols::features)   SymDockProtocolCreator (protocols::symmetric_docking)   
ChemicalShiftEvaluator (protocols::sparta)   GridSearchIterator (protocols::scoring::methods::pcs2)   MultiplePoseMover (protocols::rosetta_scripts)   ResidueSecondaryStructureFeatures (protocols::features)   SymEnergyCutRotamerTrialsMover (protocols::simple_moves::symmetry)   
ChemicalShiftEvaluatorCreator (protocols::sparta)   GridSearchIterator_Ts1 (protocols::scoring::methods::pcsTs1)   MultiplePoseMoverCreator (protocols::rosetta_scripts)   ResidueSecondaryStructureFeaturesCreator (protocols::features)   SymFoldandDockMoveRbJumpMover (protocols::symmetric_docking)   
ChiAngleNormalization (protocols::qsar::scoring_grid)   GridSearchIterator_Ts2 (protocols::scoring::methods::pcsTs2)   MultipleSigmoids (protocols::simple_filters)   ResidueSelectorLoader (protocols::jd2::parser)   SymFoldandDockMoveRbJumpMoverCreator (protocols::symmetric_docking)   
ChiralMover (protocols::simple_moves::chiral)   GridSearchIterator_Ts3 (protocols::scoring::methods::pcsTs3)   MultipleSigmoidsFilterCreator (protocols::simple_filters)   ResidueSelectorLoaderCreator (protocols::jd2::parser)   SymFoldandDockRbTrialMover (protocols::symmetric_docking)   
ChiWellRmsdEvaluator (protocols::simple_filters)   GridSearchIterator_Ts4 (protocols::scoring::methods::pcsTs4)   MultiStateAggregateFunction (protocols::multistate_design)   ResidueSetChainEnergyFilter (protocols::simple_filters)   SymFoldandDockRbTrialMoverCreator (protocols::symmetric_docking)   
ChiWellRmsdEvaluatorCreator (protocols::simple_filters)   GridSearchIteratorCA (protocols::scoring::methods::pcs2)   MultistateAggregateFunction (protocols::pack_daemon)   ResidueSetChainEnergyFilterCreator (protocols::simple_filters)   SymFoldandDockSlideTrialMover (protocols::symmetric_docking)   
Chunk (protocols::nonlocal)   GroupDiscriminator (protocols::simple_moves)   MultiStateEntity (protocols::multistate_design)   ResiduesInInterfaceFilter (protocols::simple_filters)   SymFoldandDockSlideTrialMoverCreator (protocols::symmetric_docking)   
ChunkSet (protocols::farna)   GrowLeft (protocols::forge::build)   MultiStateFitnessFunction (protocols::multistate_design)   ResiduesInInterfaceFilterCreator (protocols::simple_filters)   SymInterfaceSidechainMinMover (protocols::symmetric_docking)   
ChunkTrialMover (protocols::hybridization)   GrowLigand (protocols::ligand_docking)   MultistateFitnessFunction (protocols::pack_daemon)   ResidueTorsionRestraints (protocols::ligand_docking)   SymmetricFragmentMover (protocols::simple_moves)   
CircularPermutation (protocols::fldsgn)   GrowLigandCreator (protocols::ligand_docking)   MultiStatePacker (protocols::multistate_design)   ResidueTotalScoresFeatures (protocols::features)   SymmetricMotifFilter (protocols::simple_filters)   
CircularPermutationCreator (protocols::fldsgn)   GrowPeptides (protocols::seeded_abinitio)   MultiTempTrialCounter (protocols::canonical_sampling)   ResidueTotalScoresFeaturesCreator (protocols::features)   SymmetricMotifFilterCreator (protocols::simple_filters)   
ClaimerMessage (protocols::topology_broker)   GrowPeptidesCreator (protocols::seeded_abinitio)   MultiThreadingJob (protocols::jd2)   ResidueTypeConstraintMover (protocols::simple_moves)   SymmetricRmsdEvaluator (protocols::simple_filters)   
ClaimingMover (protocols::environment)   GrowRight (protocols::forge::build)   MultiThreadingMover (protocols::comparative_modeling)   ResidueTypeConstraintMoverCreator (protocols::simple_moves)   SymmetricRMSMover (protocols::simple_moves::symmetry)   
ClaimStrength (protocols::environment::claims)   GuardedLoopsFromFile (protocols::loops)   Mutant (protocols::pmut_scan)   ResidueTypesFeatures (protocols::features)   SymmetryClaim (protocols::topology_broker::claims)   
ClashCountCalculator (protocols::toolbox::pose_metric_calculators)   GunnCost (protocols::simple_moves)   Mutate1Randomizer (protocols::genetic_algorithm)   ResidueTypesFeaturesCreator (protocols::features)   SymmetryClaimer (protocols::topology_broker)   
ClashWithTargetFilter (protocols::protein_interface_design::filters)   GunnCost (protocols::frag_picker::scores)   MutateResidue (protocols::simple_moves)   ResidueVicinityCstGeneratorCreator (protocols::forge::remodel)   SymmetrySlider (protocols::simple_moves::symmetry)   
ClashWithTargetFilterCreator (protocols::protein_interface_design::filters)   GunnCostScore (protocols::frag_picker::scores)   MutateResidueCreator (protocols::simple_moves)   ResidueVicinityInfo (protocols::forge::remodel)   SymMinMover (protocols::simple_moves::symmetry)   
ClassicAbinitio (protocols::abinitio)   GunnTuple (protocols::simple_moves)   MutationData (protocols::pmut_scan)   ResidueVicinityRCG (protocols::forge::remodel)   SymMinMoverCreator (protocols::simple_moves::symmetry)   
ClassicFragmentMover (protocols::simple_moves)   GunnTuple (protocols::frag_picker::scores)   MyAtom (protocols::fldsgn)   ResInteractions (protocols::toolbox::match_enzdes_util)   SymPackRotamersMover (protocols::simple_moves::symmetry)   
ClassicGrid (protocols::qsar::scoring_grid)   
  H  
MyHash (protocols::motif_hash)   ResolutionSwitcher (protocols::abinitio)   SymPackRotamersMoverCreator (protocols::simple_moves::symmetry)   
ClassicGridCreator (protocols::qsar::scoring_grid)   MyPred (protocols::motif_hash)   Resonance (protocols::noesy_assign)   SymRestrictTaskForDocking (protocols::symmetric_docking)   
ClassicMatchAlgorithm (protocols::match::downstream)   H3CterInsert (protocols::antibody)   
  N  
ResonanceList (protocols::noesy_assign)   SymRotamerTrialsMover (protocols::simple_moves::symmetry)   
ClassicRelax (protocols::relax)   H3PerturbCCD (protocols::antibody)   ResPairMotif (protocols::motif_hash)   SymRotamerTrialsMoverCreator (protocols::simple_moves::symmetry)   
ClassicRelaxCreator (protocols::relax)   H3RefineCCD (protocols::antibody)   NamedAtomPairConstraintCreator (protocols::constraints_additional)   ResPairMotifs (protocols::motif_hash)   SymShakeStructureMover (protocols::simple_moves::symmetry)   
ClearConstraintsMover (protocols::simple_moves)   HbaGrid (protocols::qsar::scoring_grid)   NatbiasHelicesSheetPotential (protocols::fldsgn::potentials::sspot)   RestrictByCalculatorsOperation (protocols::toolbox::task_operations)   SymSidechainMinMover (protocols::symmetric_docking)   
ClearConstraintsMoverCreator (protocols::simple_moves)   HbaGridCreator (protocols::qsar::scoring_grid)   NatbiasHelixPairPotential (protocols::fldsgn::potentials::sspot)   RestrictByCalculatorsOperationCreator (protocols::toolbox::task_operations)   
  T  
CloseFold (protocols::seeded_abinitio)   HbdGrid (protocols::qsar::scoring_grid)   NatbiasSecondaryStructureEnergy (protocols::fldsgn::potentials::sspot)   RestrictChainToRepackingOperation (protocols::toolbox::task_operations)   
CloseFoldCreator (protocols::seeded_abinitio)   HbdGridCreator (protocols::qsar::scoring_grid)   NatbiasSecondaryStructureEnergyCreator (protocols::fldsgn::potentials::sspot)   RestrictChainToRepackingOperationCreator (protocols::toolbox::task_operations)   TabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
CloseOneCDRLoop (protocols::antibody)   HBondAcceptorFilter (protocols::ligand_docking)   NatbiasSheetPotential (protocols::fldsgn::potentials::sspot)   RestrictConservedLowDdgOperation (protocols::toolbox::task_operations)   TagDefinition (protocols::stepwise::screener)   
CloseOneMover (protocols::antibody_legacy)   HBondAcceptorFilterCreator (protocols::ligand_docking)   NatbiasStrandPairPotential (protocols::fldsgn::potentials::sspot)   RestrictConservedLowDdgOperationCreator (protocols::toolbox::task_operations)   TagPoseWithRefinementStatsMover (protocols::cryst)   
ClosureProblem (protocols::kinematic_closure)   HBondDonorFilter (protocols::ligand_docking)   NativeEvaluatorCreator (protocols::simple_filters)   RestrictDesignToProteinDNAInterface (protocols::dna)   TagPoseWithRefinementStatsMoverCreator (protocols::cryst)   
ClosureSolution (protocols::kinematic_closure)   HBondDonorFilterCreator (protocols::ligand_docking)   NativeRMSD_Screener (protocols::stepwise::screener)   RestrictDesignToProteinDNAInterfaceCreator (protocols::dna)   TailsScoreMover (protocols::simple_moves)   
CloudPDBWriter (protocols::match::output)   HBondFeatures (protocols::features)   NcbbDockDesignProtocol (protocols::ncbb)   RestrictIdentitiesAtAlignedPositionsOperation (protocols::toolbox::task_operations)   TalosSSSimilarity (protocols::frag_picker::scores)   
Cluster (protocols::cluster)   HBondFeaturesCreator (protocols::features)   NcbbDockDesignProtocolCreator (protocols::ncbb)   RestrictIdentitiesAtAlignedPositionsOperationCreator (protocols::toolbox::task_operations)   TargetPocketGrid (protocols::pockets)   
Cluster_Member (protocols::stepwise::sampling::rna)   HBondParameterFeatures (protocols::features)   NcontactsCalculator (protocols::fldsgn)   RestrictInterGroupVectorOperation (protocols::toolbox::task_operations)   TargetRotamerCoords (protocols::match::downstream)   
ClusterBase (protocols::cluster)   HBondParameterFeaturesCreator (protocols::features)   NcontactsFilter (protocols::fldsgn::filters)   RestrictInterGroupVectorOperationCreator (protocols::toolbox::task_operations)   TaskAwareCsts (protocols::protein_interface_design::movers)   
ClusterBase (protocols::toolbox)   HbondsToAtomFilter (protocols::protein_interface_design::filters)   NcontactsFilterCreator (protocols::fldsgn::filters)   RestrictNativeResiduesOperation (protocols::toolbox::task_operations)   TaskAwareCstsCreator (protocols::protein_interface_design::movers)   
ClusterData (protocols::antibody::clusters)   HbondsToAtomFilterCreator (protocols::protein_interface_design::filters)   NCSResMapping (protocols::simple_moves::symmetry)   RestrictNativeResiduesOperationCreator (protocols::toolbox::task_operations)   TaskAwareMinMover (protocols::simple_moves)   
ClusterOptions (protocols::toolbox)   HbondsToResidueFilter (protocols::protein_interface_design::filters)   NeighborDependentTabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   RestrictNonSurfaceToRepackingOperation (protocols::toolbox::task_operations)   TaskAwareMinMoverCreator (protocols::simple_moves)   
ClusterPhilStyle (protocols::cluster)   HbondsToResidueFilterCreator (protocols::protein_interface_design::filters)   NeighborDependentTorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   RestrictNonSurfaceToRepackingOperationCreator (protocols::toolbox::task_operations)   TaskOperationLoader (protocols::jd2::parser)   
ClusterPhilStyle (protocols::toolbox)   HbsMover (protocols::simple_moves::hbs)   Neighborhood (protocols::neighbor)   RestrictOperationsBase (protocols::toolbox::task_operations)   TaskOperationLoaderCreator (protocols::jd2::parser)   
ClusterPhilStyle_Loop (protocols::cluster)   HbsPatcher (protocols::simple_moves::hbs)   NeighborhoodByDistanceCalculator (protocols::toolbox::pose_metric_calculators)   RestrictResiduesToRepackingOperation (protocols::toolbox::task_operations)   TaskOperationMPM (protocols::match)   
ClusterPhilStyle_PoseReporter (protocols::cluster)   HbsRandomSmallMover (protocols::simple_moves::hbs)   NeighborsByDistanceCalculator (protocols::toolbox::pose_metric_calculators)   RestrictResiduesToRepackingOperationCreator (protocols::toolbox::task_operations)   TemperatureController (protocols::canonical_sampling)   
ClusterPoseSelector (protocols::pose_selectors)   Heat_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   NeighborTypeFilter (protocols::simple_filters)   RestrictToAlignedSegmentsOperation (protocols::toolbox::task_operations)   TemperedDocking (protocols::docking)   
ClusterPoseSelectorCreator (protocols::pose_selectors)   HeavyAtomFilter (protocols::filters)   NeighborTypeFilterCreator (protocols::simple_filters)   RestrictToAlignedSegmentsOperationCreator (protocols::toolbox::task_operations)   TemperedDockingCreator (protocols::docking)   
RigidChunkClaimer::CM_SuggestFixResidue (protocols::topology_broker)   HeavyAtomFilter (protocols::ligand_docking)   NestedEnergyTermDDGMutationOptEData (protocols::optimize_weights)   RestrictToCDRH3Loop (protocols::toolbox::task_operations)   Template (protocols::abinitio)   
CmdLineData (protocols::topology_broker)   HeavyAtomFilterCreator (protocols::ligand_docking)   NestedEnergyTermPNatAAOptEPositionData (protocols::optimize_weights)   RestrictToCDRH3LoopCreator (protocols::toolbox::task_operations)   TemplateFragmentClaimer (protocols::topology_broker)   
CoarseRNA_DeNovoProtocol (protocols::coarse_rna)   HeavyAtomNormalization (protocols::qsar::scoring_grid)   NetChargeFilter (protocols::simple_filters)   RestrictToInterface (protocols::toolbox::task_operations)   TemplateHistory (protocols::hybridization)   
CoarseRNA_Fragments (protocols::coarse_rna)   HedgeArchive (protocols::abinitio)   NetChargeFilterCreator (protocols::simple_filters)   RestrictToInterfaceCreator (protocols::toolbox::task_operations)   TemplateJumpClaimer (protocols::topology_broker)   
CoarseRNA_LoopCloser (protocols::coarse_rna)   HelicalFragment (protocols::features::helixAssembly)   NMerPSSMEnergyFilter (protocols::simple_filters)   RestrictToInterfaceOperation (protocols::toolbox::task_operations)   TemplateJumpSetup (protocols::abinitio)   
COFilter (protocols::simple_filters)   HelicalGaussianMover (protocols::rbsegment_relax)   NMerPSSMEnergyFilterCreator (protocols::simple_filters)   RestrictToInterfaceOperationCreator (protocols::toolbox::task_operations)   Templates (protocols::abinitio)   
ColorGradient (protocols::qsar)   HelicalPeptideLengthMover (protocols::simple_moves)   NMerSVMEnergyFilter (protocols::simple_filters)   RestrictToInterfaceVectorOperation (protocols::toolbox::task_operations)   TensorsOptimizer (protocols::scoring::methods::pcs)   
Combine_Tags_Info (protocols::stepwise::sampling::rna)   Helix (protocols::fldsgn::topology)   NMerSVMEnergyFilterCreator (protocols::simple_filters)   RestrictToInterfaceVectorOperationCreator (protocols::toolbox::task_operations)   TensorsOptimizer (protocols::scoring::methods::pcs2)   
CombineChainsMover (protocols::domain_assembly)   HelixBundleFeatures (protocols::features::helixAssembly)   Node (protocols::toolbox)   RestrictToLoopsAndNeighbors (protocols::toolbox::task_operations)   TensorsOptimizer_Ts1 (protocols::scoring::methods::pcsTs1)   
CombinedConstraintEvaluator (protocols::constraints_additional)   HelixBundleFeaturesCreator (protocols::features::helixAssembly)   NoesyModule (protocols::noesy_assign)   RestrictToLoopsAndNeighborsCreator (protocols::toolbox::task_operations)   TensorsOptimizer_Ts2 (protocols::scoring::methods::pcsTs2)   
CombinedConstraintEvaluatorCreator (protocols::constraints_additional)   HelixKinkFilter (protocols::fldsgn::filters)   NonlocalContactsCalculator (protocols::toolbox::pose_metric_calculators)   RestrictToMoveMapChiOperation (protocols::toolbox::task_operations)   TensorsOptimizer_Ts3 (protocols::scoring::methods::pcsTs3)   
CombinedFilter (protocols::filters)   HelixKinkFilterCreator (protocols::fldsgn::filters)   NonlocalFrags (protocols::frag_picker::nonlocal)   RestrictToNeighborhoodOperation (protocols::toolbox::task_operations)   TensorsOptimizer_Ts4 (protocols::scoring::methods::pcsTs4)   
CombinedFilterCreator (protocols::filters)   HelixPairing (protocols::fldsgn::topology)   NonlocalPair (protocols::frag_picker::nonlocal)   RestrictToNeighborhoodOperationCreator (protocols::toolbox::task_operations)   TensorsOptimizerFix (protocols::scoring::methods::pcs2)   
CombinedTaskOperation (protocols::flxbb)   HelixPairingFilter (protocols::fldsgn::filters)   NonPlaidFingerprint (protocols::pockets)   RestrictToTerminiOperation (protocols::toolbox::task_operations)   TensorsOptimizerSvd (protocols::scoring::methods::pcs2)   
COMCoordinateConstraint (protocols::constraints_additional)   HelixPairingFilterCreator (protocols::fldsgn::filters)   NonSequentialNeighborsFilter (protocols::simple_filters)   RestrictToTerminiOperationCreator (protocols::toolbox::task_operations)   TerminusDistanceFilter (protocols::simple_filters)   
CompareByScoreCombination (protocols::frag_picker)   HelixPairingSet (protocols::fldsgn::topology)   NonSequentialNeighborsFilterCreator (protocols::simple_filters)   ResTypeFragmentMover (protocols::simple_moves)   TerminusDistanceFilterCreator (protocols::simple_filters)   
CompareQueryPosition (protocols::frag_picker)   HelixRotate (protocols::nonlocal)   NoOpRotamer (protocols::rotamer_sampler)   ResTypeSequence_lt (protocols::dna)   TestPattern (protocols::hotspot_hashing)   
CompareScoreComponent (protocols::frag_picker)   HelixScore (protocols::sic_dock)   NoOutputJobOutputter (protocols::jd2)   ReturnSidechainMover (protocols::simple_moves)   TetherLigand (protocols::ligand_docking)   
CompareTags (protocols::jd2)   HierarchicalLevel (protocols::canonical_sampling::mc_convergence_checks)   NoOutputJobOutputterCreator (protocols::jd2)   Reversion (protocols::dna)   TheozymeInvrotTree (protocols::toolbox::match_enzdes_util)   
CompareTotalScore (protocols::frag_picker)   HighResDocker (protocols::ligand_docking)   NoPoseXYX_Func (protocols::sic_dock)   Revert (protocols::protein_interface_design)   ThermodynamicMover (protocols::canonical_sampling)   
ComparisonGrid (protocols::pockets)   HighResDockerCreator (protocols::ligand_docking)   NormalizedEvaluatedArchive (protocols::jd2::archive)   RGFilter (protocols::simple_filters)   ThermodynamicObserver (protocols::canonical_sampling)   
CompleteConnectionsFilter (protocols::ligand_docking)   Hit (protocols::match)   NormalMode (protocols::normalmode)   RigidBodyDeterministicSpinMover (protocols::rigid)   Thermostat (protocols::md)   
CompleteConnectionsFilterCreator (protocols::ligand_docking)   HitHasher (protocols::match)   NormalModeMinimizer (protocols::normalmode)   RigidBodyDofPerturbMover (protocols::rigid)   ThreadingJob (protocols::comparative_modeling)   
MPIArchiveJobDistributor::CompletionMessage (protocols::jd2::archive)   HitNeighborFinder (protocols::match)   NormalModeMinimizerCreator (protocols::normalmode)   RigidBodyDofRandomizeMover (protocols::rigid)   ThreadingJobInputter (protocols::comparative_modeling)   
ComposeSearchPatterns (protocols::hotspot_hashing)   HolesFilter (protocols::simple_filters)   NormalModeMultifunc (protocols::normalmode)   RigidBodyDofRandomTransMover (protocols::rigid)   ThreadingJobInputterCreator (protocols::comparative_modeling)   
CompositeFragmentSelector (protocols::frag_picker)   HolesFilterCreator (protocols::simple_filters)   NormalModeRelaxMover (protocols::normalmode)   RigidBodyDofSeqPerturbMover (protocols::rigid)   ThreadingMover (protocols::comparative_modeling)   
CompositionMover (protocols::moves)   HotspotDisjointedFoldTreeMover (protocols::protein_interface_design::movers)   NPDPropCalculator (protocols::pack_daemon)   RigidBodyDofSeqRandomizeMover (protocols::rigid)   ThreadSequenceOperation (protocols::toolbox::task_operations)   
CompoundFilter (protocols::filters)   HotspotDisjointedFoldTreeMoverCreator (protocols::protein_interface_design::movers)   NPDPropCalculatorCreator (protocols::pack_daemon)   RigidBodyDofSeqTransMover (protocols::rigid)   ThreadSequenceOperationCreator (protocols::toolbox::task_operations)   
CompoundFilterCreator (protocols::filters)   HotspotHasherMover (protocols::protein_interface_design::movers)   NtoC_RCG (protocols::forge::constraints)   RigidBodyDofTransMover (protocols::rigid)   TimeEvaluator (protocols::evaluation)   
CompoundTranslate (protocols::ligand_docking)   HotspotHasherMoverCreator (protocols::protein_interface_design::movers)   NtoCCstGeneratorCreator (protocols::forge::constraints)   RigidBodyInfo (protocols::docking)   TimeFilter (protocols::filters)   
CompoundTranslateCreator (protocols::ligand_docking)   HotspotStub (protocols::hotspot_hashing)   NullDesignMover (protocols::protein_interface_design::movers)   RigidBodyMotionMover (protocols::rigid)   TimeFilterCreator (protocols::filters)   
ComputeLigandRDF (protocols::ligand_docking)   HotspotStubSet (protocols::hotspot_hashing)   NullMover (protocols::moves)   RigidBodyMoveBaseRSO (protocols::toolbox::rotamer_set_operations)   Timer (protocols::checkpoint)   
ComputeLigandRDFCreator (protocols::ligand_docking)   HPatchCalculator (protocols::toolbox::pose_metric_calculators)   NullOpener (protocols::loop_modeling::openers)   RigidBodyMover (protocols::rigid)   TMalign (protocols::hybridization)   
ComputeTotalDistCst (protocols::abinitio)   HPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   NumberHBondsCalculator (protocols::toolbox::pose_metric_calculators)   RigidBodyMoveRSO (protocols::toolbox::rotamer_set_operations)   TopCountOfAllInputs (protocols::features)   
ConcurrencyTest (protocols::features::helixAssembly)   HSPairPotential (protocols::fldsgn::potentials::sspot)   NumNeighborsMPM (protocols::match)   RigidBodyPerturbMover (protocols::rigid)   TopCountOfEachInput (protocols::features)   
ConcurrencyTestCreator (protocols::features::helixAssembly)   HSSTriplet (protocols::fldsgn::topology)   
  O  
RigidBodyPerturbNoCenterMover (protocols::rigid)   TopEntitySet (protocols::pack_daemon)   
ConformationViewer (protocols::viewer)   HSSTripletFilter (protocols::fldsgn::filters)   RigidBodyPerturbNoCenterMoverCreator (protocols::rigid)   TopNByProperty (protocols::pose_selectors)   
ConformerSwitchMover (protocols::docking)   HSSTripletFilterCreator (protocols::fldsgn::filters)   O2M_MutateMover (protocols::simple_moves)   RigidBodyRandomizeMover (protocols::rigid)   TopNByPropertyCreator (protocols::pose_selectors)   
ConformerSwitchMoverCreator (protocols::docking)   HSSTripletSet (protocols::fldsgn::topology)   O2PrimePacker (protocols::stepwise::sampling::rna::o2prime)   RigidBodyRotamer (protocols::rotamer_sampler::rigid_body)   TopologyBroker (protocols::topology_broker)   
ConnectRight (protocols::forge::build)   HybridizeFoldtreeDynamic (protocols::hybridization)   O2PrimeScreener (protocols::stepwise::screener)   RigidBodyRotamerValueRange (protocols::rotamer_sampler::rigid_body)   TopologyBrokerMover (protocols::protein_interface_design::movers)   
ConsensusDesignMover (protocols::simple_moves)   HybridizeProtocol (protocols::hybridization)   OccupiedSpaceHash (protocols::match)   RigidBodyRotamerWithResidueAlternatives (protocols::rotamer_sampler::rigid_body)   TopologyBrokerMoverCreator (protocols::protein_interface_design::movers)   
ConsensusDesignMoverCreator (protocols::simple_moves)   HybridizeProtocolCreator (protocols::hybridization)   OopCreatorMover (protocols::ncbb::oop)   RigidBodyRotamerWithResidueList (protocols::rotamer_sampler::rigid_body)   TopologyClaimer (protocols::topology_broker)   
ConservativeDesignOperation (protocols::antibody::design)   HybridizeSetup (protocols::hybridization)   OopCreatorMoverCreator (protocols::ncbb::oop)   RigidBodySampler (protocols::stepwise::sampling::legacy)   TopologyClaimerFactory (protocols::topology_broker)   
ConservedPosMutationFilter (protocols::simple_filters)   HybridizeSetupMover (protocols::hybridization)   OopDockDesignProtocol (protocols::ncbb::oop)   RigidBodySpinMover (protocols::rigid)   TopPercentOfAllInputs (protocols::features)   
ConservedPosMutationFilterCreator (protocols::simple_filters)   HybridizeSetupMoverCreator (protocols::hybridization)   OopDockDesignProtocolCreator (protocols::ncbb::oop)   RigidBodyTransMover (protocols::rigid)   TopPercentOfEachInput (protocols::features)   
ConstAbinitioMoverWeight (protocols::topology_broker::weights)   HydrophobicityProfileSimilarity (protocols::frag_picker::scores)   OopDPuckMinusMover (protocols::simple_moves::oop)   RigidBodyTransMoverCreator (protocols::rigid)   Torsion (protocols::protein_interface_design::filters)   
ConstantScoreBase (protocols::qsar::scoring_grid)   HydrophobicitySimilarity (protocols::frag_picker::scores)   OopDPuckPlusMover (protocols::simple_moves::oop)   RigidChunkClaimer (protocols::topology_broker)   Torsion_Info (protocols::stepwise::sampling::rna)   
ConstPattern (protocols::hotspot_hashing)   
  I  
OopMover (protocols::simple_moves::oop)   RigidLigandBuilder (protocols::match::downstream)   TorsionBinIO (protocols::frag_picker)   
Constraint (protocols::md)   OopPatcher (protocols::simple_moves::oop)   RigidScore (protocols::sic_dock)   TorsionBinPool (protocols::frag_picker::quota)   
ConstraintClaimer (protocols::topology_broker)   IdealGeometryOpener (protocols::loop_modeling::openers)   OopPuckMinusMover (protocols::simple_moves::oop)   RigidSearchMover (protocols::ligand_docking)   TorsionBinSimilarity (protocols::frag_picker::scores)   
ConstraintedOptimizationWeightFunc (protocols::optimize_weights)   IdealizeHelicesMover (protocols::rbsegment_relax)   OopPuckPlusMover (protocols::simple_moves::oop)   RingConformationMover (protocols::simple_moves)   TorsionClaim (protocols::environment::claims)   
ConstraintEvaluator (protocols::constraints_additional)   IdealizeHelicesMoverCreator (protocols::rbsegment_relax)   OopRandomPuckMover (protocols::simple_moves::oop)   RingData (protocols::sparta)   TorsionCreator (protocols::protein_interface_design::filters)   
ConstraintEvaluatorCreator (protocols::constraints_additional)   IdealizeMover (protocols::idealize)   OopRandomSmallMover (protocols::simple_moves::oop)   RmsdEvaluator (protocols::simple_filters)   TorsionDOFMover (protocols::simple_moves)   
ConstraintEvaluatorWrapper (protocols::topology_broker)   IdealizeMoverCreator (protocols::idealize)   OP_const_iterator (protocols::toolbox)   RmsdEvaluatorCreator (protocols::simple_filters)   TorsionElement (protocols::environment::claims)   
ConstraintEvaluatorWrapperCreator (protocols::topology_broker)   IdealizeNonPhiPsi (protocols::kinematic_closure::perturbers)   OpenerCollection (protocols::loop_modeling::openers)   RmsdFilter (protocols::protein_interface_design::filters)   TorsionFeature (protocols::comparative_modeling::features)   
ConstraintFileCstGeneratorCreator (protocols::forge::constraints)   IfMover (protocols::moves)   Operator (protocols::simple_filters)   RmsdFilterCreator (protocols::protein_interface_design::filters)   TorsionFragment (protocols::frags)   
ConstraintFileRCG (protocols::forge::constraints)   IfMoverCreator (protocols::moves)   OperatorFilterCreator (protocols::simple_filters)   RMSDReporter (protocols::pose_reporters)   TorsionFragmentLibrary (protocols::frags)   
ConstraintFragmentMover (protocols::simple_moves)   IfThenFilter (protocols::filters)   OptEData (protocols::optimize_weights)   RMSDReporterCreator (protocols::pose_reporters)   TorsionFragmentMover (protocols::frags)   
ConstraintFragmentSampler (protocols::abinitio)   IfThenFilterCreator (protocols::filters)   OptEMultifunc (protocols::optimize_weights)   RmsdTargetEvaluatorCreator (protocols::simple_filters)   TorsionNormalModeMover (protocols::normalmode)   
ConstrainToIdealMover (protocols::simple_moves)   IGLigandDesignEdgeUpweighter (protocols::toolbox)   OptEPositionData (protocols::optimize_weights)   RMSVallData (protocols::frags)   TorsionRestrictedKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
ConstraintPreparer (protocols::abinitio::abscript)   IgnoreSubsetConstraintSet (protocols::comparative_modeling)   OptEPositionDataFactory (protocols::optimize_weights)   RNA_AddDeleteMonteCarlo (protocols::stepwise::monte_carlo::rna)   TorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
ConstraintPreparerCreator (protocols::abinitio::abscript)   Implements   OptEVariableExpression (protocols::optimize_weights)   RNA_AnalyticLoopCloser (protocols::stepwise::sampling::rna::legacy)   TorsionSet (protocols::farna)   
ConstraintScoreCutoffFilter (protocols::simple_filters)   Implements   OptimizeThreadingMover (protocols::rbsegment_relax)   RNA_BaseCentroidChecker (protocols::stepwise::sampling::rna::checker)   TorsionSweepingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
ConstraintScoreCutoffFilterCreator (protocols::simple_filters)   ImplicitFastClashCheck (protocols::scoring)   OptimizeThreadingMoverCreator (protocols::rbsegment_relax)   RNA_ChiRotamer (protocols::rotamer_sampler::rna)   TotalSasaFilter (protocols::simple_filters)   
ConstraintSetMover (protocols::simple_moves)   ImportUnboundRotamersOperation (protocols::toolbox::task_operations)   OrbitalsFeatures (protocols::features)   RNA_ChunkLibrary (protocols::farna)   TotalSasaFilterCreator (protocols::simple_filters)   
ConstraintSetMoverCreator (protocols::simple_moves)   ImportUnboundRotamersOperationCreator (protocols::toolbox::task_operations)   OrbitalsFeaturesCreator (protocols::features)   RNA_DataReader (protocols::farna)   TrajectoryRecorder (protocols::canonical_sampling)   
ConstraintSetScore (protocols::sic_dock)   IndependentLoopMover (protocols::loops::loop_mover)   OrderedSequentialSymmetrySlider (protocols::simple_moves::symmetry)   RNA_DeNovoProtocol (protocols::farna)   TransferBuffer (protocols::canonical_sampling::mc_convergence_checks)   
ConstScore (protocols::frag_picker::scores)   InnerJob (protocols::jd2)   OriginalBackboneBuildPoint (protocols::match::upstream)   RNA_FragmentMover (protocols::farna)   Transform (protocols::ligand_docking)   
Contact (protocols::contact_map)   InnerMultiThreadingJob (protocols::jd2)   OrSelector (protocols::pose_selectors)   RNA_Fragments (protocols::farna)   Transform_info (protocols::ligand_docking)   
Contact (protocols::frag_picker)   InputStreamRotamer (protocols::rotamer_sampler::input_streams)   OrSelectorCreator (protocols::pose_selectors)   RNA_HelixAssembler (protocols::stepwise::sampling::rna::helix)   Transformation (protocols::protein_interface_design)   
ContactCounts (protocols::frag_picker)   InputStreamWithResidueInfo (protocols::stepwise::sampling::protein)   OTFFlexbbEdge (protocols::flexpack::interaction_graph)   RNA_JumpLibrary (protocols::farna)   Transformation   
ContactMap (protocols::contact_map)   Inputter (protocols::inputter)   OTFFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   RNA_KicSampler (protocols::rotamer_sampler::rna)   TransformCreator (protocols::ligand_docking)   
ContactMapCreator (protocols::contact_map)   InputterStream (protocols::inputter)   OTFFlexbbNode (protocols::flexpack::interaction_graph)   RNA_KinematicCloser (protocols::rotamer_sampler::rna)   TransientCutpointHandler (protocols::stepwise::monte_carlo::rna)   
ContactMapEvaluator (protocols::simple_filters)   InsertChunkMover (protocols::hybridization)   OtherContextScoreFunction (protocols::flexpack)   RNA_LoopCloser (protocols::farna)   Translate (protocols::ligand_docking)   
ContactMapEvaluatorCreator (protocols::simple_filters)   InSetExpression (protocols::pack_daemon)   RRReporterSQLite::OutputLevel (protocols::rotamer_recovery)   RNA_McMultiSuite (protocols::rotamer_sampler::rna)   Translate_info (protocols::ligand_docking)   
ContactPartner (protocols::contact_map)   IntegrationTestBreaker (protocols::stepwise::screener)   Outputter (protocols::outputter)   RNA_McSugar (protocols::rotamer_sampler::rna)   TranslateCreator (protocols::ligand_docking)   
ContactStruct (protocols::normalmode)   InteratomicVarianceMatrix (protocols::toolbox)   OutputWriter (protocols::match::output)   RNA_McSuite (protocols::rotamer_sampler::rna)   TreeBuilder (protocols::nonlocal)   
ContingentAcceptMover (protocols::simple_moves)   InterbondAngleScore (protocols::frag_picker::scores)   
  P  
RNA_Minimizer (protocols::farna)   TreeBuilderFactory (protocols::nonlocal)   
ContingentAcceptMoverCreator (protocols::simple_moves)   InterchainEnvEnergy (protocols::scoring::methods)   RNA_NucleosideRotamer (protocols::rotamer_sampler::rna)   Trial   
ContingentFilter (protocols::filters)   InterchainEnvEnergyCreator (protocols::scoring::methods)   PackDaemon (protocols::pack_daemon)   RNA_O2PrimeMover (protocols::stepwise::monte_carlo::rna)   TrialCounter (protocols::moves)   
ContingentFilterCreator (protocols::filters)   InterchainPairEnergy (protocols::scoring::methods)   PackerNeighborGraphFilter (protocols::simple_filters)   RNA_Pairing (protocols::farna)   TrialMover (protocols::moves)   
ConvergenceCheck (protocols::moves::mc_convergence_checks)   InterchainPairEnergyCreator (protocols::scoring::methods)   PackingState (protocols::multistate_design)   RNA_PairingTemplate (protocols::farna)   TrisBpyScore (protocols::sic_dock::scores)   
CoordConstraintClaimer (protocols::topology_broker)   InterchainPotential (protocols::scoring)   PackRotamersMover (protocols::simple_moves)   RNA_Relaxer (protocols::farna)   TrueFilter (protocols::filters)   
CoordinateConstraintKC (protocols::abinitio)   Interface (protocols::scoring)   PackRotamersMoverCreator (protocols::simple_moves)   RNA_SecStructInfo (protocols::farna)   TrueFilterCreator (protocols::filters)   
CoordinateCst (protocols::seeded_abinitio)   Interface (protocols::ligand_docking::ligand_options)   PackRotamersMoverLazy (protocols::simple_moves)   RNA_StructureParameters (protocols::farna)   TruncatedScoreEvaluator (protocols::simple_filters)   
CoordinateCstCreator (protocols::seeded_abinitio)   InterfaceAnalyzerMover (protocols::analysis)   PackRotamersMoverLazyCreator (protocols::simple_moves)   RNA_SugarRotamer (protocols::rotamer_sampler::rna)   TryRotamers (protocols::protein_interface_design::movers)   
CopyDofMover (protocols::simple_moves)   InterfaceAnalyzerMoverCreator (protocols::analysis)   PackRotamersMoverPartGreedy (protocols::enzdes)   RNA_SuiteRotamer (protocols::rotamer_sampler::rna)   TryRotamersCreator (protocols::protein_interface_design::movers)   
CopyDofRotamer (protocols::rotamer_sampler::copy_dofs)   InterfaceBindingEnergyDensityFilter (protocols::simple_filters)   PackRotamersMoverPartGreedyCreator (protocols::enzdes)   RNA_TorsionMover (protocols::stepwise::monte_carlo::rna)   Tumble (protocols::simple_moves)   
CORdata (protocols::sparta)   InterfaceBindingEnergyDensityFilterCreator (protocols::simple_filters)   PackstatCalculator (protocols::toolbox::pose_metric_calculators)   RNA_TorsionScreener (protocols::rotamer_sampler::screener)   TumbleCreator (protocols::simple_moves)   
CoreDunbrackFilter (protocols::fldsgn::filters)   InterfaceBuilder (protocols::ligand_docking)   PackStatFilter (protocols::simple_filters)   RNA_VDW_BinChecker (protocols::stepwise::sampling::rna::checker)   
  U  
CoreDunbrackFilterCreator (protocols::fldsgn::filters)   InterfaceBuilderLoader (protocols::ligand_docking)   PackStatFilterCreator (protocols::simple_filters)   RollMover (protocols::rigid)   
CorrectionVisitor (protocols::sic_dock)   InterfaceBuilderLoaderCreator (protocols::ligand_docking)   PackStatMover (protocols::analysis)   RollMoverCreator (protocols::rigid)   UDPSocketClient (protocols::moves)   
CountFromLeft (protocols::forge::build)   InterfaceData (protocols::analysis)   PairFeatures (protocols::features)   Rose (protocols::sic_dock)   UnconstrainedTorsionsMover (protocols::ligand_docking)   
CovalentCompliance (protocols::noesy_assign)   InterfaceFeatures (protocols::features)   PairFeaturesCreator (protocols::features)   RosettaScriptsParser (protocols::rosetta_scripts)   UnfoldedStateEnergyCalculatorJobDistributor (protocols::unfolded_state_energy_calculator)   
CovalentConnectionReplaceInfo (protocols::toolbox::match_enzdes_util)   InterfaceFeaturesCreator (protocols::features)   PairingLibrary (protocols::jumping)   RotamerAny (protocols::rotamer_sampler)   UnfoldedStateEnergyCalculatorMover (protocols::unfolded_state_energy_calculator)   
CovalentResidueNetwork (protocols::toolbox)   InterfaceHolesFilter (protocols::protein_interface_design::filters)   PairingStatEntry (protocols::abinitio)   RotamerBase (protocols::rotamer_sampler)   UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (protocols::unfolded_state_energy_calculator)   
CreateMembranePoseMover (protocols::membrane)   InterfaceHolesFilterCreator (protocols::protein_interface_design::filters)   PairingStatistics (protocols::abinitio)   RotamerBoltzCalculator (protocols::toolbox::pose_metric_calculators)   UniformPerturber (protocols::kinematic_closure::perturbers)   
CreateMembranePoseMoverCreator (protocols::membrane)   InterfaceInfo (protocols::scoring)   PairingTemplate (protocols::jumping)   RotamerBoltzmannWeight (protocols::simple_filters)   UniformPolicy (protocols::nonlocal)   
CrossPeak (protocols::noesy_assign)   InterfaceInfo (protocols::ligand_docking::ligand_options)   PalesEvaluator (protocols::simple_filters)   RotamerBoltzmannWeightFeatures (protocols::features)   UniformSphereTransMover (protocols::rigid)   
CrossPeak3D (protocols::noesy_assign)   InterfaceRecapitulationMover (protocols::protein_interface_design::movers)   PalesEvaluatorCreator (protocols::simple_filters)   RotamerBoltzmannWeightFeaturesCreator (protocols::features)   UnrecognizedAtomFeatures (protocols::features)   
CrossPeak4D (protocols::noesy_assign)   InterfaceRecapitulationMoverCreator (protocols::protein_interface_design::movers)   ParallelBetaPairingPreferenceFilter (protocols::fldsgn::filters)   RotamerBoltzmannWeightFilterCreator (protocols::simple_filters)   UnrecognizedAtomFeaturesCreator (protocols::features)   
CrossPeakInfo (protocols::noesy_assign)   InterfaceSasaFilter (protocols::simple_filters)   ParallelBetaPairingPreferenceFilterCreator (protocols::fldsgn::filters)   RotamerComb (protocols::rotamer_sampler)   UpdateSolventMover (protocols::cryst)   
CrossPeakList (protocols::noesy_assign)   InterfaceSasaFilterCreator (protocols::simple_filters)   ParetoOptMutationMover (protocols::design_opt)   RotamerDNAHBondFilter (protocols::dna)   UpdateSolventMoverCreator (protocols::cryst)   
CrystalContactsOperation (protocols::toolbox::task_operations)   InterfaceScoreCalculator (protocols::ligand_docking)   ParetoOptMutationMoverCreator (protocols::design_opt)   RotamerDumpMover (protocols::RotamerDump)   UpstreamBuilder (protocols::match::upstream)   
CrystalContactsOperationCreator (protocols::toolbox::task_operations)   InterfaceScoreCalculatorCreator (protocols::ligand_docking)   ParsedProtocol (protocols::rosetta_scripts)   RotamerFeatures (protocols::features)   UpstreamCollisionFilter (protocols::match::output)   
CS2ndShift (protocols::frag_picker)   InterfaceSidechainMinMover (protocols::docking)   ParsedProtocolCreator (protocols::rosetta_scripts)   RotamerFeaturesCreator (protocols::features)   UpstreamDownstreamCollisionFilter (protocols::match::output)   
CSScore (protocols::frag_picker::scores)   InterfaceTaskOperation (protocols::toolbox::task_operations)   Parser (protocols::jd2)   RotamerInitializer (protocols::features)   UpstreamHitCacher (protocols::match::output)   
CSTalosIO (protocols::frag_picker)   InterGroupNeighborsCalculator (protocols::toolbox::pose_metric_calculators)   ParserJobInputter (protocols::protein_interface_design)   RotamerOneTorsion (protocols::rotamer_sampler)   UpstreamResidueProcessor (protocols::match::upstream)   
CstResInteractions (protocols::toolbox::match_enzdes_util)   InterlockAroma (protocols::flxbb)   ParserJobInputterCreator (protocols::protein_interface_design)   RotamerOneValue (protocols::rotamer_sampler)   UpstreamResTypeGeometry (protocols::match::upstream)   
CustomScoreSelector (protocols::frag_picker)   InterlockAromaCreator (protocols::flxbb)   PartialSecondarySimilarity (protocols::frag_picker::scores)   RotamerOneValueComb (protocols::rotamer_sampler)   UserDefinedGroupDiscriminator (protocols::simple_moves)   
CutBiasClaim (protocols::environment::claims)   InterlockingAromaFilter (protocols::fldsgn::filters)   PartialThreadingMover (protocols::comparative_modeling)   RotamerRecovery (protocols::rotamer_recovery)   UDPSocketClient::UUID (protocols::moves)   
CutBiasClaimer (protocols::topology_broker)   InterlockingAromaFilterCreator (protocols::fldsgn::filters)   PartitionAggregateFunction (protocols::multistate_design)   RotamerRecovery (protocols::toolbox::pose_metric_calculators)   
  V  
CutBiasElement (protocols::environment::claims)   InternalWorkingResidueParameter (protocols::stepwise::sampling::rna)   PartitionedSearchPattern (protocols::hotspot_hashing)   RotamerRecoveryFactory (protocols::rotamer_recovery)   
CutChainMover (protocols::simple_moves)   Interval (protocols::forge::build)   PatchdockReader (protocols::protein_interface_design)   RotamerRecoveryFeatures (protocols::features)   VallChunk (protocols::frag_picker)   
CutChainMoverCreator (protocols::simple_moves)   Interval (protocols::jumping)   PatchdockTransform (protocols::protein_interface_design::movers)   RotamerRecoveryFeaturesCreator (protocols::features)   VallChunkFilter (protocols::frag_picker)   
CutClaim (protocols::topology_broker::claims)   InverseRotamersCstGeneratorCreator (protocols::forge::constraints)   PatchdockTransformCreator (protocols::protein_interface_design::movers)   RotamerRecoveryMover (protocols::rotamer_recovery)   VallData (protocols::frags)   
CutElement (protocols::environment::claims)   InverseRotamersRCG (protocols::forge::constraints)   PatchOperation (protocols::canonical_sampling)   RotamerRecoveryMoverCreator (protocols::rotamer_recovery)   VallProvider (protocols::frag_picker)   
CCluster::Cxyz (protocols::pockets)   InvGeometricFunc (protocols::moves)   PCA (protocols::evaluation)   RotamerRecoveryRegistrator (protocols::rotamer_recovery)   VallResidue (protocols::frag_picker)   
PCluster::Cxyz (protocols::pockets)   InvrotCollector (protocols::toolbox::match_enzdes_util)   PcaEvaluator (protocols::abinitio)   RotamerSized (protocols::rotamer_sampler)   ValueEvaluator (protocols::enzdes)   
CycleMover (protocols::moves)   InvrotTarget (protocols::toolbox::match_enzdes_util)   PCluster (protocols::pockets)   RotamerSizedAny (protocols::rotamer_sampler)   VariableVectorExpression (protocols::pack_daemon)   
CyclicMover (protocols::moves)   InvrotTree (protocols::toolbox::match_enzdes_util)   PClusterSet (protocols::pockets)   RotamerSizedComb (protocols::rotamer_sampler)   VarianceStatisticsArchive (protocols::jd2::archive)   
  D  
InvrotTreeCstGeneratorCreator (protocols::forge::constraints)   PCS_data (protocols::scoring::methods::pcs)   RotamerSubsetRepacker (protocols::pack_daemon)   VarLengthBuild (protocols::forge::components)   
InvrotTreeNode (protocols::toolbox::match_enzdes_util)   PCS_data_input (protocols::scoring::methods::pcs)   RotamerTrialsMinMover (protocols::simple_moves)   VDW_BinScreener (protocols::stepwise::screener)   
DaemonSet (protocols::pack_daemon)   InvrotTreeNodeBase (protocols::toolbox::match_enzdes_util)   PCS_data_input_manager (protocols::scoring::methods::pcs)   RotamerTrialsMinMoverCreator (protocols::simple_moves)   VDW_RepScreeninfo (protocols::stepwise::sampling::rna::checker)   
DarcElectrostaticsBase (protocols::pockets)   InvrotTreeRCG (protocols::forge::constraints)   PCS_data_input_manager_Ts1 (protocols::scoring::methods::pcsTs1)   RotamerTrialsMover (protocols::simple_moves)   VdwGrid (protocols::qsar::scoring_grid)   
DarcParticleSwarmMinimizer (protocols::pockets)   IRCollection (protocols::motifs)   PCS_data_input_manager_Ts2 (protocols::scoring::methods::pcsTs2)   RotamerTrialsMoverCreator (protocols::simple_moves)   VdwGridCreator (protocols::qsar::scoring_grid)   
DatabaseEntryWorkUnit (protocols::wum)   IRmsdFilter (protocols::protein_interface_design::filters)   PCS_data_input_manager_Ts3 (protocols::scoring::methods::pcsTs3)   RotamerTrialsRefiner (protocols::loop_modeling::refiners)   Vec1Hash (protocols::genetic_algorithm)   
DatabaseFilter (protocols::features)   IRmsdFilterCreator (protocols::protein_interface_design::filters)   PCS_data_input_manager_Ts4 (protocols::scoring::methods::pcsTs4)   Rotate (protocols::ligand_docking)   Vec3 (protocols::sic_dock)   
DatabaseJobInputter (protocols::features)   LoggedFragmentMover::Item (protocols::simple_moves)   PCS_data_input_Ts1 (protocols::scoring::methods::pcsTs1)   Rotate_info (protocols::ligand_docking)   VectorExpression (protocols::pack_daemon)   
DatabaseJobInputterCreator (protocols::features)   IteratedConvergenceMover (protocols::moves)   PCS_data_input_Ts2 (protocols::scoring::methods::pcsTs2)   RotateCreator (protocols::ligand_docking)   VectorExpressionCreator (protocols::pack_daemon)   
DatabaseJobOutputter (protocols::features)   IteratedConvergenceMoverCreator (protocols::moves)   PCS_data_input_Ts3 (protocols::scoring::methods::pcsTs3)   RotateJumpAxisMover (protocols::rigid)   VectorFunction (protocols::pack_daemon)   
DatabaseJobOutputterCreator (protocols::features)   IterativeAbrelax (protocols::abinitio)   PCS_data_input_Ts4 (protocols::scoring::methods::pcsTs4)   Rotates (protocols::ligand_docking)   VectorFunction2 (protocols::pack_daemon)   
DatabaseQueryWorkUnitManager (protocols::wum)   IterativeBase (protocols::abinitio)   PCS_data_per_lanthanides (protocols::scoring::methods::pcs)   RotatesCreator (protocols::ligand_docking)   VectorPair (protocols::hotspot_hashing)   
DatabaseThread (protocols::toolbox::task_operations)   IterativeCentroid (protocols::abinitio)   PCS_data_per_lanthanides_Ts1 (protocols::scoring::methods::pcsTs1)   RotationSearchPattern (protocols::hotspot_hashing)   VicinityPerturber (protocols::kinematic_closure::perturbers)   
DatabaseThreadCreator (protocols::toolbox::task_operations)   IterativeFullatom (protocols::abinitio)   PCS_data_per_lanthanides_Ts2 (protocols::scoring::methods::pcsTs2)   RotData (protocols::MakeRotLib)   VicinitySamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
DataBuffer (protocols::canonical_sampling::mc_convergence_checks)   IterativeOptEDriver (protocols::optimize_weights)   PCS_data_per_lanthanides_Ts3 (protocols::scoring::methods::pcsTs3)   RPF_ScoreEvaluator (protocols::simple_filters)   VIP_Mover (protocols::vip)   
DataLoader (protocols::jd2::parser)   IterativeVectorExpression (protocols::pack_daemon)   PCS_data_per_lanthanides_Ts4 (protocols::scoring::methods::pcsTs4)   RRComparer (protocols::rotamer_recovery)   VIP_Report (protocols::vip)   
DataLoaderCreator (protocols::jd2::parser)   
  J  
PCS_data_Ts1 (protocols::scoring::methods::pcsTs1)   RRComparerAutomorphicRMSD (protocols::rotamer_recovery)   VirtResClaim (protocols::environment::claims)   
DataLoaderFactory (protocols::jd2::parser)   PCS_data_Ts2 (protocols::scoring::methods::pcsTs2)   RRComparerAutomorphicRMSDCreator (protocols::rotamer_recovery)   VirtualRootMover (protocols::simple_moves)   
DataLoaderRegistrator (protocols::jd2::parser)   JCoupling (protocols::frag_picker::scores)   PCS_data_Ts3 (protocols::scoring::methods::pcsTs3)   RRComparerChiDiff (protocols::rotamer_recovery)   VirtualRootMoverCreator (protocols::simple_moves)   
DataPoint (protocols::cluster)   JCouplingIO (protocols::frag_picker)   PCS_data_Ts4 (protocols::scoring::methods::pcsTs4)   RRComparerChiDiffCreator (protocols::rotamer_recovery)   VLB (protocols::protein_interface_design::movers)   
DbTrajectoryReader (protocols::canonical_sampling)   JD2ResourceManager (protocols::jd2)   PCS_Energy (protocols::scoring::methods::pcs)   RRComparerCreator (protocols::rotamer_recovery)   VLBCreator (protocols::protein_interface_design::movers)   
DbTrajectoryReader (protocols::trajectory)   JD2ResourceManagerCreator (protocols::jd2)   PCS_Energy_parameters_manager (protocols::scoring::methods::pcs)   RRComparerElecDensDiff (protocols::rotamer_recovery)   VMax (protocols::pack_daemon)   
DbTrajectoryRecorder (protocols::canonical_sampling)   JD2ResourceManagerJobInputter (protocols::jd2)   PCS_Energy_parameters_manager_Ts1 (protocols::scoring::methods::pcsTs1)   RRComparerElecDensDiffCreator (protocols::rotamer_recovery)   VMaxBy (protocols::pack_daemon)   
DbTrajectoryRecorderCreator (protocols::canonical_sampling)   JD2ResourceManagerJobInputterCreator (protocols::jd2)   PCS_Energy_parameters_manager_Ts2 (protocols::scoring::methods::pcsTs2)   RRComparerRotBins (protocols::rotamer_recovery)   VMin (protocols::pack_daemon)   
DbTrajectoryWriter (protocols::trajectory)   Job (protocols::jd2)   PCS_Energy_parameters_manager_Ts3 (protocols::scoring::methods::pcsTs3)   RRComparerRotBinsCreator (protocols::rotamer_recovery)   VMinBy (protocols::pack_daemon)   
DDGBindOptEData (protocols::optimize_weights)   JobDataFeatures (protocols::features)   PCS_Energy_parameters_manager_Ts4 (protocols::scoring::methods::pcsTs4)   RRProtocol (protocols::rotamer_recovery)   VoxelSetIterator (protocols::match)   
DdgFilter (protocols::simple_filters)   JobDataFeaturesCreator (protocols::features)   PCS_Energy_Ts1 (protocols::scoring::methods::pcsTs1)   RRProtocolCreator (protocols::rotamer_recovery)   
  W  
DdgFilterCreator (protocols::simple_filters)   JobDistributor (protocols::jd2)   PCS_Energy_Ts2 (protocols::scoring::methods::pcsTs2)   RRProtocolMinPack (protocols::rotamer_recovery)   
DDGMutationOptEData (protocols::optimize_weights)   JobDistributorFactory (protocols::jd2)   PCS_Energy_Ts3 (protocols::scoring::methods::pcsTs3)   RRProtocolMinPackCreator (protocols::rotamer_recovery)   WalkingBondAnglePerturber (protocols::kinematic_closure::perturbers)   
DDomainParse (protocols::hybridization)   JobInputter (protocols::jd2)   PCS_Energy_Ts4 (protocols::scoring::methods::pcsTs4)   RRProtocolMover (protocols::rotamer_recovery)   WalkingPerturber (protocols::kinematic_closure::perturbers)   
DebugArchive (protocols::jd2::archive)   JobInputterCreator (protocols::jd2)   PCS_file_data (protocols::scoring::methods::pcs)   RRProtocolMoverCreator (protocols::rotamer_recovery)   WatsonCrickRotamerCouplings (protocols::dna)   
DebugOut_MpiFileBuffer (protocols::jd2)   JobInputterFactory (protocols::jd2)   PCS_file_data_Ts1 (protocols::scoring::methods::pcsTs1)   RRProtocolPackRotamers (protocols::rotamer_recovery)   WatsonCrickRotamerCouplingsCreator (protocols::dna)   
DecomposeAndReweightEnergiesCalculator (protocols::toolbox::pose_metric_calculators)   JobInputterRegistrator (protocols::jd2)   PCS_file_data_Ts2 (protocols::scoring::methods::pcsTs2)   RRProtocolPackRotamersCreator (protocols::rotamer_recovery)   WeightedFragmentSmoothTrialMover (protocols::hybridization)   
DecoySetEvaluation (protocols::toolbox)   JobOutputter (protocols::jd2)   PCS_file_data_Ts3 (protocols::scoring::methods::pcsTs3)   RRProtocolReferenceStructure (protocols::rotamer_recovery)   WeightedFragmentTrialMover (protocols::hybridization)   
DefineMovableLoops (protocols::seeded_abinitio)   JobOutputterCreator (protocols::jd2)   PCS_file_data_Ts4 (protocols::scoring::methods::pcsTs4)   RRProtocolReferenceStructureCreator (protocols::rotamer_recovery)   WeightRangeConstraint (protocols::optimize_weights)   
DefineMovableLoopsCreator (protocols::seeded_abinitio)   JobOutputterFactory (protocols::jd2)   PCS_FragDistance (protocols::frag_picker::scores)   RRProtocolRelax (protocols::rotamer_recovery)   WhileMover (protocols::moves)   
DeleteMover (protocols::stepwise::monte_carlo::rna)   JobOutputterObserver (protocols::jd2)   PCS_line_data (protocols::scoring::methods::pcs)   RRProtocolRelaxCreator (protocols::rotamer_recovery)   WholeBodyRotationMover (protocols::rigid)   
DelphiElectrostatics (protocols::pockets)   JobOutputterRegistrator (protocols::jd2)   PCS_line_data_Ts1 (protocols::scoring::methods::pcsTs1)   RRProtocolRotamerTrials (protocols::rotamer_recovery)   WholeBodyTranslationMover (protocols::rigid)   
DeltaFilter (protocols::simple_filters)   JointScore (protocols::sic_dock)   PCS_line_data_Ts2 (protocols::scoring::methods::pcsTs2)   RRProtocolRotamerTrialsCreator (protocols::rotamer_recovery)   WidthFirstSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
DeltaFilterCreator (protocols::simple_filters)   JointSequenceOperation (protocols::toolbox::task_operations)   PCS_line_data_Ts3 (protocols::scoring::methods::pcsTs3)   RRProtocolRTMin (protocols::rotamer_recovery)   WobbleMover (protocols::simple_moves)   
DenseIGRepacker (protocols::pack_daemon)   JointSequenceOperationCreator (protocols::toolbox::task_operations)   PCS_line_data_Ts4 (protocols::scoring::methods::pcsTs4)   RRProtocolRTMinCreator (protocols::rotamer_recovery)   WorkUnit (protocols::wum2)   
DensityMorphingMover (protocols::electron_density)   JScoreEvaluator (protocols::simple_filters)   PCS_tensor (protocols::scoring::methods::pcs)   RRReporter (protocols::rotamer_recovery)   WorkUnit_BatchRelax (protocols::relax)   
DensityMorphingMoverCreator (protocols::electron_density)   JScoreEvaluatorCreator (protocols::simple_filters)   PCS_tensor_Ts1 (protocols::scoring::methods::pcsTs1)   RRReporterCreator (protocols::rotamer_recovery)   WorkUnit_BatchRelax_and_PostRescore (protocols::relax)   
DensityScoringClaimer (protocols::topology_broker)   JSON_RPC (protocols::rpc)   PCS_tensor_Ts2 (protocols::scoring::methods::pcsTs2)   RRReporterHuman (protocols::rotamer_recovery)   WorkUnit_ElScripts (protocols::wum2)   
DenyPdbIdFilter (protocols::frag_picker)   JSONFormattedLoopsFileReader (protocols::loops)   PCS_tensor_Ts3 (protocols::scoring::methods::pcsTs3)   RRReporterHumanCreator (protocols::rotamer_recovery)   WorkUnit_LoopHash (protocols::loophash)   
DesignableResiduesFilter (protocols::protein_interface_design::filters)   Jump_point (protocols::stepwise::sampling::rna)   PCS_tensor_Ts4 (protocols::scoring::methods::pcsTs4)   RRReporterSimple (protocols::rotamer_recovery)   WorkUnit_MoverWrapper (protocols::wum)   
DesignableResiduesFilterCreator (protocols::protein_interface_design::filters)   RigidChunkClaimer::JumpCalculator (protocols::topology_broker)   PcsDataCenter (protocols::scoring::methods::pcs2)   RRReporterSimpleCreator (protocols::rotamer_recovery)   WorkUnit_SilentStructStore (protocols::wum)   
DesignAroundOperation (protocols::toolbox::task_operations)   JumpClaim (protocols::topology_broker::claims)   PcsDataCenterManager (protocols::scoring::methods::pcs2)   RRReporterSQLite (protocols::rotamer_recovery)   WorkUnit_Wait (protocols::wum2)   
DesignAroundOperationCreator (protocols::toolbox::task_operations)   JumpClaim (protocols::environment::claims)   PcsDataCenterManagerSingleton (protocols::scoring::methods::pcs2)   RRReporterSQLiteCreator (protocols::rotamer_recovery)   WorkUnit_Wait (protocols::wum)   
DesignInstructionsParser (protocols::antibody::design)   JumpSetup::JumpDef (protocols::jumping)   PcsDataLanthanide (protocols::scoring::methods::pcs2)   RTElement (protocols::environment::claims)   WorkUnitBase (protocols::wum)   
DesignMinimizeHbonds (protocols::protein_interface_design::movers)   ResiduePairJumpSetup::JumpDef (protocols::jumping)   PcsEnergy (protocols::scoring::methods::pcs2)   
  S  
WorkUnitList (protocols::wum)   
DesignMinimizeHbondsCreator (protocols::protein_interface_design::movers)   JumpElement (protocols::environment::claims)   PcsEnergyController (protocols::topology_broker)   WorkUnitManager (protocols::wum)   
DesignProteinBackboneAroundDNA (protocols::dna)   JumpEvaluator (protocols::simple_filters)   PcsEnergyCreator (protocols::scoring::methods::pcs2)   SaltBridgeCalculator (protocols::toolbox::pose_metric_calculators)   WorkUnitQueue (protocols::wum)   
DesignProteinBackboneAroundDNACreator (protocols::dna)   JumpingFoldConstraints (protocols::abinitio)   PcsEnergyParameter (protocols::scoring::methods::pcs2)   SaltBridgeFeatures (protocols::features)   WorkUnitQueue_Swapped (protocols::wum)   
DesignRepackMover (protocols::simple_moves)   JumpingFoldConstraintsWrapper (protocols::abinitio)   PcsEnergyParameterManager (protocols::scoring::methods::pcs2)   SaltBridgeFeaturesCreator (protocols::features)   WrappedOptEExpressionCreator (protocols::optimize_weights)   
DesignTask (protocols::flxbb)   JumpNrEvaluator (protocols::simple_filters)   PcsGridSearchParameter (protocols::scoring::methods::pcs2)   SameChiBinComboGrouper (protocols::match::output)   WrapperOptEMultifunc (protocols::optimize_weights)   
DesignTask_Layer (protocols::flxbb)   JumpNrEvaluatorCreator (protocols::simple_filters)   PcsGridSearchParameterManager (protocols::scoring::methods::pcs2)   SameRotamerComboGrouper (protocols::match::output)   WriteFileSFB (protocols::jd2)   
DesignTask_Normal (protocols::flxbb)   JumpOutMover (protocols::moves)   PcsInputCenter (protocols::scoring::methods::pcs2)   SameSequenceAndDSPositionGrouper (protocols::match::output)   WriteKinemageOutputter (protocols::match::output)   
DesignVsNativeComparison (protocols::enzdes)   JumpRotamer (protocols::rotamer_sampler)   PcsInputCenterManager (protocols::scoring::methods::pcs2)   SameSequenceGrouper (protocols::match::output)   WriteLigandMolFile (protocols::ligand_docking)   
DetectProteinLigandInterface (protocols::enzdes)   JumpRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   PcsInputFile (protocols::scoring::methods::pcs2)   SameStrand (protocols::jumping)   WriteLigandMolFileCreator (protocols::ligand_docking)   
DetectProteinLigandInterfaceOperationCreator (protocols::enzdes)   JumpRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   PcsInputLine (protocols::scoring::methods::pcs2)   SampleApplier (protocols::stepwise::screener)   WriteOut_MpiFileBuffer (protocols::jd2)   
DetectSymmetry (protocols::simple_moves::symmetry)   JumpSample (protocols::jumping)   PcsTensor (protocols::scoring::methods::pcs2)   SampleStrategyData (protocols::match::upstream)   WriteUpstreamCoordinateKinemage (protocols::match::output)   
DetectSymmetryMoverCreator (protocols::simple_moves::symmetry)   JumpSampleData (protocols::abinitio::abscript)   PDB (protocols::sparta)   SamplingWeights (protocols::antibody::design)   WriteUpstreamHitKinemage (protocols::match::output)   
DGBindOptEData (protocols::optimize_weights)   JumpSampleDataCreator (protocols::abinitio::abscript)   PdbDataFeatures (protocols::features)   SandwichFeatures (protocols::features::strand_assembly)   WorkUnitBase::WU_Header (protocols::wum)   
DiffAtomSasaFilter (protocols::enzdes)   JumpSelector (protocols::jumping)   PdbDataFeaturesCreator (protocols::features)   SandwichFeaturesCreator (protocols::features::strand_assembly)   WUQueue (protocols::wum2)   
DiffAtomSasaFilterCreator (protocols::enzdes)   JumpSetup (protocols::jumping)   PDBDumpMover (protocols::moves)   SandwichFragment (protocols::features::strand_assembly)   
  X  
DihedralConstraintsScore (protocols::frag_picker::scores)   JumpsFromAllPairings (protocols::jumping)   PdbIdChunkFilter (protocols::frag_picker)   SaneDockingProtocol (protocols::docking::stateless)   
DimerPairing (protocols::fldsgn::topology)   JumpSelector::JumpWeightDef (protocols::jumping)   PDBInputter (protocols::inputter)   SaneMinMover (protocols::simple_moves)   XformScore (protocols::motif_hash)   
DimerPairings (protocols::fldsgn::topology)   
  K  
PDBJobInputter (protocols::jd2)   SaneMinMoverCreator (protocols::simple_moves)   XfoxmScore (protocols::sic_dock)   
DiscreteRandomizer (protocols::genetic_algorithm)   PDBJobInputterCreator (protocols::jd2)   SaveAndRetrieveSidechains (protocols::protein_interface_design::movers)   Xfrag (protocols::motif_hash)   
FragsToAtomDist::DistanceRecord (protocols::noesy_assign)   KCluster (protocols::toolbox)   PDBJobOutputter (protocols::jd2)   SaveAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   XfragSet (protocols::motif_hash)   
DistanceResidueNetwork (protocols::toolbox)   KClusterData (protocols::toolbox)   PDBJobOutputterCreator (protocols::jd2)   SavePoseConstraintToFileFilter (protocols::simple_filters)   Xfres (protocols::motif_hash)   
DistanceScoreMover (protocols::noesy_assign)   KClusterElement (protocols::toolbox)   PDBLandmark (protocols::antibody)   SavePoseConstraintToFileFilterCreator (protocols::simple_filters)   
  Z  
DistributionMap (protocols::ligand_docking)   KicMover (protocols::kinematic_closure)   PdbLogger (protocols::loop_modeling::loggers)   SavePoseMover (protocols::rosetta_scripts)   
DisulfideDistance (protocols::frag_picker::scores)   KinematicAbinitio (protocols::abinitio)   PDBOutput (protocols::dna)   SavePoseMoverCreator (protocols::rosetta_scripts)   ZincHeterodimerMover (protocols::metal_interface)   
DisulfideEntropyFilter (protocols::simple_filters)   KinematicControl (protocols::abinitio)   PDBOutputter (protocols::outputter)   SAXSScoreFilter (protocols::simple_filters)   ZincSiteFinder (protocols::metal_interface)   
DisulfideEntropyFilterCreator (protocols::simple_filters)   KinematicMover (protocols::loops::loop_closure::kinematic_closure)   PDBReloadMover (protocols::simple_moves)   ScaffoldBuildPoint (protocols::match::upstream)   
  _  
DisulfideFilter (protocols::protein_interface_design::filters)   KinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   PDBReloadMoverCreator (protocols::simple_moves)   ScaleAnnealerTemperatureOperation (protocols::optimize_weights)   
DisulfideFilterCreator (protocols::protein_interface_design::filters)   KinematicTaskControl (protocols::abinitio)   PDBTrajectoryRecorder (protocols::canonical_sampling)   ScaleMapIntensities (protocols::electron_density)   _BoolMover (protocols::moves)   
DisulfideIdentity (protocols::frag_picker::scores)   KinematicWrapper (protocols::loops::loop_closure::kinematic_closure)   PDBTrajectoryRecorderCreator (protocols::canonical_sampling)   ScaleMapIntensitiesCreator (protocols::electron_density)   _HashEntry (protocols::abinitio)   
DisulfideMover (protocols::protein_interface_design::movers)   KinFunGroupTK (protocols::kinmatch)   PDBWriter (protocols::match::output)   ScoreCutoffFilter (protocols::simple_filters)   _MergableEntries (protocols::abinitio)   
DisulfideMoverCreator (protocols::protein_interface_design::movers)   KMedoid (protocols::toolbox)   PDDFEnergy (protocols::scoring::methods::saxs)   ScoreCutoffFilterCreator (protocols::simple_filters)   
  a  
DisulfJumpClaimer (protocols::topology_broker)   KRSQuery (protocols::kinmatch)   PDDFEnergyCreator (protocols::scoring::methods::saxs)   ScoreEvaluator (protocols::simple_filters)   
DisulfPairing (protocols::jumping)   
  L  
PDDFScoreFilter (protocols::simple_filters)   ScoreEValuator (protocols::frag_picker::scores)   access_ptr (protocols::jd2::utility::pointer)   
DisulfPairingLibrary (protocols::jumping)   PeakAssignment (protocols::noesy_assign)   ScoreFunctionFeatures (protocols::features)   
  b  
DisulfTemplate (protocols::jumping)   LAMBEGO_IO (protocols::frag_picker)   PeakAssignmentParameters (protocols::noesy_assign)   ScoreFunctionFeaturesCreator (protocols::features)   
DiversifyCrmsdByClustering (protocols::frag_picker)   LAMBEGO_Similarity (protocols::frag_picker::scores)   PeakAssignmentResidueMap (protocols::noesy_assign)   ScoreFunctionLoader (protocols::jd2::parser)   LoopHashMap::by_index (protocols::loophash)   
DiversifyCrmsdSelector (protocols::frag_picker)   LargeFragWeight (protocols::topology_broker::weights)   PeakCalibrator (protocols::noesy_assign)   ScoreFunctionLoaderCreator (protocols::jd2::parser)   
  c  
DiversifyDihedralsSelector (protocols::frag_picker)   LayerDesignOperation (protocols::flxbb)   PeakCalibratorMap (protocols::noesy_assign)   ScoreMap (protocols::jd2)   
DiversifyStoredRBConfs (protocols::enzdes)   LayerDesignOperationCreator (protocols::flxbb)   PeakFileFormat (protocols::noesy_assign)   ScoreMover (protocols::simple_moves)   compare_base_bin (protocols::stepwise::sampling::rna::rigid_body)   
DME_FilterMover (protocols::simple_moves)   LayerOperations (protocols::toolbox::task_operations)   PeakFileFormat_Base (protocols::noesy_assign)   ScoreMoverCreator (protocols::simple_moves)   compare_int_pair (protocols::stepwise::sampling::rna::rigid_body)   
DNABase (protocols::dna)   LazySilentFileJobInputter (protocols::jd2)   PeakFileFormat_Sparky (protocols::noesy_assign)   ScoreNormalization (protocols::qsar::scoring_grid)   
  d  
DNABasepair (protocols::dna)   LazySilentFileJobInputterCreator (protocols::jd2)   PeakFileFormat_xeasy (protocols::noesy_assign)   ScoreOnlyJobOutputter (protocols::jd2)   
DNABasestep (protocols::dna)   LazySortedVector1 (protocols::frag_picker)   PeakFileFormat_xpk (protocols::noesy_assign)   ScoreOnlyJobOutputterCreator (protocols::jd2)   ddG (protocols::simple_moves)   
DnaChains (protocols::dna)   LeapIndex (protocols::loophash)   PeptideStapleDesignMover (protocols::protein_interface_design::movers)   ScoreTypeFeatures (protocols::features)   ddGCreator (protocols::simple_moves)   
DnaDesignDef (protocols::dna)   LegacyKicSampler (protocols::loop_modeling::samplers)   PeptideStapleDesignMoverCreator (protocols::protein_interface_design::movers)   ScoreTypeFeaturesCreator (protocols::features)   ddGData (protocols::ddG)   
DnaInterfaceFinder (protocols::dna)   LegacyLeapIndex (protocols::loophash)   PeptideStapleMover (protocols::simple_moves)   ScoreTypeFilter (protocols::simple_filters)   ddGMover (protocols::ddg)   
DnaInterfaceMinMover (protocols::dna)   LegacyRootClaim (protocols::topology_broker::claims)   PeriodicMover (protocols::loop_modeling::utilities)   ScoreTypeFilterCreator (protocols::simple_filters)   downstream_hit (protocols::match)   
DnaInterfaceMinMoverCreator (protocols::dna)   LHRepulsiveRamp (protocols::antibody)   PerNativeRRReporterHuman (protocols::rotamer_recovery)   ScoreVsRmsd (protocols::loop_modeling::loggers)   
  f  
DnaInterfaceMultiStateDesign (protocols::dna)   LHRepulsiveRampLegacy (protocols::antibody)   PerResidueInterfaceData (protocols::analysis)   ScoringGridLoader (protocols::qsar::scoring_grid)   
DnaInterfaceMultiStateDesignCreator (protocols::dna)   LHSnugFitLegacy (protocols::antibody)   PerturbChiSidechainMover (protocols::simple_moves::sidechain_moves)   ScoringGridLoaderCreator (protocols::qsar::scoring_grid)   find_SilentStructOPs (protocols::wum)   
DnaInterfacePacker (protocols::dna)   Ligand_info (protocols::ligand_docking)   PerturbChiSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   ScoringSecMatchRPE (protocols::match::downstream)   
  h  
DnaInterfacePackerCreator (protocols::dna)   LigandArea (protocols::ligand_docking)   Perturber (protocols::kinematic_closure::perturbers)   ScreeningFeatures (protocols::features)   
DnaNeighbor (protocols::dna)   LigandAreaLoader (protocols::ligand_docking)   PerturberSet (protocols::kinematic_closure::perturbers)   ScreeningFeaturesCreator (protocols::features)   hash_upstream_hit (protocols::match::downstream)   
DNAParameters (protocols::dna)   LigandAreaLoaderCreator (protocols::ligand_docking)   PerturbRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   ScreeningJobInputter (protocols::jd2)   hConvergenceCheck (protocols::abinitio)   
DnaPosition (protocols::dna)   LigandBaseProtocol (protocols::ligand_docking)   PerturbRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   ScreeningJobInputterCreator (protocols::jd2)   hConvergenceCheck (protocols::hybridization)   
DockAndRetrieveSidechains (protocols::protein_interface_design::movers)   LigandConformer (protocols::toolbox::match_enzdes_util)   Phi (protocols::frag_picker::scores)   SearchPattern (protocols::hotspot_hashing)   
  i  
DockAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   LigandConformerBuilder (protocols::match::downstream)   PhiPsiRmsd (protocols::frag_picker::scores)   SearchPatternExpansion (protocols::hotspot_hashing)   
DockDesignFilterFactory (protocols::protein_interface_design)   LigandDesign (protocols::ligand_docking)   PhiPsiSquareWell (protocols::frag_picker::scores)   SearchPatternRotSetOp (protocols::hotspot_hashing)   RemodelMover::instruction_flags (protocols::forge::remodel)   
DockingEnsemble (protocols::docking)   LigandDesignCreator (protocols::ligand_docking)   PhiPsiTalosIO (protocols::frag_picker)   SearchPatternTransform (protocols::hotspot_hashing)   
  m  
DockingEnsemblePrepackProtocol (protocols::docking)   LigandDockMain (protocols::ligand_docking)   PhosphateMove (protocols::stepwise::sampling::rna::phosphate)   SecMatchEvaluatorFactory (protocols::match::downstream)   
DockingHighRes (protocols::docking)   LigandDockProtocol (protocols::ligand_docking)   PhosphateMover (protocols::stepwise::sampling::rna::phosphate)   SecMatchResiduePairEvaluator (protocols::match::downstream)   match_dspos1 (protocols::match)   
DockingHighResFilter (protocols::docking)   LigandMotifSearch (protocols::motifs)   PhosphateScreener (protocols::stepwise::screener)   SecondaryIdentity (protocols::frag_picker::scores)   match_lite_equals (protocols::match)   
DockingHighResLegacy (protocols::docking)   LigandPropertyScore (protocols::qsar::scoring_grid)   PiPiCalculator (protocols::toolbox::pose_metric_calculators)   SecondaryMatcherToDownstreamResidue (protocols::match::downstream)   match_lite_hasher (protocols::match)   
DockingInitialPerturbation (protocols::docking)   LigandPropertyScoreCreator (protocols::qsar::scoring_grid)   PivotPicker (protocols::kinematic_closure::pivot_pickers)   SecondaryMatcherToUpstreamResidue (protocols::match::downstream)   missing_fraction_sorter_biggest_first (protocols::frag_picker::quota)   
DockingInitialPerturbationCreator (protocols::docking)   LigBurialFilter (protocols::enzdes)   PlaceFragments (protocols::seeded_abinitio)   SecondaryMatchProtocol (protocols::enzdes)   motif2scaffold_data (protocols::motif_grafting::movers)   
DockingLowRes (protocols::docking)   LigBurialFilterCreator (protocols::enzdes)   PlacementAuctionMover (protocols::protein_interface_design::movers)   SecondaryMatchUpstreamResProcessor (protocols::match::downstream)   motif2scaffold_indexes (protocols::motif_grafting::movers)   
DockingLowResEnsemble (protocols::docking)   LigDSasaFilter (protocols::enzdes)   PlacementAuctionMoverCreator (protocols::protein_interface_design::movers)   SecondarySimilarity (protocols::frag_picker::scores)   
  n  
DockingLowResFilter (protocols::docking)   LigDSasaFilterCreator (protocols::enzdes)   PlacementMinimizationMover (protocols::protein_interface_design::movers)   SecondaryStructureCountFilter (protocols::fldsgn::filters)   
DockingNoRepack1 (protocols::toolbox::task_operations)   LigInterfaceEnergyFilter (protocols::enzdes)   PlacementMinimizationMoverCreator (protocols::protein_interface_design::movers)   SecondaryStructureCountFilterCreator (protocols::fldsgn::filters)   nmer_svm_res_data (protocols::simple_filters)   
DockingNoRepack2 (protocols::toolbox::task_operations)   LigInterfaceEnergyFilterCreator (protocols::enzdes)   PlaceOnLoop (protocols::protein_interface_design::movers)   SecondaryStructureFilter (protocols::fldsgn::filters)   
  o  
DockingPrepackProtocol (protocols::docking)   LimitAromaChi2_RotamerSetOperation (protocols::toolbox::task_operations)   PlaceOnLoopCreator (protocols::protein_interface_design::movers)   SecondaryStructureFilterCreator (protocols::fldsgn::filters)   
DockingProtocol (protocols::docking)   LimitAromaChi2Operation (protocols::toolbox::task_operations)   PlaceProbeMover (protocols::hotspot_hashing::movers)   SecondaryStructureMPM (protocols::match)   output_data_struct (protocols::stepwise::sampling::rna)   
DockingProtocolCreator (protocols::docking)   LimitAromaChi2OperationCreator (protocols::toolbox::task_operations)   PlaceSimultaneouslyMover (protocols::protein_interface_design::movers)   SecondaryStructurePool (protocols::frag_picker::quota)   
  p  
DockingSlideIntoContact (protocols::docking)   LimitHitsPerRotamerFilter (protocols::match::output)   PlaceSimultaneouslyMoverCreator (protocols::protein_interface_design::movers)   SecondaryStructureSegment (protocols::features)   
CentroidRelax::parameters (protocols::relax)   
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