Rosetta 3.5
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  A  
DistanceFunc (core::scoring::custom_pair_distance)   IterativeOptEDriver (protocols::optimize_weights)   PeakCalibrator (protocols::noesy_assign)   ScoreTypeFilterCreator (protocols::simple_filters)   
DistanceHistogram (core::scoring::saxs)   IterativeVectorExpression (protocols::pack_daemon)   PeakCalibratorMap (protocols::noesy_assign)   ScoreTypeManager (core::scoring)   
A   DistancePairConstraint (core::scoring::constraints)   SilentFileData::iterator (core::io::silent)   PeakFileFormat (protocols::noesy_assign)   ScoringGridLoader (protocols::qsar::scoring_grid)   
A   FragsToAtomDist::DistanceRecord (protocols::noesy_assign)   RawFileData::iterator (core::io::raw_data)   PeakFileFormat_Base (protocols::noesy_assign)   ScoringGridLoaderCreator (protocols::qsar::scoring_grid)   
A   DistanceScoreMover (protocols::noesy_assign)   
  J  
PeakFileFormat_Sparky (protocols::noesy_assign)   ScoringManager (core::scoring)   
A   DistributionMap (protocols::ligand_docking)   PeakFileFormat_xeasy (protocols::noesy_assign)   ScoringScheme (core::sequence)   
A   DisulfideAtomIndices (core::scoring::disulfides)   JCoupling (protocols::frag_picker::scores)   PeakFileFormat_xpk (protocols::noesy_assign)   ScoringSchemeFactory (core::sequence)   
AACompositionEnergy (protocols::fldsgn::potentials)   DisulfideDistance (protocols::frag_picker::scores)   JCouplingIO (protocols::frag_picker)   PeptideBondedEnergyContainer (core::scoring)   ScoringSecMatchRPE (protocols::match::downstream)   
AACompositionEnergyCreator (protocols::fldsgn::potentials)   DisulfideFile (core::io::raw_data)   JD2ResourceManager (protocols::jd2)   PeptideBondedNeighborConstIterator (core::scoring)   SDFParser (core::chemical::sdf)   
Ab_TemplateInfo (protocols::antibody2)   DisulfideFilter (protocols::protein_interface_design::filters)   JD2ResourceManagerCreator (protocols::jd2)   PeptideBondedNeighborIterator (core::scoring)   SearchPattern (protocols::hotspot_hashing)   
ABEGO (core::util)   DisulfideFilterCreator (protocols::protein_interface_design::filters)   JD2ResourceManagerJobInputter (protocols::jd2)   PeptideBondEnergy (core::scoring::methods)   SearchPatternExpansion (protocols::hotspot_hashing)   
ABEGO_SS_Config (protocols::frag_picker::quota)   DisulfideIdentity (protocols::frag_picker::scores)   JD2ResourceManagerJobInputterCreator (protocols::jd2)   PeptideBondEnergyCreator (core::scoring::methods)   SearchPatternRotSetOp (protocols::hotspot_hashing)   
ABEGO_SS_Map (protocols::frag_picker::quota)   DisulfideMatchingDatabase (core::scoring::disulfides)   JJH_Minimizer (core::optimization)   PeptideStapleDesignMover (protocols::protein_interface_design::movers)   SearchPatternTransform (protocols::hotspot_hashing)   
ABEGO_SS_Pool (protocols::frag_picker::quota)   DisulfideMatchingEnergy (core::scoring::disulfides)   Job (protocols::jd2)   PeptideStapleDesignMoverCreator (protocols::protein_interface_design::movers)   SecMatchEvaluatorFactory (protocols::match::downstream)   
ABEGO_SS_Score (protocols::frag_picker::scores)   DisulfideMatchingEnergyComponents (core::scoring::disulfides)   JobDataFeatures (protocols::features)   PeptideStapleMover (protocols::simple_moves)   SecMatchResiduePairEvaluator (protocols::match::downstream)   
ABEGOEval (core::fragment::picking_old::vall::eval)   DisulfideMatchingEnergyContainer (core::scoring::disulfides)   JobDataFeaturesCreator (protocols::features)   PeriodicBoundFunc (core::scoring::constraints)   SecondaryIdentity (protocols::frag_picker::scores)   
ABEGOManager (core::util)   DisulfideMatchingEnergyCreator (core::scoring::disulfides)   JobDistributor (protocols::jd2)   PeriodicFunc (core::scoring::constraints)   SecondaryMatcherToDownstreamResidue (protocols::match::downstream)   
AbinitioBaseFilter (protocols::simple_filters)   DisulfideMatchingNeighborConstIterator (core::scoring::disulfides)   JobDistributorFactory (protocols::jd2)   PerNativeRRReporterHuman (protocols::rotamer_recovery)   SecondaryMatcherToUpstreamResidue (protocols::match::downstream)   
AbinitioMoverWeight (protocols::topology_broker::weights)   DisulfideMatchingNeighborIterator (core::scoring::disulfides)   JobInputter (protocols::jd2)   PerSphereAccumulator (core::scoring::packstat)   SecondaryMatchProtocol (protocols::enzdes)   
AbrelaxApplication (protocols::abinitio)   DisulfideMatchingPotential (core::scoring::disulfides)   JobInputterCreator (protocols::jd2)   PerturbChiSidechainMover (protocols::simple_moves::sidechain_moves)   SecondaryMatchUpstreamResProcessor (protocols::match::downstream)   
AbrelaxMover (protocols::abinitio)   DisulfideMover (protocols::protein_interface_design::movers)   JobInputterFactory (protocols::jd2)   PerturbChiSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   SecondarySimilarity (protocols::frag_picker::scores)   
AbstractArchiveBase (protocols::jd2::archive)   DisulfideMoverCreator (protocols::protein_interface_design::movers)   JobInputterRegistrator (protocols::jd2)   PerturbRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   SecondaryStructure (core::fragment)   
AbstractRotamerTrie (core::conformation)   DisulfJumpClaimer (protocols::topology_broker)   JobOutputter (protocols::jd2)   PerturbRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   SecondaryStructureEnergy (core::scoring::methods)   
access_ptr (utility::pointer)   DisulfMinData (core::scoring::disulfides)   JobOutputterCreator (protocols::jd2)   pHEnergy (core::scoring::methods)   SecondaryStructureEnergyCreator (core::scoring::methods)   
Accumulator (core::scoring::packstat)   DisulfPairing (protocols::jumping)   JobOutputterFactory (protocols::jd2)   pHEnergyCreator (core::scoring::methods)   SecondaryStructureFilter (protocols::fldsgn::filters)   
ActiveSiteGrid (protocols::match::downstream)   DisulfPairingLibrary (protocols::jumping)   JobOutputterRegistrator (protocols::jd2)   Phi (protocols::frag_picker::scores)   SecondaryStructureFilterCreator (protocols::fldsgn::filters)   
AdaptiveScoreHistogram (protocols::frag_picker::scores)   DisulfResNeighbConstIterator (core::scoring::disulfides)   JointScore (protocols::sic_dock)   PhiPsiRmsd (protocols::frag_picker::scores)   SecondaryStructureMPM (protocols::match)   
AddAllPositionsMPM (protocols::match)   DisulfResNeighbIterator (core::scoring::disulfides)   JointSequenceOperation (protocols::toolbox::task_operations)   PhiPsiSquareWell (protocols::frag_picker::scores)   SecondaryStructurePool (protocols::frag_picker::quota)   
AddAssemblyConstraints (protocols::domain_assembly)   DisulfTemplate (protocols::jumping)   JointSequenceOperationCreator (protocols::toolbox::task_operations)   PhiPsiTalosIO (protocols::frag_picker)   SecondaryStructurePotential (core::scoring)   
AddAtom (core::chemical)   DiversifyCrmsdByClustering (protocols::frag_picker)   JScoreEvaluator (protocols::simple_filters)   PIKAA (core::pack::task)   SecondaryStructureSegment (protocols::features)   
AddBehaviorRLT (core::pack::task::operation)   DiversifyCrmsdSelector (protocols::frag_picker)   JScoreEvaluatorCreator (protocols::simple_filters)   PIKNA (core::pack::task)   SecondaryStructureSegmentFeatures (protocols::features)   
AddBehaviorRLTCreator (core::pack::task::operation)   DiversifyDihedralsSelector (protocols::frag_picker)   JSONFormattedLoopsFileReader (protocols::loops)   PIKRNA (core::pack::task)   SecondaryStructureSegmentFeaturesCreator (protocols::features)   
AddBond (core::chemical)   DiversifyStoredRBConfs (protocols::enzdes)   Jump (core::kinematics)   PiPiCalculator (protocols::toolbox::pose_metric_calculators)   SecondaryStructureWeights (core::scoring)   
AddCavitiesMover (protocols::simple_moves)   DME_FilterMover (protocols::simple_moves)   Jump_point (protocols::swa::rna)   PlaceFragments (protocols::seeded_abinitio)   SecStructGen (core::fragment::picking_old::vall::gen)   
AddChainBreak (protocols::protein_interface_design::movers)   DNA_BaseEnergy (core::scoring::methods)   JumpAtom (core::kinematics::tree)   PlacementAuctionMover (protocols::protein_interface_design::movers)   SecstructSRFD (core::fragment)   
AddChainBreakCreator (protocols::protein_interface_design::movers)   DNA_BaseEnergyCreator (core::scoring::methods)   RigidChunkClaimer::JumpCalculator (protocols::topology_broker)   PlacementAuctionMoverCreator (protocols::protein_interface_design::movers)   SeedFoldTree (protocols::seeded_abinitio)   
AddChi (core::chemical)   DNA_BasePotential (core::scoring::dna)   JumpClaim (protocols::topology_broker)   PlacementMinimizationMover (protocols::protein_interface_design::movers)   SeedFoldTreeCreator (protocols::seeded_abinitio)   
AddChiRotamer (core::chemical)   DNABase (protocols::dna)   JumpClaimer (protocols::topology_broker)   PlacementMinimizationMoverCreator (protocols::protein_interface_design::movers)   SeedSetupMover (protocols::seeded_abinitio)   
AddConnect (core::chemical)   DNABasepair (protocols::dna)   ResiduePairJumpSetup::JumpDef (protocols::jumping)   PlaceOnLoop (protocols::protein_interface_design::movers)   SeedSetupMoverCreator (protocols::seeded_abinitio)   
AddConstraintsToCurrentConformationMover (protocols::simple_moves)   DNABasestep (protocols::dna)   JumpSetup::JumpDef (protocols::jumping)   PlaceOnLoopCreator (protocols::protein_interface_design::movers)   Segment (protocols::forge::remodel)   
AddConstraintsToCurrentConformationMoverCreator (protocols::simple_moves)   DNABFormPotential (core::scoring::dna)   JumpEvaluator (protocols::simple_filters)   PlaceProbeMover (protocols::hotspot_hashing::movers)   SegmentHybridizer (protocols::seeded_abinitio)   
AddEdgeVisitor (core::conformation)   DnaChains (protocols::dna)   JumpID (core::id)   PlaceSimultaneouslyMover (protocols::protein_interface_design::movers)   SegmentHybridizerCreator (protocols::seeded_abinitio)   
addedH (core::chemical::sdf)   DNAChiEnergy (core::scoring::dna)   JumpingFoldConstraints (protocols::abinitio)   PlaceSimultaneouslyMoverCreator (protocols::protein_interface_design::movers)   SegmentInsert (protocols::forge::build)   
AddHydrogen (protocols::ligand_docking)   DNAChiEnergyCreator (core::scoring::dna)   JumpingFoldConstraintsWrapper (protocols::abinitio)   PlaceStubMover (protocols::protein_interface_design::movers)   SegmentRebuild (protocols::forge::build)   
AddHydrogens (protocols::ligand_docking)   DnaDesignDef (protocols::dna)   JumpingFrame (core::fragment)   PlaceStubMoverCreator (protocols::protein_interface_design::movers)   SegmentSwap (protocols::forge::build)   
AddHydrogensCreator (protocols::ligand_docking)   DnaInterfaceFinder (protocols::dna)   JumpNrEvaluator (protocols::simple_filters)   PlaceSurfaceProbe (protocols::hotspot_hashing::movers)   SelectBySASAOperation (protocols::toolbox::task_operations)   
AdditionalBackgroundNodesInteractionGraph (core::pack::interaction_graph)   DnaInterfaceMinMover (protocols::dna)   JumpNrEvaluatorCreator (protocols::simple_filters)   PlaceSurfaceProbeCreator (protocols::hotspot_hashing::movers)   SelectBySASAOperationCreator (protocols::toolbox::task_operations)   
AddLigandMotifRotamers (protocols::enzdes)   DnaInterfaceMinMoverCreator (protocols::dna)   JumpOutMover (protocols::moves)   PlaidFingerprint (protocols::pockets)   SelectedResPredicate (core::scoring)   
AddLigandMotifRotamersOperationCreator (protocols::enzdes)   DnaInterfaceMultiStateDesign (protocols::dna)   JumpRotamerSidechainMover (protocols::simple_moves::sidechain_moves)   PlainPdbJobDistributor (protocols::jobdist)   SelectGdtEvaluator (protocols::simple_filters)   
AddOrRemoveMatchCsts (protocols::enzdes)   DnaInterfaceMultiStateDesignCreator (protocols::dna)   JumpRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves)   PlainRawJobDistributor (protocols::jobdist)   SelectMaxsubEvaluator (protocols::simple_filters)   
AddOrRemoveMatchCstsCreator (protocols::enzdes)   DnaInterfacePacker (protocols::dna)   JumpSample (protocols::jumping)   PlainSilentFileJobDistributor (protocols::jobdist)   Selector_AA (core::chemical)   
AddProperty (core::chemical)   DnaInterfacePackerCreator (protocols::dna)   JumpSelector (protocols::jumping)   PNatAAOptEPositionData (protocols::optimize_weights)   Selector_CMDFLAG (core::chemical)   
AddProtonChi (core::chemical)   DnaNeighbor (protocols::dna)   JumpSetup (protocols::jumping)   PNatAAOptERotamerData (protocols::optimize_weights)   Selector_MATCH_VARIANTS (core::chemical)   
AddRigidBodyLigandConfs (protocols::enzdes)   DNAParameters (protocols::dna)   JumpsFromAllPairings (protocols::jumping)   PNatLigPoseOptEData (protocols::optimize_weights)   Selector_NAME1 (core::chemical)   
AddRigidBodyLigandConfsCreator (protocols::enzdes)   DnaPosition (protocols::dna)   JumpSelector::JumpWeightDef (protocols::jumping)   PNatRotOptEPositionData (protocols::optimize_weights)   Selector_NAME3 (core::chemical)   
AddSearchPatternRotSetOp (protocols::hotspot_hashing)   DNATorsionEnergy (core::scoring::dna)   
  K  
PNatRotOptERotamerData (protocols::optimize_weights)   Selector_NO_VARIANTS (core::chemical)   
AddSidechainConstraintsToHotspots (protocols::protein_interface_design::movers)   DNATorsionEnergyCreator (core::scoring::dna)   PNatStructureOptEData (protocols::optimize_weights)   Selector_PROPERTY (core::chemical)   
AddSidechainConstraintsToHotspotsCreator (protocols::protein_interface_design::movers)   DNATorsionPotential (core::scoring::dna)   KarplusFunc (core::scoring::constraints)   PocketConstraint (protocols::pockets)   Selector_VARIANT_TYPE (core::chemical)   
Adduct (core::chemical)   DockAndRetrieveSidechains (protocols::protein_interface_design::movers)   KCluster (protocols::toolbox)   PocketConstraintCreator (protocols::pockets)   SelectRDC_Evaluator (protocols::simple_filters)   
AlaScan (protocols::simple_filters)   DockAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   KClusterData (protocols::toolbox)   PocketGrid (protocols::pockets)   SelectResiduesByLayer (protocols::toolbox)   
AlaScanFilterCreator (protocols::simple_filters)   DockDesignFilterFactory (protocols::protein_interface_design)   KClusterElement (protocols::toolbox)   Point (core::scoring::packstat)   SelectRmsdEvaluator (protocols::simple_filters)   
Align_RmsdEvaluator (protocols::comparative_modeling)   DockDesignParser (protocols::jd2)   KinematicAbinitio (protocols::abinitio)   PointGraphEdgeData (core::conformation)   SelfNeighInfo (core::scoring)   
Align_RotamerEvaluator (protocols::comparative_modeling)   DockingEnsemble (protocols::docking)   KinematicControl (protocols::abinitio)   PointGraphVertexData (core::conformation)   SemiExplicitWaterUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   
Aligner (core::sequence)   DockingEnsemblePrepackProtocol (protocols::docking)   KinematicMover (protocols::loops::loop_closure::kinematic_closure)   PointMutationCalculator (protocols::design_opt)   SemiRotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)   
AlignerFactory (core::sequence)   DockingHighRes (protocols::docking)   KinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   PointMutScanDriver (protocols::pmut_scan)   SeparateDnaFromNonDna (protocols::dna)   
AlignEvaluator (protocols::evaluation)   DockingHighResFilter (protocols::docking)   KinematicTaskControl (protocols::abinitio)   PointPair (core::scoring::packstat)   SeparateDnaFromNonDnaCreator (protocols::dna)   
AlignmentCluster (protocols::comparative_modeling)   DockingHighResLegacy (protocols::docking)   KinematicWrapper (protocols::loops::loop_closure::kinematic_closure)   PoissonBoltzmannEnergy (core::scoring::methods)   SeqprofConsensusOperation (protocols::toolbox::task_operations)   
AlignmentClustering (protocols::comparative_modeling)   DockingInitialPerturbation (protocols::docking)   KinFunGroupTK (protocols::kinmatch)   PoissonBoltzmannEnergyCreator (core::scoring::methods)   SeqprofConsensusOperationCreator (protocols::toolbox::task_operations)   
AlignmentID (protocols::id)   DockingInitialPerturbationCreator (protocols::docking)   KMedoid (protocols::toolbox)   PoissonBoltzmannPotential (core::scoring)   Sequence (core::sequence)   
AlignmentSet (protocols::comparative_modeling)   DockingLowRes (protocols::docking)   KofNConstraint (core::scoring::constraints)   POLAR (core::pack::task)   SequenceAlignment (core::sequence)   
AlignPoseToInvrotTreeMover (protocols::toolbox::match_enzdes_util)   DockingLowResEnsemble (protocols::docking)   KofNConstraintCreator (core::scoring::constraints)   Policy (protocols::nonlocal)   SequenceAlignmentHasher (core::sequence)   
AlignRmsdTargetEvaluatorCreator (protocols::comparative_modeling)   DockingLowResFilter (protocols::docking)   KromerMann (core::scoring::electron_density)   PolicyFactory (protocols::nonlocal)   SequenceClaim (protocols::topology_broker)   
ALLAA (core::pack::task)   DockingNoRepack1 (protocols::toolbox::task_operations)   KRSQuery (protocols::kinmatch)   Poly (protocols::sasa_scores)   SequenceClaimer (protocols::topology_broker)   
ALLAAwc (core::pack::task)   DockingNoRepack1 (core::pack::task::operation)   
  L  
Polynomial_1d (core::scoring::hbonds)   SequenceComparison (protocols::toolbox::pose_metric_calculators)   
ALLAAxc (core::pack::task)   DockingNoRepack2 (protocols::toolbox::task_operations)   Pool_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   SequenceCoupling (core::sequence)   
AllowedSeqposForGeomCst (protocols::toolbox::match_enzdes_util)   DockingNoRepack2 (core::pack::task::operation)   L1ScoringScheme (core::sequence)   Pool_Evaluator (protocols::canonical_sampling::mc_convergence_checks)   SequenceCoupling1BDConstraint (protocols::constraints_additional)   
AllowInsert (protocols::toolbox)   DockingPrepackProtocol (protocols::docking)   LAMBEGO_IO (protocols::frag_picker)   Pool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   SequenceCoupling1BDConstraintCreator (protocols::constraints_additional)   
AllowPdbIdFilter (protocols::frag_picker)   DockingProtocol (protocols::docking)   LAMBEGO_Similarity (protocols::frag_picker::scores)   PoolData (protocols::canonical_sampling::mc_convergence_checks)   SequenceCouplingConstraint (protocols::constraints_additional)   
AllResFilter (core::pack::task::operation)   DockingProtocolCreator (protocols::docking)   LargeFragWeight (protocols::topology_broker::weights)   PoolEvaluatorCreator (protocols::simple_filters)   SequenceCouplingConstraintCreator (protocols::constraints_additional)   
AllResFilterCreator (core::pack::task::operation)   DockingScoreFunction (core::scoring)   LayerDesignOperation (protocols::flxbb)   Pose (core::pose)   SequenceCouplingCreator (core::sequence)   
AllResiduesChanged (protocols::abinitio)   DockingSlideIntoContact (protocols::docking)   LayerDesignOperationCreator (protocols::flxbb)   pose_data_struct2 (protocols::swa::rna)   SequenceCreator (core::sequence)   
AllResiduesChanged (protocols::hybridization)   DockMCMCycle (protocols::docking)   LayerOperations (protocols::toolbox::task_operations)   PoseBalls (core::scoring::packing)   SequenceDependentRefEnergy (core::scoring::methods)   
Alternating   DockMCMProtocol (protocols::docking)   LazyEdge (core::pack::interaction_graph)   PoseBallsLite (core::scoring::packing)   SequenceDependentRefEnergyCreator (core::scoring::methods)   
AlternativePairings (protocols::abinitio)   DockMinMover (protocols::docking)   LazyInteractionGraph (core::pack::interaction_graph)   PoseCommentsFeatures (protocols::features)   SequenceFactory (core::sequence)   
AlterSpecDisruptionDriver (protocols::pmut_scan)   DockSetupMover (protocols::docking)   LazyNode (core::pack::interaction_graph)   PoseCommentsFeaturesCreator (protocols::features)   SequenceIdentity (protocols::frag_picker::scores)   
AmberPeriodicFunc (core::scoring::constraints)   DockSetupMoverCreator (protocols::docking)   LazySilentFileJobInputter (protocols::jd2)   PoseCondition (protocols::moves)   SequenceMapping (core::id)   
AmbigCSScore (protocols::frag_picker::scores)   DockTaskFactory (protocols::docking)   LazySilentFileJobInputterCreator (protocols::jd2)   PoseConformationFeatures (protocols::features)   SequenceMover (protocols::moves)   
AmbiguousConstraint (core::scoring::constraints)   DOF_Constraint (core::scoring::constraints)   LazySilentFilePoseInputStream (core::import_pose::pose_stream)   PoseConformationFeaturesCreator (protocols::features)   SequenceProfile (core::sequence)   
AmbiguousConstraintCreator (core::scoring::constraints)   DOF_DataPoint (core::optimization)   LazySortedVector1 (protocols::frag_picker)   PoseEvaluator (protocols::evaluation)   SequenceProfileConstraint (core::scoring::constraints)   
AmbiguousMultiConstraint (protocols::constraints_additional)   DOF_ID (core::id)   lbfgs_iteration_data (core::optimization)   PoseFilter (protocols::swa)   SequenceProfileConstraintCreator (core::scoring::constraints)   
AmbiguousNMRConstraint (core::scoring::constraints)   DOF_ID_Map (core::id)   LeapIndex (protocols::loophash)   PoseFilter_RMSD_Screen (protocols::swa)   SequenceProfileCreator (core::sequence)   
AmbiguousNMRConstraintCreator (core::scoring::constraints)   DOF_ID_Range (core::id)   LeeRichards (core::scoring::packstat)   PoseFoundResiduesCombination (protocols::enzdes)   SequenceProfileMover (protocols::simple_moves)   
AmbiguousNMRDistanceConstraint (core::scoring::constraints)   DOF_Node (core::optimization)   LegacyLeapIndex (protocols::loophash)   PoseFromPDBLoader (core::import_pose)   SequenceProfileMoverCreator (protocols::simple_moves)   
AmbiguousNMRDistanceConstraintCreator (core::scoring::constraints)   DofClaim (protocols::topology_broker)   LengthEvent (core::conformation::signals)   PoseFromPDBLoaderCreator (core::import_pose)   SequenceRecoveryFilter (protocols::protein_interface_design::filters)   
AminoAcidNeighborSparseMatrix (core::pack::interaction_graph)   DOFHistogramRecorder (protocols::simple_moves)   LengthEventCollector (core::pose::datacache)   PoseInfoFilter (protocols::simple_filters)   SequenceRecoveryFilterCreator (protocols::protein_interface_design::filters)   
An   DomainAssembly (protocols::abinitio)   LengthGen (core::fragment::picking_old::vall::gen)   PoseInfoFilterCreator (protocols::simple_filters)   SequenceRegistrator (core::sequence)   
An   DomainAssembly (protocols::hybridization)   LHRepulsiveRamp (protocols::antibody2)   PoseInputStream (core::import_pose::pose_stream)   SequenceShiftMover (protocols::rbsegment_relax)   
AnalyticEtableEnergy (core::scoring::etable)   DomainAssemblyCreator (protocols::abinitio)   LHRepulsiveRampLegacy (protocols::antibody2)   PoseInputStreamJobInputter (protocols::jd2)   SequentialSymmetrySlider (protocols::simple_moves::symmetry)   
AnalyticEtableEvaluator (core::scoring::etable)   DotSphere (core::pack::interaction_graph)   LHSnugFitLegacy (protocols::antibody2)   PoseInputStreamJobInputterCreator (protocols::jd2)   SerializedLoop (protocols::loops)   
Anchor (protocols::anchored_design)   DoubleDenseIGRepacker (protocols::pack_daemon)   Librarian (core::fragment::picking_old::concepts)   PoseInserter (protocols::match::output)   SetAACompositionPotential (protocols::fldsgn::potentials)   
Anchor_ribose_stub (protocols::swa::rna)   DoubleDensePDEdge (core::pack::interaction_graph)   Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary (core::fragment::picking_old::concepts)   PoseMatchOutputWriter (protocols::match::output)   SetAACompositionPotentialCreator (protocols::fldsgn::potentials)   
AnchoredDesignMover (protocols::anchored_design)   DoubleDensePDInteractionGraph (core::pack::interaction_graph)   Library (core::fragment::picking_old::concepts)   PoseMetricCalculator (core::pose::metrics)   SetAtomicCharge (core::chemical)   
AnchoredGraftMover (protocols::grafting)   DoubleDensePDNode (core::pack::interaction_graph)   Library_VallSections (core::fragment::picking_old::concepts)   PoseMetricContainer (core::pose::metrics)   SetAtomTree (protocols::protein_interface_design::movers)   
AnchoredPerturbMover (protocols::anchored_design)   DoubleLayerKinematicAbinitio (protocols::abinitio)   Ligand_info (protocols::ligand_docking)   PoseMetricEvaluator (protocols::simple_filters)   SetAtomTreeCreator (protocols::protein_interface_design::movers)   
AnchoredRefineMover (protocols::anchored_design)   DoubleLazyEdge (core::pack::interaction_graph)   LigandArea (protocols::ligand_docking)   PoseNumberedLoopFileReader (protocols::loops)   SetAtomType (core::chemical)   
AnchorMoversData (protocols::anchored_design)   DoubleLazyInteractionGraph (core::pack::interaction_graph)   LigandAreaLoader (protocols::ligand_docking)   PoseOutputStream (core::import_pose::pose_stream)   SetBackboneHeavyatom (core::chemical)   
AngleConstraint (core::scoring::constraints)   DoubleLazyNode (core::pack::interaction_graph)   LigandAreaLoaderCreator (protocols::ligand_docking)   PosePackData (core::scoring::packstat)   SetCatalyticResPackBehavior (protocols::enzdes)   
AngleConstraintCreator (core::scoring::constraints)   DownJumpSRFD (core::fragment)   LigandBaseProtocol (protocols::ligand_docking)   PositionConservedResiduesStore (core::pose::datacache)   SetCatalyticResPackBehaviorCreator (protocols::enzdes)   
ANN (protocols::sparta)   downstream_hit (protocols::match)   LigandConformer (protocols::toolbox::match_enzdes_util)   PositionDdGInfo (core::io::PositionDdGInfo)   SetChiMover (protocols::simple_moves::sidechain_moves)   
AnnealerFactory (core::pack::annealer)   DownstreamAlgorithm (protocols::match::downstream)   LigandConformerBuilder (protocols::match::downstream)   PositionSpecificRandomizer (protocols::genetic_algorithm)   SetChiMoverCreator (protocols::simple_moves::sidechain_moves)   
AnnotatedFragData (core::fragment)   DownstreamBuilder (protocols::match::downstream)   LigandDesign (protocols::ligand_docking)   PositionType (protocols::dna)   SetICoor (core::chemical)   
AnnotatedSequence (core::sequence)   DownstreamCoordinateKinemageWriter (protocols::match::output)   LigandDesignCreator (protocols::ligand_docking)   PostDockAssemblyScorer (protocols::domain_assembly)   SetIGTypeOperation (protocols::toolbox::task_operations)   
Antibody (protocols::antibody)   DownstreamRMSEvaluator (protocols::match::output)   LigandDockMain (protocols::ligand_docking)   PosType (protocols::multistate_design)   SetIGTypeOperationCreator (protocols::toolbox::task_operations)   
AntibodyInfo (protocols::antibody2)   DP_Matrix (core::sequence)   LigandDockProtocol (protocols::ligand_docking)   PosTypeCreator (protocols::multistate_design)   SetIO_String (core::chemical)   
AntibodyModeler (protocols::antibody)   DPScoringScheme (core::sequence)   LigandMotifSearch (protocols::motifs)   PowExpression (protocols::pack_daemon)   SetMMAtomType (core::chemical)   
AntibodyModelerProtocol (protocols::antibody2)   DS_Node (core::graph)   LigBurialFilter (protocols::enzdes)   PPoly (protocols::sasa_scores)   SetNbrAtom (core::chemical)   
AnyResFilter (core::pack::task::operation)   Dssp (core::scoring::dssp)   LigBurialFilterCreator (protocols::enzdes)   PQR (core::scoring)   SetNbrRadius (core::chemical)   
AnyResFilterCreator (core::pack::task::operation)   DsspMover (protocols::moves)   LigDSasaFilter (protocols::enzdes)   PrecomputedFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   SetOrientAtom (core::chemical)   
APBSConfig (core::scoring)   DsspMoverCreator (protocols::moves)   LigDSasaFilterCreator (protocols::enzdes)   PrecomputedPairEnergiesEdge (core::pack::interaction_graph)   SetPolymerConnectAtom (core::chemical)   
APBSResult (core::scoring)   DummyClass (protocols::toolbox)   LigInterfaceEnergyFilter (protocols::enzdes)   PrecomputedPairEnergiesInteractionGraph (core::pack::interaction_graph)   SetReturningPackRotamersMover (protocols::simple_moves)   
APBSWrapper (core::scoring)   DumpPdb (protocols::simple_moves)   LigInterfaceEnergyFilterCreator (protocols::enzdes)   PrecomputedPairEnergiesNode (core::pack::interaction_graph)   SetRotamerCouplings (core::pack::task::operation)   
APCluster (protocols::cluster)   DumpPdbCreator (protocols::simple_moves)   LimitAromaChi2_RotamerSetOperation (protocols::toolbox::task_operations)   PredesignPerturbMover (protocols::enzdes)   SetRotamerCouplingsCreator (core::pack::task::operation)   
APOLA (core::pack::task)   DunbrackConstraint (core::pack::dunbrack)   LimitAromaChi2Operation (protocols::toolbox::task_operations)   PredesignPerturbMoverCreator (protocols::enzdes)   SetRotamerLinks (core::pack::task::operation)   
APOLAR (core::pack::task)   DunbrackConstraintCreator (core::pack::dunbrack)   LimitAromaChi2OperationCreator (protocols::toolbox::task_operations)   Predicate (core::scoring)   SetRotamerLinksCreator (core::pack::task::operation)   
AppendMainchainAtom (core::chemical)   DunbrackEnergy (core::pack::dunbrack)   LimitHitsPerRotamerFilter (protocols::match::output)   PredictedBurialEvaluator (protocols::simple_filters)   SetSecStructEnergies (protocols::fldsgn::potentials)   
AppendResidueRotamerSet (core::pack::task::operation)   DunbrackEnergyCreator (core::pack::dunbrack)   Line (core::util)   PredictedBurialFnEvaluatorCreator (protocols::simple_filters)   SetSecStructEnergiesCreator (protocols::fldsgn::potentials)   
AppendResidueRotamerSetCreator (core::pack::task::operation)   DunbrackRotamer (core::pack::dunbrack)   LinearChainbreakEnergy (core::scoring::methods)   PrepackMover (protocols::protein_interface_design::movers)   SetTemperatureFactor (protocols::protein_interface_design::movers)   
AppendRotamer (core::pack::task::operation)   DunbrackRotamerMeanSD (core::pack::dunbrack)   LinearChainbreakEnergyCreator (core::scoring::methods)   PrepackMoverCreator (protocols::protein_interface_design::movers)   SetTemperatureFactorCreator (protocols::protein_interface_design::movers)   
AppendRotamerCreator (core::pack::task::operation)   DunbrackRotamerSampleData (core::pack::dunbrack)   LinearFunc (protocols::moves)   PrependMainchainAtom (core::chemical)   SetTorsion (protocols::simple_moves)   
AppendRotamerSet (core::pack::task::operation)   DunbrackSCSampler (protocols::match::upstream)   LinearMemEdge (core::pack::interaction_graph)   PreserveCBeta (core::pack::task::operation)   SetTorsionCreator (protocols::simple_moves)   
AppendRotamerSetCreator (core::pack::task::operation)   DynamicAggregateFunction (protocols::pack_daemon)   LinearMemNode (core::pack::interaction_graph)   PreserveCBetaCreator (core::pack::task::operation)   SetupForDensityScoringMover (protocols::electron_density)   
ApplyRandomStoredRBConf (protocols::enzdes)   
  E  
LinearMemoryInteractionGraph (core::pack::interaction_graph)   PreventChainFromRepackingOperation (protocols::toolbox::task_operations)   SetupForDensityScoringMoverCreator (protocols::electron_density)   
ArchiveBase (protocols::jd2::archive)   LinearPenaltyFunction (core::scoring::constraints)   PreventChainFromRepackingOperationCreator (protocols::toolbox::task_operations)   SetupForFibrilMover (protocols::fibril)   
ArchiveManager (protocols::jd2::archive)   Edge (core::kinematics)   LineMinimizationAlgorithm (core::optimization)   PreventRepacking (core::pack::task::operation)   SetupForSymmetryMover (protocols::simple_moves::symmetry)   
ArchiveMasterBase (protocols::mpi)   Edge (core::graph)   LineObject (protocols::forge::remodel)   PreventRepackingCreator (core::pack::task::operation)   SetupForSymmetryMoverCreator (protocols::simple_moves::symmetry)   
AreaAccumulator (core::scoring::packstat)   EdgeBase (core::pack::interaction_graph)   LinkerScore (protocols::sic_dock)   PreventRepackingRLT (core::pack::task::operation)   SetupHotspotConstraintsLoopsMover (protocols::protein_interface_design::movers)   
ArmijoLineMinimization (core::optimization)   EdgeList (core::graph)   LinkInformation (core::io::pdb)   PreventRepackingRLTCreator (core::pack::task::operation)   SetupHotspotConstraintsLoopsMoverCreator (protocols::protein_interface_design::movers)   
Array0 (core::graph)   EdgeListConstIterator (core::graph)   LK_BallEnergy (core::scoring::methods)   PreventResiduesFromRepackingOperation (protocols::toolbox::task_operations)   SetupHotspotConstraintsMover (protocols::protein_interface_design::movers)   
Array2D (core::scoring::packstat)   EdgeListElement (core::graph)   LK_BallEnergyCreator (core::scoring::methods)   PreventResiduesFromRepackingOperationCreator (protocols::toolbox::task_operations)   SetupHotspotConstraintsMoverCreator (protocols::protein_interface_design::movers)   
ArrayPool (core::graph)   EdgeListIterator (core::graph)   LK_CosThetaEnergy (core::scoring::methods)   ProbSortClass (core::pack::dunbrack)   SetupNCSMover (protocols::simple_moves::symmetry)   
ArrayPoolElement (core::graph)   EdgeStandScore (protocols::sic_dock)   LK_CosThetaEnergyCreator (core::scoring::methods)   ProcessorFactory (protocols::match::output)   SetupNCSMoverCreator (protocols::simple_moves::symmetry)   
AssembleLinkerMover (protocols::domain_assembly)   EggshellGrid (protocols::pockets)   LK_hack (core::scoring::methods)   ProClosureEnergy (core::scoring::methods)   SetupPoissonBoltzmannPotential (protocols::pb_potential)   
AssignOrbitals (core::chemical::orbitals)   EItem (core::optimization)   LK_hackCreator (core::scoring::methods)   ProClosureEnergyCreator (core::scoring::methods)   SetupPoissonBoltzmannPotentialCreator (protocols::pb_potential)   
AssignToClustersMover (protocols::cluster)   ElecAtom (core::scoring::hackelec)   LK_SigmoidalFunc (core::scoring::methods)   ProfilerMover (protocols::moves)   SF_Replica (protocols::toolbox)   
AsymFoldandDockClaimer (protocols::topology_broker)   ElecDensAllAtomCenEnergy (core::scoring::electron_density)   LKB_ResidueInfo (core::scoring::methods)   ProfileScore (protocols::frag_picker::scores)   SG_Dist_Func (core::scoring::disulfides)   
AsymFoldandDockMoveRbJumpMover (protocols::simple_moves::asym_fold_and_dock)   ElecDensAllAtomCenEnergyCreator (core::scoring::electron_density)   LKB_ResiduesInfo (core::scoring::methods)   ProfileScoreBlosum62 (protocols::frag_picker::scores)   SGSG_Dihedral_Func (core::scoring::disulfides)   
AsymFoldandDockRbTrialMover (protocols::simple_moves::asym_fold_and_dock)   ElecDensAtomwiseEnergy (core::scoring::electron_density_atomwise)   LnExpression (protocols::pack_daemon)   ProfileScoreDistWeight (protocols::frag_picker::scores)   ShakeStructureMover (protocols::simple_moves)   
Atom (core::conformation)   ElecDensAtomwiseEnergyCreator (core::scoring::electron_density_atomwise)   LoadPDBMover (protocols::simple_moves)   ProfileScoreL1 (protocols::frag_picker::scores)   ShapeComplementarityCalculator (core::scoring::sc)   
Atom (core::kinematics::tree)   ElecDensCenEnergy (core::scoring::electron_density)   LoadPDBMoverCreator (protocols::simple_moves)   ProfileScoreStructL1 (protocols::frag_picker::scores)   ShapeComplementarityCalculatorException (core::scoring::sc)   
Atom (core::scoring::sc)   ElecDensCenEnergyCreator (core::scoring::electron_density)   LoadUnboundRotMover (protocols::simple_moves)   ProfileScoreSubMatrix (protocols::frag_picker::scores)   ShapeComplementarityFilter (protocols::simple_filters)   
Atom (core::chemical)   ElecDensEnergy (core::scoring::electron_density)   LoadUnboundRotMoverCreator (protocols::simple_moves)   ProfSimScoringScheme (core::sequence)   ShapeComplementarityFilterCreator (protocols::simple_filters)   
Atom_ (core::kinematics::tree)   ElecDensEnergyCreator (core::scoring::electron_density)   LocalCoordinateConstraint (core::scoring::constraints)   ProlineFixMover (protocols::simple_moves)   SharedSilentData (core::io::silent)   
Atom_Bin (protocols::swa::rna)   ElectronDensity (core::scoring::electron_density)   LocalCoordinateConstraintCreator (core::scoring::constraints)   ProlinePhiScore (protocols::frag_picker::scores)   ShearMinCCDTrial (protocols::loops::loop_mover::refine)   
AtomAngleSecMatchRPE (protocols::match::downstream)   ElectronDensityAtomwise (core::scoring::electron_density_atomwise)   LocalInserter (protocols::loophash)   ProteinBackboneAtomAtomPairFeatures (protocols::features)   ShearMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
AtomAtomPairFeatures (protocols::features)   ElectronDensityLoader (core::scoring::electron_density)   LocalInserter_SimpleMin (protocols::loophash)   ProteinBackboneAtomAtomPairFeaturesCreator (protocols::features)   ShearMover (protocols::simple_moves)   
AtomAtomPairFeaturesCreator (protocols::features)   ElectronDensityLoaderCreator (core::scoring::electron_density)   LoggedFragmentMover (protocols::simple_moves)   ProteinBackboneBuildPoint (protocols::match::upstream)   ShearMoverCreator (protocols::simple_moves)   
AtomBasedConstraintsScore (protocols::frag_picker::scores)   ElectronDensityOptions (core::scoring::electron_density)   LongRangeTwoBodyEnergy (core::scoring::methods)   ProteinBackboneTorsionAngleFeatures (protocols::features)   Sheet (protocols::fldsgn::topology)   
AtomCountFilter (protocols::ligand_docking)   ElectronDensityOptionsCreator (core::scoring::electron_density)   Loop (protocols::loops)   ProteinBackboneTorsionAngleFeaturesCreator (protocols::features)   SheetBuilder (protocols::jumping)   
AtomCountFilterCreator (protocols::ligand_docking)   Element (core::chemical)   Loop (protocols::fldsgn::topology)   ProteinBondGeometryFeatures (protocols::features)   SheetConstraintsRCG (protocols::fldsgn)   
AtomDihedralSecMatchRPE (protocols::match::downstream)   ElementSet (core::chemical)   Loop_lt (protocols::loops)   ProteinBondGeometryFeaturesCreator (protocols::features)   SheetCstGeneratorCreator (protocols::fldsgn)   
AtomDistanceSecMatchRPE (protocols::match::downstream)   elementToType (core::chemical::sdf)   LoopAnalyzerMover (protocols::analysis)   ProteinCore (protocols::toolbox::task_operations)   SheetFilter (protocols::simple_filters)   
AtomGeometrySecMatchRPE (protocols::match::downstream)   EMapVector (core::scoring)   LoopAnchorFeatures (protocols::features)   ProteinCoreFilterCreator (protocols::toolbox::task_operations)   SheetFoldTypeManager (protocols::fldsgn::topology)   
AtomGraphEdgeData (core::conformation)   EMPTY (core::pack::task)   LoopAnchorFeaturesCreator (protocols::features)   ProteinInterfaceDesignOperation (protocols::toolbox::task_operations)   SheetSet (protocols::fldsgn::topology)   
AtomGraphVertexData (core::conformation)   EmptyVertexData (protocols::toolbox::pose_metric_calculators)   LoopBuildMover (protocols::loop_build)   ProteinInterfaceDesignOperationCreator (protocols::toolbox::task_operations)   SheetTopologyFilter (protocols::fldsgn::filters)   
AtomicContactCountFilter (protocols::protein_interface_design::filters)   EndPoint (protocols::wum2)   LoopClosure (protocols::loops::loop_closure::ccd)   ProteinInterfaceMultiStateDesignMover (protocols::protein_interface_design::movers)   SheetTopologyFilterCreator (protocols::fldsgn::filters)   
AtomicContactCountFilterCreator (protocols::protein_interface_design::filters)   Energies (core::scoring)   LoopFinder (protocols::protein_interface_design::movers)   ProteinInterfaceMultiStateDesignMoverCreator (protocols::protein_interface_design::movers)   SheetTranslate (protocols::nonlocal)   
AtomicContactFilter (protocols::simple_filters)   EnergiesData (protocols::toolbox::pose_metric_calculators)   LoopFinderCreator (protocols::protein_interface_design::movers)   ProteinLigandInterfaceUpweighter (protocols::enzdes)   ShortestPathInFoldTree (core::kinematics)   
AtomicContactFilterCreator (protocols::simple_filters)   EnergyCutRotamerTrialsMinMover (protocols::simple_moves)   LoopFragmentClaimer (protocols::topology_broker)   ProteinLigandInterfaceUpweighterOperationCreator (protocols::enzdes)   ShortLoopClosure (protocols::loops::loop_closure::ccd)   
AtomicDistanceFilter (protocols::simple_filters)   EnergyCutRotamerTrialsMover (protocols::simple_moves)   LoopFromFileData (protocols::loops)   ProteinResidueConformationFeatures (protocols::features)   ShortRangeTwoBodyEnergy (core::scoring::methods)   
AtomicDistanceFilterCreator (protocols::simple_filters)   EnergyDependentCalculator (core::pose::metrics)   LoopHashDiversifier (protocols::loophash)   ProteinResidueConformationFeaturesCreator (protocols::features)   ShoveResidueMover (protocols::protein_interface_design::movers)   
AtomICoor (core::chemical)   EnergyEdge (core::scoring)   LoopHashDiversifierCreator (protocols::loophash)   ProteinRMSDFeatures (protocols::features)   ShoveResidueMoverCreator (protocols::protein_interface_design::movers)   
AtomID (core::id)   EnergyEval (core::fragment::picking_old::vall::eval)   LoopHashLibrary (protocols::loophash)   ProteinRMSDFeaturesCreator (protocols::features)   ShowViolation (protocols::abinitio)   
AtomID_Map (core::id)   EnergyEvent (core::pose::signals)   LoopHashMap (protocols::loophash)   ProteinSCSampler (protocols::match::upstream)   ShuffleFileSystemJobDistributor (protocols::jd2)   
AtomInformation (core::io::pdb)   EnergyGraph (core::scoring)   LoopHashMoverWrapper (protocols::loophash)   ProteinSilentReport (protocols::features)   SICFast (protocols::sic_dock)   
AtomInResidueAtomInResiduePairFeatures (protocols::features)   EnergyMethod (core::scoring::methods)   LoopHashMoverWrapperCreator (protocols::loophash)   ProteinSilentStruct_SinglePrecCreator (core::io::silent)   SICPatternAtTransform (protocols::hotspot_hashing)   
AtomInResidueAtomInResiduePairFeaturesCreator (protocols::features)   EnergyMethodCreator (core::scoring::methods)   LoopHashRelaxProtocol (protocols::loophash)   ProteinSilentStruct_Template (core::io::silent)   SidechainContactDistCutoff (protocols::frag_picker)   
AtomNeighbor (core::scoring)   EnergyMethodOptions (core::scoring::methods)   LoopHashSampler (protocols::loophash)   ProteinSilentStructCreator (core::io::silent)   SidechainMCMover (protocols::simple_moves::sidechain_moves)   
AtomNode (core::optimization)   EnergyMethodRegistrator (core::scoring::methods)   LoopJumpFoldCst (protocols::abinitio)   ProteinUpstreamBuilder (protocols::match::upstream)   SidechainMCMoverCreator (protocols::simple_moves::sidechain_moves)   
AtomPairConstraint (core::scoring::constraints)   EnergyNames (core::io::silent)   LoopLengthChange (protocols::protein_interface_design::movers)   Protocol (protocols::abinitio)   SidechainMetropolisHastingsMover (protocols::canonical_sampling)   
AtomPairConstraintCreator (core::scoring::constraints)   EnergyNode (core::scoring)   LoopLengthChangeCreator (protocols::protein_interface_design::movers)   ProtocolFeatures (protocols::features)   SidechainMetropolisHastingsMoverCreator (protocols::canonical_sampling)   
AtomPairConstraintsData (protocols::frag_picker::scores)   EnergyPerResidueFilter (protocols::simple_filters)   LoopMover (protocols::loops::loop_mover)   ProtocolFeaturesCreator (protocols::features)   SidechainMinMover (protocols::docking)   
AtomPairConstraintsScore (protocols::frag_picker::scores)   EnergyPerResidueFilterCreator (protocols::simple_filters)   LoopMover_Perturb_CCD (protocols::loops::loop_mover::perturb)   PseudoBond (core::conformation)   SidechainMover (protocols::simple_moves::sidechain_moves)   
AtomPairEnergy (core::scoring::etable)   EnsembleConstraints (protocols::cluster)   LoopMover_Perturb_CCDCreator (protocols::loops::loop_mover::perturb)   PseudoBondCollection (core::conformation)   SidechainMoverBase (protocols::simple_moves::sidechain_moves)   
AtomPairFuncList (core::scoring::custom_pair_distance)   EnsembleConstraints_Simple (protocols::cluster)   LoopMover_Perturb_KIC (protocols::loops::loop_mover::perturb)   PseudocontactShiftEnergyController (protocols::topology_broker)   SidechainMoverCreator (protocols::simple_moves::sidechain_moves)   
AtomRadiusMap (core::scoring::packstat)   EnsembleEnergy (protocols::scoring::methods)   LoopMover_Perturb_KICCreator (protocols::loops::loop_mover::perturb)   PseudocontactShiftEnergyCreator (protocols::scoring::methods::pcs)   SidechainRmsdFilter (protocols::simple_filters)   
PDBInfo::AtomRecord (core::pose)   EnsembleEnergyCreator (protocols::scoring::methods)   LoopMover_Perturb_QuickCCD (protocols::loops::loop_mover::perturb)   Psi (protocols::frag_picker::scores)   SidechainRmsdFilterCreator (protocols::simple_filters)   
atoms_and_func_struct (core::scoring::custom_pair_distance)   Entity (protocols::genetic_algorithm)   LoopMover_Perturb_QuickCCD_Moves (protocols::loops::loop_mover::perturb)   PSSMOptEPositionData (protocols::optimize_weights)   SidechainStateAssignment (core::pack::scmin)   
AtomTree (core::kinematics)   EntityCorrespondence (protocols::pack_daemon)   LoopMover_Perturb_QuickCCD_MovesCreator (protocols::loops::loop_mover::perturb)   PValuedFragmentScoreManager (protocols::frag_picker::scores)   Sigmoid (protocols::simple_filters)   
AtomTreeCollection (core::pack::scmin)   EntityElement (protocols::genetic_algorithm)   LoopMover_Perturb_QuickCCDCreator (protocols::loops::loop_mover::perturb)   PyContextIndependentOneBodyEnergy (core::scoring::methods)   SigmoidFilterCreator (protocols::simple_filters)   
AtomTreeDiff (core::import_pose::atom_tree_diffs)   EntityElementCreator (protocols::genetic_algorithm)   LoopMover_Refine_Backrub (protocols::loops::loop_mover::refine)   PyContextIndependentTwoBodyEnergy (core::scoring::methods)   SigmoidFunc (core::scoring::constraints)   
AtomTreeDiffJobDistributor (protocols::jobdist)   EntityElementFactory (protocols::genetic_algorithm)   LoopMover_Refine_BackrubCreator (protocols::loops::loop_mover::refine)   PyEnergyMethodRegistrator (core::scoring::methods)   SigmoidWeightedCenList (core::scoring)   
AtomTreeDiffJobInputter (protocols::jd2)   EntityElementRegistrator (protocols::genetic_algorithm)   LoopMover_Refine_CCD (protocols::loops::loop_mover::refine)   PyMolMover (protocols::moves)   SilentEnergy (core::io::silent)   
AtomTreeDiffJobInputterCreator (protocols::jd2)   EntityElementsEqual (protocols::genetic_algorithm)   LoopMover_Refine_CCDCreator (protocols::loops::loop_mover::refine)   PyMolObserver (protocols::moves)   SilentFileData (core::io::silent)   
AtomTreeDiffJobOutputter (protocols::jd2)   EntityFunc (protocols::pack_daemon)   LoopMover_Refine_KIC (protocols::loops::loop_mover::refine)   
  Q  
SilentFileInputter (protocols::inputter)   
AtomTreeDiffJobOutputterCreator (protocols::jd2)   EntityFuncExpressionCreator (protocols::pack_daemon)   LoopMover_Refine_KICCreator (protocols::loops::loop_mover::refine)   SilentFileJobInputter (protocols::jd2)   
AtomTreeMinimizer (core::optimization)   EntityHistoryLT (protocols::pack_daemon)   LoopMover_SlidingWindow (protocols::loop_build)   qsarCreator (protocols::qsar)   SilentFileJobInputterCreator (protocols::jd2)   
AtomTreeMultifunc (core::optimization)   EntityRandomizer (protocols::genetic_algorithm)   LoopMover_SlidingWindowCreator (protocols::loop_build)   qsarMap (protocols::qsar)   SilentFileJobOutputter (protocols::jd2)   
AtomTreeSCMinMinimizerMap (core::pack::scmin)   Entry   LoopMoverFactory (protocols::loops)   qsarMover (protocols::qsar)   SilentFileJobOutputterCreator (protocols::jd2)   
AtomType (core::chemical)   EnvEnergy (core::scoring::methods)   LoopMoverFromCommandLine (protocols::protein_interface_design::movers)   qsarOptData (protocols::qsar)   SilentFileLoader (core::io::silent)   
AtomTypeDatabaseIO (core::chemical)   EnvEnergyCreator (core::scoring::methods)   LoopMoverFromCommandLineCreator (protocols::protein_interface_design::movers)   qsarOptFunc (protocols::qsar)   SilentFileLoaderCreator (core::io::silent)   
atomTyper (core::chemical::sdf)   EnvPairPotential (core::scoring)   LoopOver (protocols::protein_interface_design::movers)   qsarPoint (protocols::qsar)   SilentFileOptions (core::io::silent)   
AtomTypeSet (core::chemical)   EnvSmoothEnergy (core::scoring::methods)   LoopOverCreator (protocols::protein_interface_design::movers)   Quat (protocols::simple_filters)   SilentFileOptionsCreator (core::io::silent)   
AtomTypesFeatures (protocols::features)   EnvSmoothEnergyCreator (core::scoring::methods)   LoopRebuild (protocols)   QuickRepacker (protocols::pack_daemon)   SilentFileOutputter (protocols::outputter)   
AtomTypesFeaturesCreator (protocols::features)   EnzConstraintIO (protocols::toolbox::match_enzdes_util)   LoopRefine (protocols)   quota_limits_sorter_biggest_first (protocols::frag_picker::quota)   SilentFilePoseInputStream (core::import_pose::pose_stream)   
AtomVDW (core::scoring)   EnzConstraintParameters (protocols::toolbox::match_enzdes_util)   LoopRefineInnerCycle (protocols::loops::loop_mover::refine)   quota_limits_sorter_smallest_first (protocols::frag_picker::quota)   SilentObserver (protocols::viewer)   
AtomWithDOFChange (core::kinematics)   EnzCstTemplateRes (protocols::toolbox::match_enzdes_util)   LoopRefineInnerCycleContainer (protocols::loops::loop_mover::refine)   QuotaCollector (protocols::frag_picker::quota)   SilentStruct (core::io::silent)   
AtrGrid (protocols::qsar::scoring_grid)   EnzCstTemplateResAtoms (protocols::toolbox::match_enzdes_util)   LoopRefineInnerCycleContainerCreator (protocols::loops::loop_mover::refine)   QuotaConfig (protocols::frag_picker::quota)   SilentStructCreator (core::io::silent)   
AtrGridCreator (protocols::qsar::scoring_grid)   EnzCstTemplateResCache (protocols::toolbox::match_enzdes_util)   LoopRefineInnerCycleFactory (protocols::loops::loop_mover::refine)   QuotaDebug (protocols::frag_picker)   SilentStructFactory (core::io::silent)   
AUTO (core::pack::task)   EnzdesBaseProtocol (protocols::enzdes)   LoopRelaxMover (protocols::comparative_modeling)   QuotaPool (protocols::frag_picker::quota)   SilentStructRegistrator (core::io::silent)   
AutomorphismIterator (core::chemical)   EnzdesCacheableObserver (protocols::toolbox::match_enzdes_util)   LoopRelaxMoverCreator (protocols::comparative_modeling)   QuotaSelector (protocols::frag_picker::quota)   SilentStructStore (protocols::wum)   
AutoRBMover (protocols::rbsegment_relax)   EnzdesConstraintReporter (protocols::enzdes)   LoopRelaxThreadingMover (protocols::comparative_modeling)   
  R  
SilentTrajectoryRecorder (protocols::canonical_sampling)   
AverageDegreeFilter (protocols::protein_interface_design::filters)   EnzdesCstCache (protocols::toolbox::match_enzdes_util)   LoopRemodel (protocols::protein_interface_design::movers)   SilentTrajectoryRecorderCreator (protocols::canonical_sampling)   
AverageDegreeFilterCreator (protocols::protein_interface_design::filters)   EnzdesCstParamCache (protocols::toolbox::match_enzdes_util)   LoopRemodelCreator (protocols::protein_interface_design::movers)   APBSConfig::R_PARAM (core::scoring)   SillyCountStruct (protocols::swa::rna)   
  B  
EnzdesFixBBProtocol (protocols::enzdes)   LoopRlxMover (protocols::antibody)   RadiusOfGyrationFeatures (protocols::features)   SimAnnealerBase (core::pack::annealer)   
EnzdesFlexBBProtocol (protocols::enzdes)   LoopRmsdEvaluator (protocols::simple_filters)   RadiusOfGyrationFeaturesCreator (protocols::features)   Simple   
BackboneDB (protocols::loophash)   EnzdesFlexibleRegion (protocols::enzdes)   Loops (protocols::loops)   Ramachandran (core::scoring)   SimpleDerivCheckResult (core::optimization)   
BackboneMover (protocols::simple_moves)   EnzdesJobInputter (protocols::enzdes)   LoopsDatabaseDefiner (protocols::loops::loops_definers)   Ramachandran2B (core::scoring)   SimpleEdge (core::pack::interaction_graph)   
BackboneSampler (protocols::enzdes)   EnzdesJobInputterCreator (protocols::enzdes)   LoopsDatabaseDefinerCreator (protocols::loops::loops_definers)   RamachandranEnergy (core::scoring::methods)   SimpleInteractionGraph (core::pack::interaction_graph)   
BackboneSamplerCreator (protocols::enzdes)   EnzdesJobOutputter (protocols::enzdes)   LoopsDefiner (protocols::loops::loops_definers)   RamachandranEnergy2B (core::scoring::methods)   SimpleNode (core::pack::interaction_graph)   
BackboneSegment (protocols::loophash)   EnzdesJobOutputterCreator (protocols::enzdes)   LoopsDefinerCreator (protocols::loops::loops_definers)   RamachandranEnergy2BCreator (core::scoring::methods)   SimplePDB (core::scoring::packstat)   
BackboneStubConstraint (core::scoring::constraints)   EnzdesLoopInfo (protocols::toolbox::match_enzdes_util)   LoopsDefinerFactory (protocols::loops::loops_definers)   RamachandranEnergyCreator (core::scoring::methods)   SimplePDB_Atom (core::scoring::packstat)   
BackgroundNode (core::pack::interaction_graph)   EnzdesLoopsFile (protocols::toolbox::match_enzdes_util)   LoopsDefinerLoader (protocols::loops::loops_definers)   RamaScore (protocols::frag_picker::scores)   SimpleScoringScheme (core::sequence)   
BackgroundToFirstClassEdge (core::pack::interaction_graph)   EnzdesScorefileFilter (protocols::enzdes)   LoopsDefinerLoaderCreator (protocols::loops::loops_definers)   RampingFunc (protocols::moves)   SimpleSequenceCreator (core::sequence)   
BackrubDDMover (protocols::protein_interface_design::movers)   EnzdesScorefileFilterCreator (protocols::enzdes)   LoopsDefinerRegistrator (protocols::loops::loops_definers)   RampingMover (protocols::moves)   SimpleSequenceData (core::io::silent)   
BackrubDDMoverCreator (protocols::protein_interface_design::movers)   EnzdesSeqRecoveryCache (protocols::toolbox::match_enzdes_util)   LoopsExplicitDefiner (protocols::loops::loops_definers)   RampingMoverCreator (protocols::moves)   SimpleTreeBuilder (protocols::nonlocal)   
BackrubMover (protocols::backrub)   EnzRepackMinimize (protocols::enzdes)   LoopsExplicitDefinerCreator (protocols::loops::loops_definers)   RandomConformerMover (protocols::ligand_docking)   SimulatedTempering (protocols::canonical_sampling)   
BackrubMoverCreator (protocols::backrub)   EnzRepackMinimizeCreator (protocols::enzdes)   LoopsFileData (protocols::loops)   RandomConformers (protocols::ligand_docking)   SimulatedTemperingCreator (protocols::canonical_sampling)   
BackrubSegment (protocols::backrub)   EnzScoreFilter (protocols::enzdes)   LoopsFileDefiner (protocols::loops::loops_definers)   RandomConformersCreator (protocols::ligand_docking)   SingleDownstreamResidueWriter (protocols::match::output)   
BackrubSidechainMover (protocols::backrub)   EnzScoreFilterCreator (protocols::enzdes)   LoopsFileDefinerCreator (protocols::loops::loops_definers)   RandomMover (protocols::moves)   SingleFileBuffer (protocols::jd2)   
BackrubSidechainMoverCreator (protocols::backrub)   Etable (core::scoring::etable)   LoopsFileFallbackConfiguration (protocols::loops)   RandomMoverCreator (protocols::moves)   SingleFragmentMover (protocols::nonlocal)   
Ball (core::scoring::packing)   EtableAtom (core::scoring::etable::etrie)   LoopsFileFallbackConfigurationCreator (protocols::loops)   RandomMutation (protocols::protein_interface_design::movers)   SingleFragmentMoverCreator (protocols::nonlocal)   
Base_bin (protocols::swa::rna)   EtableEnergyCreator (core::scoring::etable)   LoopsFileIO (protocols::loops)   RandomMutationCreator (protocols::protein_interface_design::movers)   SingleGrid (protocols::qsar::scoring_grid)   
Base_pair (core::scoring::rna)   EtableEvaluator (core::scoring::etable)   LoopsFileLoader (protocols::loops)   RandomSheetBuilder (protocols::jumping)   SingleLigandRotamerLibrary (core::pack::dunbrack)   
Base_stack (core::scoring::rna)   EtableFunc (core::scoring::constraints)   LoopsFileLoaderCreator (protocols::loops)   RandomSymmetrySlider (protocols::simple_moves::symmetry)   SingleMotif (protocols::motifs)   
BaseCacheUnit (core::fragment)   EtableOptions (core::scoring::etable)   LoopsFileOptions (protocols::loops)   RangeFilter (protocols::simple_filters)   SingleResidueDunbrackLibrary (core::pack::dunbrack)   
BaseDisulfPairingLibrary (protocols::jumping)   EtableParamsOnePair (core::scoring::etable)   LoopsFileOptionsCreator (protocols::loops)   RangeFilterCreator (protocols::simple_filters)   SingleResidueDunbrackLibraryConcrete (core::pack::dunbrack)   
BaseEtableEnergy (core::scoring::etable)   Euler_angles (protocols::swa::rna)   LR_AtomData (core::scoring::packstat)   RationalLoopComparator (protocols::loops)   SingleResidueFragData (core::fragment)   
BaseJobDistributor (protocols::jobdist)   EvaluatedArchive (protocols::jd2::archive)   LR_MP_AtomData (core::scoring::packstat)   RationalMonteCarlo (protocols::simple_moves::rational_mc)   SingleResidueInvrotTarget (protocols::toolbox::match_enzdes_util)   
BaseJumpSetup (protocols::jumping)   EvaluatedTrialMover (protocols::simple_filters)   LREnergyContainer (core::scoring)   RawFileData (core::io::raw_data)   SingleResidueMultifunc (core::optimization)   
BasePairingLibrary (protocols::jumping)   EvaluatorCreator (protocols::evaluation)   LSMSearchPattern (protocols::hotspot_hashing)   RawStruct (core::io::raw_data)   SingleResidueRotamerLibrary (core::pack::dunbrack)   
BasePairType (protocols::rna)   EvaluatorFactory (protocols::evaluation)   
  M  
ray_distance_derivs (protocols::pockets)   SingleResidueTorsionFragmentLibrary (protocols::frags)   
BasePartner (core::scoring::dna)   EvaluatorRegistrator (protocols::evaluation)   RB_lt (protocols::rbsegment_relax)   SingleState (protocols::multistate_design)   
BasicJob (protocols::jobdist)   Event (core::scoring::packstat)   MainChainTorsionSet (protocols::swa::protein)   RBResidueRange (protocols::rbsegment_relax)   SingleStateEntityData (protocols::multistate_design)   
BasicSimAnnealerRepacker (protocols::pack_daemon)   EX (core::pack::task)   MainChainTorsionSet (protocols::swa)   RBSegment (protocols::rbsegment_relax)   SingleStateFitnessFunction (protocols::multistate_design)   
Batch (protocols::jd2::archive)   EX_CUTOFF (core::pack::task)   MakeABEGO_SS_Score (protocols::frag_picker::scores)   RBSegmentMover (protocols::rbsegment_relax)   SingleStructureData (protocols::optimize_weights)   
BatchEvaluator (protocols::simple_filters)   ExactOccludedHbondSolEnergy (core::scoring::geometric_solvation)   MakeAmbigCSScore (protocols::frag_picker::scores)   RBSegmentRelax (protocols::rbsegment_relax)   SingleValuePoseEvaluator (protocols::evaluation)   
BatchFeatures (protocols::features)   ExactOccludedHbondSolEnergyCreator (core::scoring::geometric_solvation)   MakeAtomPairConstraintsScore (protocols::frag_picker::scores)   RBSegmentRelaxImpl (protocols)   SinXOverX (core::scoring::saxs)   
BatchFeaturesCreator (protocols::features)   ExactResidueMatcher (core::conformation)   MakeBFactor (protocols::frag_picker::scores)   RDC (core::scoring)   SiteConstraint (core::scoring::constraints)   
BatchJobInputter (protocols::jd2)   ExcludedResPredicate (core::scoring)   MakeConstScore (protocols::frag_picker::scores)   RDC_Evaluator (protocols::simple_filters)   SiteConstraintCreator (core::scoring::constraints)   
BatchNrEvaluator (protocols::simple_filters)   EXCN_Archive (protocols::jd2::archive)   MakeCSScore (protocols::frag_picker::scores)   RDC_Rohl (core::scoring)   SiteConstraintResidues (core::scoring::constraints)   
BB_BB_EnergyInvoker (core::scoring::etable)   EXCN_AssignmentNotFound (protocols::noesy_assign)   MakeDihedralConstraintsScore (protocols::frag_picker::scores)   RdcEvaluatorCreator (protocols::simple_filters)   SiteConstraintResiduesCreator (core::scoring::constraints)   
BB_Pos (protocols::fldsgn::topology)   EXCN_AtomNotFound (core::id)   MakeDisulfideDistance (protocols::frag_picker::scores)   RDCScore (protocols::frag_picker::scores)   SkipViolFunc (core::scoring::constraints)   
BB_Pos (core::scoring)   EXCN_BadInput (utility::excn)   MakeDisulfideIdentity (protocols::frag_picker::scores)   RdcSelectEvaluatorCreator (protocols::simple_filters)   Slice (core::scoring::packstat)   
BBClaim (protocols::topology_broker)   EXCN_bbdb_Merge_Failed (protocols::loophash)   MakeFragmentAllAtomCrmsd (protocols::frag_picker::scores)   RdcTargetEvaluatorCreator (protocols::simple_filters)   SlicedPoseJobParameters (protocols::swa::rna)   
BBConRotMover (protocols::simple_moves)   EXCN_Converged (protocols::moves)   MakeFragmentCrmsd (protocols::frag_picker::scores)   ReadResfile (core::pack::task::operation)   SlideIntoSurface (protocols::surface_docking)   
BBData (protocols::loophash)   EXCN_Converged (protocols::moves::mc_convergence_checks)   MakeFragmentCrmsdResDepth (protocols::frag_picker::scores)   ReadResfileAndObeyLengthEvents (core::pack::task::operation)   SlideTogether (protocols::ligand_docking)   
BBDepCartBondedParameters (core::scoring::methods)   EXCN_DB_IO_Failed (protocols::loophash)   MakeFragmentDME (protocols::frag_picker::scores)   ReadResfileAndObeyLengthEventsCreator (core::pack::task::operation)   SlideTogetherCreator (protocols::ligand_docking)   
BBDepNRChiSample (core::pack::dunbrack)   EXCN_FailedBroking (protocols::topology_broker)   MakeFragmentScoringMethod (protocols::frag_picker::scores)   ReadResfileCreator (core::pack::task::operation)   SlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
BBDepScoreInterpData (core::pack::dunbrack)   EXCN_FileFormat (protocols::noesy_assign)   MakeGunnCostScore (protocols::frag_picker::scores)   ReadResfileFromDB (protocols::toolbox::task_operations)   SmallAtNb (core::scoring)   
BBDepSemiRotamericData (core::pack::dunbrack)   EXCN_FilterFailed (protocols::topology_broker)   MakeHydrophobicityProfileSimilarity (protocols::frag_picker::scores)   ReadResfileFromDBCreator (protocols::toolbox::task_operations)   SmallFragWeight (protocols::topology_broker::weights)   
BBDofs (protocols::protein_interface_design::movers)   EXCN_Heat_Converged (protocols::canonical_sampling::mc_convergence_checks)   MakeHydrophobicitySimilarity (protocols::frag_picker::scores)   RecoverSideChainsMover (protocols::comparative_modeling)   SmallMinCCDTrial (protocols::loops::loop_mover::refine)   
BBExtraData (protocols::loophash)   EXCN_Input (protocols::topology_broker)   MakeInterbondAngleScore (protocols::frag_picker::scores)   RedefineChi (core::chemical)   SmallMinCCDTrialCreator (protocols::loops::loop_mover::refine)   
BBG8T3AMover (protocols::simple_moves)   EXCN_Invalid_Hashmap (protocols::loophash)   MakeJCoupling (protocols::frag_picker::scores)   ReferenceCount (utility::pointer)   SmallMover (protocols::simple_moves)   
BBGaussianMover (protocols::simple_moves)   EXCN_InvalidFoldTree (core::kinematics)   MakeLAMBEGO_Similarity (protocols::frag_picker::scores)   ReferenceCountMI (utility::pointer)   SmallMoverCreator (protocols::simple_moves)   
BBIndepCartBondedParameters (core::scoring::methods)   EXCN_Loop_not_closed (protocols::loops)   MakeMidPhiOut (protocols::frag_picker::scores)   ReferenceEnergy (core::scoring::methods)   SmoothCenPairEnergy (core::scoring::methods)   
BBIndNRChiSample (core::pack::dunbrack)   EXCN_Msg_Exception (utility::excn)   MakeMidPsiOut (protocols::frag_picker::scores)   ReferenceEnergyCreator (core::scoring::methods)   SmoothCenPairEnergyCreator (core::scoring::methods)   
BBIndSemiRotamericData (core::pack::dunbrack)   EXCN_No_Extra_Data_To_Write (protocols::loophash)   MakePartialSecondarySimilarity (protocols::frag_picker::scores)   ReferenceEnergyNoncanonical (core::scoring::methods)   SmoothEnvEnergy (core::scoring::methods)   
BBTorsionAndAnglesSRFD (core::fragment)   EXCN_NoesyAssign (protocols::noesy_assign)   MakePCS_FragDistance (protocols::frag_picker::scores)   ReferenceEnergyNoncanonicalCreator (core::scoring::methods)   SmoothEnvEnergyCreator (core::scoring::methods)   
BBTorsionSRFD (core::fragment)   EXCN_Pool_Converged (protocols::canonical_sampling::mc_convergence_checks)   MakePhi (protocols::frag_picker::scores)   RefineBetaBarrel (protocols::antibody2)   SmoothEnvPairPotential (core::scoring)   
BDR (protocols::forge::components)   EXCN_TopologyBroker (protocols::topology_broker)   MakePhiPsiRmsd (protocols::frag_picker::scores)   RefineOneCDRLoop (protocols::antibody2)   SmoothFragmentMover (protocols::simple_moves)   
BDRSegmentInfo (protocols::forge::components)   EXCN_Unknown (protocols::topology_broker)   MakePhiPsiSquareWell (protocols::frag_picker::scores)   RefineOneCDRLoopCentroid (protocols::antibody2)   SmoothFragWeight (protocols::topology_broker::weights)   
Rule::BeadAdder (core::coarse)   EXCN_UnknownAtomname (protocols::noesy_assign)   MakePolyXMover (protocols::simple_moves)   Region (protocols::nonlocal)   SmoothPolicy (protocols::nonlocal)   
Translator::BeadAtom (core::coarse)   EXCN_UnknownResonance (protocols::noesy_assign)   MakePolyXMoverCreator (protocols::simple_moves)   RegionalConnections (protocols::simple_filters)   SmoothScoreTermCoeffs (core::scoring)   
BestHotspotCstMover (protocols::protein_interface_design::movers)   EXCN_Wrong_DB_Format (protocols::loophash)   MakeProfileScore (protocols::frag_picker::scores)   RelativeConnectRight (protocols::forge::build)   SmoothSymmetricFragmentMover (protocols::simple_moves)   
BestHotspotCstMoverCreator (protocols::protein_interface_design::movers)   Exemplar (protocols::cluster)   MakeProfileScoreBlosum62 (protocols::frag_picker::scores)   RelativePoseFilter (protocols::simple_filters)   SmotifFeatures (protocols::features)   
BestMatchesCollection (protocols::match::output)   ExpExpression (protocols::pack_daemon)   MakeProfileScoreDistWeight (protocols::frag_picker::scores)   RelativePoseFilterCreator (protocols::simple_filters)   SmotifFeaturesCreator (protocols::features)   
BestTotalScoreSelector (protocols::frag_picker)   ExpiryFilter (protocols::simple_filters)   MakeProfileScoreL1 (protocols::frag_picker::scores)   RelativeSegmentFilter (protocols::protein_interface_design::filters)   SnugDock (protocols::antibody2)   
BetaAlphaBetaMotif (protocols::fldsgn::topology)   ExpiryFilterCreator (protocols::simple_filters)   MakeProfileScoreStructL1 (protocols::frag_picker::scores)   RelativeSegmentFilterCreator (protocols::protein_interface_design::filters)   SnugDockProtocol (protocols::antibody2)   
BetaAlphaBetaMotifSet (protocols::fldsgn::topology)   ExplicitWaterUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   MakeProfileScoreSubMatrix (protocols::frag_picker::scores)   RelativeSequencePosition (protocols::forge::build)   SoedingFunc (core::scoring::constraints)   
BetaTurnDetectionFeatures (protocols::features)   exposed_hydrophobic_data (core::pack::interaction_graph)   MakeProlinePhiScore (protocols::frag_picker::scores)   RelaxProtocolBase (protocols::relax)   SOGFunc (core::scoring::constraints)   
BetaTurnDetectionFeaturesCreator (protocols::features)   Expression (numeric::expression_parser)   MakePsi (protocols::frag_picker::scores)   RelaxScriptCommand (protocols::relax)   SOGFunc_Impl (core::scoring::constraints)   
BFactor (protocols::frag_picker::scores)   ExpressionCreator (numeric::expression_parser)   MakeRamaScore (protocols::frag_picker::scores)   RemarkInfo (core::pose)   SolvationGrid (protocols::qsar::scoring_grid)   
BfactorMPM (protocols::match)   ExtendAlignerSW (core::sequence)   MakeRDCScore (protocols::frag_picker::scores)   Remarks (core::pose)   SolvationGridCreator (protocols::qsar::scoring_grid)   
BiasedFragmentMover (protocols::nonlocal)   ExtendedPoseInputStream (core::import_pose::pose_stream)   MakeScoreEValuator (protocols::frag_picker::scores)   RemodelAccumulator (protocols::forge::remodel)   SolvationMetaGrid (protocols::qsar::scoring_grid)   
BigBinConstraint (core::scoring::constraints)   ExtendedPoseMover (protocols::simple_moves)   MakeSecondaryIdentity (protocols::frag_picker::scores)   RemodelConstraintGenerator (protocols::forge::remodel)   SolvationMetaGridCreator (protocols::qsar::scoring_grid)   
BigBinConstraintCreator (core::scoring::constraints)   ExtendedPoseMoverCreator (protocols::simple_moves)   MakeSecondarySimilarity (protocols::frag_picker::scores)   RemodelData (protocols::forge::remodel)   SolventAccessibility (protocols::frag_picker::scores)   
BinaryExpression (numeric::expression_parser)   Extender (protocols::star)   MakeSequenceIdentity (protocols::frag_picker::scores)   RemodelDesignMover (protocols::forge::remodel)   sort_SilentStructOPs (protocols::wum)   
BinaryProteinSilentStruct (core::io::silent)   Extent (core::fragment::picking_old::concepts)   MakeSolventAccessibility (protocols::frag_picker::scores)   RemodelEnzdesCstModule (protocols::forge::remodel)   SortPredicate (protocols::jd2::archive)   
BinaryProteinSilentStructCreator (core::io::silent)   ExtentEvaluator (core::fragment::picking_old::concepts)   MakeTalosSSSimilarity (protocols::frag_picker::scores)   RemodelLoopMover (protocols::forge::remodel)   SourcePositions (protocols::coarse_rna)   
BinaryRNASilentStruct (core::io::silent)   ExtentGenerator (core::fragment::picking_old::concepts)   MakeTorsionBinSimilarity (protocols::frag_picker::scores)   RemodelLoopMoverCreator (protocols::forge::remodel)   SparseMatrixIndex (core::pack::interaction_graph)   
BinaryRNASilentStructCreator (core::io::silent)   ExternalEvaluator (protocols::simple_filters)   MapCacheUnit (core::fragment)   RemodelMover (protocols::forge::remodel)   Sparta (protocols::sparta)   
BindingSiteConstraint (protocols::constraints_additional)   ExternalGeomSampler (protocols::toolbox::match_enzdes_util)   MapHotspot (protocols::protein_interface_design::movers)   RemodelMoverCreator (protocols::forge::remodel)   Sparta::SpartaLib (protocols::sparta)   
BindingSiteConstraintCreator (protocols::constraints_additional)   ExtraChiCutoff (core::pack::task::operation)   MapHotspotCreator (protocols::protein_interface_design::movers)   RemodelRotamerLinks (protocols::forge::remodel)   SpecialRotamerEnergy (protocols::scoring::methods)   
BindingStrainFilter (protocols::protein_interface_design::filters)   ExtraChiCutoffCreator (core::pack::task::operation)   match_dspos1 (protocols::match)   RemodelRotamerLinksCreator (protocols::forge::remodel)   SpecialRotamerEnergyCreator (protocols::scoring::methods)   
BindingStrainFilterCreator (protocols::protein_interface_design::filters)   ExtractAsymmetricPoseMover (protocols::simple_moves::symmetry)   match_lite_equals (protocols::match)   RemoveCsts (protocols::forge::constraints)   SpecialRotamerRSO (protocols::toolbox::rotamer_set_operations)   
BluePrint (protocols::jd2::parser)   ExtractAsymmetricPoseMoverCreator (protocols::simple_moves::symmetry)   match_lite_hasher (protocols::match)   RemoveCstsCreator (protocols::forge::constraints)   SpecialSegmentsObserver (core::pose::datacache)   
BluePrintBDR (protocols::fldsgn)   ExtractAsymmetricUnitMover (protocols::simple_moves::symmetry)   MatchCollisionFilter (protocols::match::output)   RemoveNorCTermMPM (protocols::match)   SpecificGeometryLibrary (protocols::jumping)   
BluePrintBDRCreator (protocols::fldsgn)   ExtractAsymmetricUnitMoverCreator (protocols::simple_moves::symmetry)   MatchConsolidator (protocols::match::output)   RenderGridsToKinemage (protocols::qsar)   SpecificResiduesNearInterfaceFilter (protocols::protein_interface_design::filters)   
Boinc (protocols::boinc)   ExtraQuadraticRepulsion (core::scoring::etable)   MatchConstraintFileInfo (protocols::toolbox::match_enzdes_util)   RenderGridsToKinemageCreator (protocols::qsar)   SpecificResiduesNearInterfaceFilterCreator (protocols::protein_interface_design::filters)   
BoincCurrentPoseObserver (protocols::boinc)   ExtraRotamers (core::pack::task::operation)   MatchConstraintFileInfoList (protocols::toolbox::match_enzdes_util)   RepackLigandSiteWithoutLigandMover (protocols::enzdes)   Sphere (core::scoring::packstat)   
BOINCJobDistributor (protocols::jd2)   ExtraRotamersCreator (core::pack::task::operation)   MatchCounter (protocols::match)   RepackMinimize (protocols::protein_interface_design::movers)   spherical_coor_triplet (protocols::pockets)   
BoincSharedMemory (protocols::boinc)   ExtraRotamersGeneric (core::pack::task::operation)   Matcher (protocols::match)   RepackMinimizeCreator (protocols::protein_interface_design::movers)   SphericalRotationSearchPattern (protocols::hotspot_hashing)   
BoltzmannFilter (protocols::protein_interface_design::filters)   ExtraRotamersGenericCreator (core::pack::task::operation)   MatcherMover (protocols::match)   RepackSidechainsMover (protocols::simple_moves)   CrossPeak::Spin (protocols::noesy_assign)   
BoltzmannFilterCreator (protocols::protein_interface_design::filters)   ExtraScoreEvaluatorCreator (protocols::simple_filters)   MatcherMoverCreator (protocols::match)   RepackSidechainsMoverCreator (protocols::simple_moves)   SpinMover (protocols::protein_interface_design::movers)   
BondData (core::chemical::sdf)   ExtraThreadingMover (protocols::comparative_modeling)   MatcherOutputStats (protocols::match)   RepackTrial (protocols::loops::loop_mover::refine)   SpinMoverCreator (protocols::protein_interface_design::movers)   
BondedAtom (core::kinematics::tree)   
  F  
MatcherTask (protocols::match)   RepackTrialCreator (protocols::loops::loop_mover::refine)   Splice (protocols::protein_interface_design::movers)   
BondID (core::id)   MatchEvaluator (protocols::match::output)   RepackWithoutLigandFilter (protocols::enzdes)   SpliceCreator (protocols::protein_interface_design::movers)   
Book (core::fragment::picking_old::concepts)   Fa_MbenvEnergy (core::scoring::methods)   MatchFilter (protocols::match::output)   RepackWithoutLigandFilterCreator (protocols::enzdes)   SpliceSegment (protocols::protein_interface_design::movers)   
Book_VallResidues (core::fragment::picking_old::concepts)   Fa_MbenvEnergyCreator (core::scoring::methods)   MatchGrouper (protocols::match::output)   RepeatMover (protocols::moves)   SplineFunc (core::scoring::constraints)   
Bookmark (core::fragment::picking_old::concepts)   Fa_MbsolvEnergy (core::scoring::methods)   MatchOutputter (protocols::match::output)   RepGrid (protocols::qsar::scoring_grid)   SplineParameters (core::scoring::etable)   
Bool3DGrid (protocols::match)   Fa_MbsolvEnergyCreator (core::scoring::methods)   MatchOutputTracker (protocols::match)   RepGridCreator (protocols::qsar::scoring_grid)   SquareWell2Func (core::scoring::constraints)   
Bool3DGridKinemageWriter (protocols::match)   FabConstraint (core::scoring::constraints)   MatchPositionModifier (protocols::match)   ReplicaExchangeMC (protocols::moves)   SquareWellFunc (core::scoring::constraints)   
BoundedCollector (protocols::frag_picker)   FabConstraintCreator (core::scoring::constraints)   MatchProcessor (protocols::match::output)   ReplicateFilter (protocols::filters)   SRelaxPose (protocols::relax)   
BoundedCollector_CompareTotalScore (protocols::frag_picker)   FACTSEnergy (core::scoring::methods)   MatchResidues (protocols::fldsgn)   ReplicateFilterCreator (protocols::filters)   SS_Base (protocols::fldsgn::topology)   
BoundedPriorityQueue (protocols::frag_picker)   FACTSPoseInfo (core::scoring)   MatchResiduesMover (protocols::fldsgn)   ReplicateTask (core::pack::task::operation)   SS_Info (core::scoring)   
BoundFunc (core::scoring::constraints)   FACTSPotential (core::scoring)   MatchResiduesMoverCreator (protocols::fldsgn)   ReplicateTaskCreator (core::pack::task::operation)   SS_Info2 (protocols::fldsgn::topology)   
BranchAngleOptimizer (protocols::branch_angle)   FACTSResidueInfo (core::scoring)   MatrixScoringScheme (core::sequence)   Report (protocols::features)   SS_Killhairpins_Info (core::scoring)   
BranchCoef1 (protocols::branch_angle)   FACTSRotamerSetInfo (core::scoring)   MaxSeqSepConstraintSet (protocols::constraints_additional)   ReportFilter (protocols::simple_filters)   SSFeature (protocols::comparative_modeling::features)   
BranchCoef2 (protocols::branch_angle)   FadeFunc (core::scoring::constraints)   MCAligner (core::sequence)   ReportFilterCreator (protocols::simple_filters)   SSPairPotential (protocols::fldsgn::potentials::sspot)   
BranchParam1 (protocols::branch_angle)   FadeInterval (core::scoring::hbonds)   MCShowMover (protocols::moves)   ReportPSSMDifferences (protocols::protein_interface_design)   Stage1Sampler (protocols::abinitio)   
BranchParam2 (protocols::branch_angle)   FaDockingSlideIntoContact (protocols::docking)   MD_Angle (protocols::cartesian)   ReportSequenceDifferences (protocols::protein_interface_design)   StandardDisulfPairingLibrary (protocols::jumping)   
BrentLineMinimization (core::optimization)   FalseFilter (protocols::filters)   MD_Bond (protocols::cartesian)   ReportToDB (protocols::features)   StandardPairingLibrary (protocols::jumping)   
Bridge (protocols::forge::build)   FalseFilterCreator (protocols::filters)   MD_HarmonicDihedral (protocols::cartesian)   ReportToDBCreator (protocols::features)   StarAbinitio (protocols::star)   
BruteFunGroupTK (protocols::kinmatch)   FASelectSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   MedalExchangeMover (protocols::medal)   RepulsiveOnlyMover (protocols::simple_moves)   StartFrom (protocols::ligand_docking)   
BUFFER (core::io::serialization)   FaSlideAwayFromSurface (protocols::surface_docking)   MedalMover (protocols::medal)   resatom_and_func_struct (core::scoring::custom_pair_distance)   StartFromCreator (protocols::ligand_docking)   
BuildAlaPose (protocols::protein_interface_design::movers)   FaSlideIntoSurface (protocols::surface_docking)   MembEtable (core::scoring::etable)   ResConnID (core::chemical)   StarTreeBuilder (protocols::nonlocal)   
BuildAlaPoseCreator (protocols::protein_interface_design::movers)   FastaInputter (protocols::inputter)   Membrane_FAEmbed (core::scoring)   ResfileCommand (core::pack::task)   StartStructClaimer (protocols::topology_broker)   
BuildInstruction (protocols::forge::build)   FastDensEnergy (core::scoring::electron_density)   Membrane_FAPotential (core::scoring)   ResfileContents (core::pack::task)   StateAccumulatingMatchFilter (protocols::match::output)   
BuildManager (protocols::forge::build)   FastDensEnergyCreator (core::scoring::electron_density)   MembraneAbinitio (protocols::abinitio)   ResFileOutputter (protocols::outputter)   StatusRequest (protocols::wum2)   
BuildPosition (protocols::motifs)   FASTER_IG_Repacker (protocols::pack_daemon)   MembraneCbetaEnergy (core::scoring::methods)   ResfileReaderException (core::pack::task)   StatusResponse (protocols::wum2)   
BuildSet (protocols::match::upstream)   FASTERAnnealer (core::pack::annealer)   MembraneCbetaEnergyCreator (core::scoring::methods)   ResFilter (core::pack::task::operation)   StealLigandMover (protocols::comparative_modeling)   
BumpGrid (protocols::match)   FASTEREdge (core::pack::interaction_graph)   MembraneCenPairEnergy (core::scoring::methods)   ResFilterComposition (core::pack::task::operation)   StealSideChainsMover (protocols::comparative_modeling)   
BumpSelector (core::pack::rotamer_set)   FASTERInteractionGraph (core::pack::interaction_graph)   MembraneCenPairEnergyCreator (core::scoring::methods)   ResFilterCreator (core::pack::task::operation)   StepWiseBetaAntiParallelJumpSampleGenerator (protocols::swa::protein)   
BurialEnergy (core::scoring::methods)   FASTERNode (core::pack::interaction_graph)   MembraneCenterPerturbationMover (protocols::rigid)   ResFilterFactory (core::pack::task::operation)   StepWiseClusterer (protocols::swa)   
BurialEnergyCreator (core::scoring::methods)   FastGapMover (protocols::loophash)   MembraneEmbed (core::scoring)   ResFilterRegistrator (core::pack::task::operation)   StepWiseCombineSampleGenerator (protocols::swa)   
BuriedPolarScore (protocols::sic_dock)   FastLinearFunc (protocols::moves)   MembraneEnvEnergy (core::scoring::methods)   ResId (protocols::moves)   StepWiseDoNothingSampleGenerator (protocols::swa)   
BuriedUnsatHbondFilter (protocols::simple_filters)   FastRelax (protocols::relax)   MembraneEnvEnergyCreator (core::scoring::methods)   ResidualDipolarCoupling (core::scoring)   StepWiseFilterer (protocols::swa)   
BuriedUnsatHbondFilterCreator (protocols::simple_filters)   FastRelaxCreator (protocols::relax)   MembraneEnvPenalties (core::scoring::methods)   ResidualDipolarCoupling_Rohl (core::scoring)   StepWiseIdentitySampleGenerator (protocols::swa)   
BuriedUnsatisfiedPolarsCalculator (protocols::toolbox::pose_metric_calculators)   FastSAXSEnergy (core::scoring::saxs)   MembraneEnvPenaltiesCreator (core::scoring::methods)   ResidualDipolarCouplingEnergy (core::scoring::methods)   StepWiseJobParameters (protocols::swa)   
LoopHashMap::by_index (protocols::loophash)   FastSAXSEnergyCreator (core::scoring::saxs)   MembraneEnvSmoothEnergy (core::scoring::methods)   ResidualDipolarCouplingEnergy_Rohl (core::scoring::methods)   StepWisePoseCombineSampleGenerator (protocols::swa)   
  C  
FaSymDockingSlideTogether (protocols::simple_moves::symmetry)   MembraneEnvSmoothEnergyCreator (core::scoring::methods)   ResidualDipolarCouplingEnergy_RohlCreator (core::scoring::methods)   StepWisePoseSampleGenerator (protocols::swa)   
FavorNativeResidue (protocols::protein_interface_design)   MembraneJump (protocols::jumping)   ResidualDipolarCouplingEnergyCreator (core::scoring::methods)   StepWisePoseSetup (protocols::swa)   
CaCbCb_Angle_Func (core::scoring::disulfides)   FavorNativeResiduePreCycle (protocols::protein_interface_design::movers)   MembraneLipo (core::scoring::methods)   ResidualDipolarCouplingEnergyRigidSegments (protocols::scoring::methods)   StepWiseProteinCCD_Closer (protocols::swa::protein)   
CaCbCbCa_Dihedral_Func (core::scoring::disulfides)   FavorNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MembraneLipoCreator (core::scoring::methods)   ResidualDipolarCouplingEnergyRigidSegments (core::scoring::methods)   StepWiseProteinFilterer (protocols::swa::protein)   
CacheableAtomID_MapVector (core::id)   FavorNonNativeResidue (protocols::protein_interface_design)   MembraneNormalPerturbationMover (protocols::rigid)   ResidualDipolarCouplingEnergyRigidSegmentsCreator (protocols::scoring::methods)   StepWiseProteinFragmentSampleGenerator (protocols::swa::protein)   
CacheableDataType (core::pose::datacache)   FavorNonNativeResiduePreCycle (protocols::protein_interface_design::movers)   MembranePotential (core::scoring)   ResidualDipolarCouplingRigidSegments (protocols::scoring)   StepWiseProteinJumpSampleGenerator (protocols::swa::protein)   
CacheableObserver (core::pose::datacache)   FavorNonNativeResiduePreCycleCreator (protocols::protein_interface_design::movers)   MembraneTopology (protocols::simple_moves)   Residue (core::conformation)   StepWiseProteinLoopBridger (protocols::swa::protein)   
CacheableObserverType (core::pose::datacache)   FavorSequenceProfile (protocols::simple_moves)   MembraneTopology (core::scoring)   Residue_info (protocols::swa::rna)   StepWiseProteinMainChainSampleGenerator (protocols::swa::protein)   
CacheablePoseRawPtr (core::pose::datacache)   FavorSequenceProfileCreator (protocols::simple_moves)   MembraneTopologyClaimer (protocols::topology_broker)   ResidueAtomTreeCollection (core::pack::scmin)   StepWiseProteinPacker (protocols::swa::protein)   
CacheableSequenceProfile (core::sequence)   FB_Pose_Data (protocols::swa::rna)   MembraneTopologyCreator (protocols::simple_moves)   ResidueAtomTreeCollectionMomento (core::pack::scmin)   StepWiseProteinPoseMinimizer (protocols::swa::protein)   
CacheWrapper (core::fragment)   FeaturesReporter (protocols::features)   MetalloClaimer (protocols::topology_broker)   ResidueBBDofs (protocols::protein_interface_design::movers)   StepWiseProteinPoseSetup (protocols::swa::protein)   
CachingScoringMethod (protocols::frag_picker::scores)   FeaturesReporterCreator (protocols::features)   MetalloPlacementEnergy (core::scoring::methods)   ResidueBurialFeatures (protocols::features)   StepWiseProteinResidueSampler (protocols::swa::protein)   
CAcstGenerator (protocols::seeded_abinitio)   FeaturesReporterFactory (protocols::features)   MetaPoseEvaluator (protocols::evaluation)   ResidueBurialFeaturesCreator (protocols::features)   StepWiseProteinScreener (protocols::swa::protein)   
CAcstGeneratorCreator (protocols::seeded_abinitio)   FeaturesReporterRegistrator (protocols::features)   MetaPoseInputStream (core::import_pose::pose_stream)   ResidueBurialFilter (protocols::simple_filters)   StepWiseResidueSampler (protocols::swa)   
CalculatorFactory (core::pose::metrics)   FibrilModelingClaimer (protocols::topology_broker)   MethylNameLibrary (protocols::noesy_assign)   ResidueBurialFilterCreator (protocols::simple_filters)   StepWiseRNA_AnalyticalLoopCloseSampler (protocols::swa::rna)   
CalculatorFilter (protocols::filters)   Field (core::io::pdb)   MethylNames (protocols::noesy_assign)   ResidueCartBondedParameters (core::scoring::methods)   StepWiseRNA_Base_Sugar_Rotamer (protocols::swa::rna)   
CalculatorFilterCreator (protocols::filters)   FileBuffer (protocols::checkpoint)   MetricCalculatorFitnessFunction (protocols::multistate_design)   ResidueConformationFeatures (protocols::features)   StepWiseRNA_BaseCentroidScreener (protocols::swa::rna)   
CamShiftEvaluator (protocols::simple_filters)   FileData (core::io::pdb)   MetricRecorder (protocols::canonical_sampling)   ResidueConformationFeaturesCreator (protocols::features)   StepWiseRNA_Clusterer (protocols::swa::rna)   
CamShiftEvaluatorCreator (protocols::simple_filters)   FileDataOptions (core::io::pdb)   MetricRecorderCreator (protocols::canonical_sampling)   ResidueConnection (core::chemical)   StepWiseRNA_CombineLongLoopFilterer (protocols::swa::rna)   
SmoothPolicy::Candidate (protocols::nonlocal)   FileExistFilter (protocols::simple_filters)   MetricValueGetter (protocols::toolbox::pose_metric_calculators)   ResidueConstraints (core::scoring::constraints)   StepWiseRNA_JobParameters (protocols::swa::rna)   
CandidatesCollector (protocols::frag_picker)   FileExistFilterCreator (protocols::simple_filters)   MetropolisHastingsMover (protocols::canonical_sampling)   ResidueCoordinateChangeList (core::kinematics)   StepWiseRNA_JobParameters_Setup (protocols::swa::rna)   
CanonicalSamplingMover (protocols::canonical_sampling)   FileJobOutputter (protocols::jd2)   MetropolisHastingsMoverCreator (protocols::canonical_sampling)   ResidueCountFilter (protocols::simple_filters)   StepWiseRNA_Minimizer (protocols::swa::rna)   
CanonicalSamplingMover (protocols::moves)   FileRemoveFilter (protocols::simple_filters)   MidPhiOut (protocols::frag_picker::scores)   ResidueCountFilterCreator (protocols::simple_filters)   StepWiseRNA_PoseSetup (protocols::swa::rna)   
CarbohydrateInfo (core::chemical::carbohydrates)   FileRemoveFilterCreator (protocols::simple_filters)   MidPsiOut (protocols::frag_picker::scores)   ResidueDatabaseIO (core::chemical)   StepWiseRNA_ResidueSampler (protocols::swa::rna)   
CarbonHBondEnergy (core::scoring::carbon_hbonds)   FileSystemJobDistributor (protocols::jd2)   MinDebug (core::optimization::symmetry)   ResidueDecompositionByChainCalculator (protocols::toolbox::pose_metric_calculators)   StepWiseRNA_RotamerGenerator (protocols::swa::rna)   
CarbonHBondEnergyCreator (core::scoring::carbon_hbonds)   Filter (protocols::filters)   MinimalistFlexbbEdge (protocols::flexpack::interaction_graph)   ResidueDecompositionCalculator (protocols::toolbox::pose_metric_calculators)   StepWiseRNA_RotamerGenerator_Wrapper (protocols::swa::rna)   
CarbonHBondPotential (core::scoring::carbon_hbonds)   FilterBucket (protocols::loophash)   MinimalistFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   ResidueDistanceFilter (protocols::simple_filters)   StepWiseRNA_VDW_Bin_Screener (protocols::swa::rna)   
CartBondedParameters (core::scoring::methods)   FilterCollection (protocols::filters)   MinimalistFlexbbNode (protocols::flexpack::interaction_graph)   ResidueDistanceFilterCreator (protocols::simple_filters)   StepWiseScreener (protocols::swa)   
CartesianAtom (protocols::cartesian)   FilterCreator (protocols::filters)   MinimalRotamer (protocols::simple_moves)   ResidueFactory (core::conformation)   StochasticFilter (protocols::filters)   
CartesianBondedEnergy (core::scoring::methods)   Filterer_Count (protocols::swa::rna)   MinimizationEdge (core::scoring)   ResidueFeature (protocols::comparative_modeling::features)   StochasticFilterCreator (protocols::filters)   
CartesianBondedEnergyCreator (core::scoring::methods)   FilterFactory (protocols::filters)   MinimizationGraph (core::scoring)   ResidueFeatureFactory (protocols::comparative_modeling::features)   Strand (protocols::fldsgn::topology)   
CartesianHybridize (protocols::hybridization)   FilterMover (protocols::moves)   MinimizationNode (core::scoring)   ResidueFeatures (protocols::features)   StrandBundleFeatures (protocols::features::strand_assembly)   
CartesianMinimizer (core::optimization)   FilterRegistrator (protocols::filters)   MinimizeBackbone (protocols::ligand_docking)   ResidueFeaturesCreator (protocols::features)   StrandBundleFeaturesCreator (protocols::features::strand_assembly)   
CartesianMinimizerMap (core::optimization)   FilterScanFilter (protocols::protein_interface_design::filters)   MinimizeBackboneCreator (protocols::ligand_docking)   ResidueGridScoresFeatures (protocols::features)   StrandConstraints (protocols::abinitio)   
CartesianMultifunc (core::optimization)   FilterScanFilterCreator (protocols::protein_interface_design::filters)   MinimizeLigand (protocols::ligand_docking)   ResidueGridScoresFeaturesCreator (protocols::features)   StrandFragment (protocols::features::strand_assembly)   
CartesianSampler (protocols::hybridization)   FilterStructs (protocols::flxbb)   Minimizer (core::optimization)   ResidueGroupIGEdgeUpweighter (protocols::toolbox)   StrandPairing (core::scoring::dssp)   
CartesianSamplerCreator (protocols::hybridization)   FilterStructs_Packstat (protocols::flxbb)   MinimizerMap (core::optimization)   ResidueHasProperty (core::pack::task::operation)   StrandPairing (protocols::fldsgn::topology)   
CartesianSearchPattern (protocols::hotspot_hashing)   FilterStructs_TotalCharge (protocols::flxbb)   MinimizerMapBase (core::kinematics)   ResidueHasPropertyCreator (core::pack::task::operation)   StrandPairingSet (protocols::fldsgn::topology)   
CartGrid (core::grid)   FinalMinimizer (protocols::ligand_docking)   MinimizerOptions (core::optimization)   ResidueIEFilter (protocols::simple_filters)   StrandPairingSet (core::scoring::dssp)   
CartSCMinMinimizerMap (core::pack::scmin)   FinalMinimizerCreator (protocols::ligand_docking)   MinimizeStoredRBConfs (protocols::enzdes)   ResidueIEFilterCreator (protocols::simple_filters)   Strands (core::scoring)   
CartSCMinMultifunc (core::pack::scmin)   find_SilentStructOPs (protocols::wum)   MiniPose (core::pose)   ResidueIndexDescription (protocols::loops)   StrandTwistingMover (protocols::rbsegment_relax)   
CatPiCalculator (protocols::toolbox::pose_metric_calculators)   FingerprintBase (protocols::pockets)   MiniRelax (protocols::relax)   ResidueIndexDescriptionFromFile (protocols::loops)   StrongWolfeLineMinimization (core::optimization)   
CavityBall (core::scoring::packstat)   FingerprintMultifunc (protocols::pockets)   MinMover (protocols::simple_moves)   ResidueIndexIs (core::pack::task::operation)   StructuralSimilarityEvaluator (protocols::simple_filters)   
CavityBallCluster (core::scoring::packstat)   FirstClassEdge (core::pack::interaction_graph)   MinMoverCreator (protocols::simple_moves)   ResidueIndexIsCreator (core::pack::task::operation)   StructureDependentCalculator (core::pose::metrics)   
CB_Angle_Func (core::scoring::disulfides)   FirstClassNode (core::pack::interaction_graph)   MinMultiHarmonicFunc (core::scoring::constraints)   ResidueIndexIsnt (core::pack::task::operation)   StructureDependentPeakCalibrator (protocols::noesy_assign)   
Cb_Distance_Func (core::scoring::disulfides)   FitnessFunction (protocols::genetic_algorithm)   MinPackMover (protocols::simple_moves)   ResidueIndexIsntCreator (core::pack::task::operation)   StructureFeatures (protocols::features)   
CBScore (protocols::sic_dock)   FIX_HIS_TAUTOMER (core::pack::task)   MinPackMoverCreator (protocols::simple_moves)   ResidueInformation (core::io::pdb)   StructureFeaturesCreator (protocols::features)   
CBScoreVisitor (protocols::sic_dock)   FixbbCoupledRotamerSimAnnealer (core::pack::annealer)   MinScoreScoreFunction (core::scoring)   PDBPoseMap::ResidueKey (core::pose)   StructureFileNames (protocols::pack_daemon)   
CBSG_Dihedral_Func (core::scoring::disulfides)   FixbbLinkingRotamerSimAnnealer (core::pack::annealer)   MinValueEvaluator (protocols::simple_filters)   ResidueKinemageWriter (protocols::match::output)   StructureIndependentPeakCalibrator (protocols::noesy_assign)   
CcdLoopClosureMover (protocols::loops::loop_closure::ccd)   FixbbRotamerSets (core::pack::rotamer_set)   missing_fraction_sorter_biggest_first (protocols::frag_picker::quota)   ResidueKinWriter (core::conformation)   StructureRestrictor (protocols::moves)   
CcdMover (protocols::loops::loop_closure::ccd)   FixbbSimAnnealer (core::pack::annealer)   MissingDensityToJumpMover (protocols::simple_moves)   ResidueLacksProperty (core::pack::task::operation)   StructureScoresFeatures (protocols::features)   
CCDMoveWrapper (protocols::rbsegment_relax)   FixedBBEdge (core::pack::interaction_graph)   MixtureFunc (core::scoring::constraints)   ResidueLacksPropertyCreator (core::pack::task::operation)   StructureScoresFeaturesCreator (protocols::features)   
CDRH3Modeler (protocols::antibody)   FixedBBInteractionGraph (core::pack::interaction_graph)   MMAtomType (core::chemical)   ResidueLevelTask (core::pack::task)   StructureSimilarityEvaluatorCreator (protocols::simple_filters)   
CDRsMinPackMin (protocols::antibody2)   FixedBBNode (core::pack::interaction_graph)   MMAtomTypeSet (core::chemical)   ResidueLevelTask_ (core::pack::task)   StructureStore (protocols::abinitio)   
Cell (core::sequence)   FixedTemperatureController (protocols::canonical_sampling)   MMBondAngleEnergy (core::scoring::methods)   ResidueLoader (core::chemical)   Stub (core::kinematics)   
Cen_Distance_Func (core::scoring::disulfides)   FixTemplateJumpSetup (protocols::abinitio)   MMBondAngleEnergyCreator (core::scoring::methods)   ResidueLoaderCreator (core::chemical)   StubGenerator (protocols::hotspot_hashing)   
CenHBEnergy (core::scoring::methods)   FlatHarmonicFunc (core::scoring::constraints)   MMBondAngleLibrary (core::scoring::mm)   ResidueLoaderOptions (core::chemical)   StubID (core::id)   
CenHBEnergyCreator (core::scoring::methods)   FlexbbEdge (protocols::flexpack::interaction_graph)   MMBondAngleResidueTypeParam (core::scoring::mm)   ResidueLoaderOptionsCreator (core::chemical)   StubScoreFilter (protocols::protein_interface_design::filters)   
CenHBPotential (core::scoring)   FlexbbIGFactory (protocols::flexpack::interaction_graph)   MMBondAngleResidueTypeParamSet (core::scoring::mm)   ResidueMatcher (core::conformation)   StubScoreFilterCreator (protocols::protein_interface_design::filters)   
CenListInfo (core::scoring)   FlexbbInteractionGraph (protocols::flexpack::interaction_graph)   MMBondAngleScore (core::scoring::mm)   ResidueName3Is (core::pack::task::operation)   StubScoreLoopsFilter (protocols::protein_interface_design::filters)   
CenPairEnergy (core::scoring::methods)   FlexbbNode (protocols::flexpack::interaction_graph)   MMBondLengthEnergy (core::scoring::methods)   ResidueName3IsCreator (core::pack::task::operation)   StubScoreLoopsFilterCreator (protocols::protein_interface_design::filters)   
CenPairEnergyCreator (core::scoring::methods)   FlexbbRotamerSet (protocols::flexpack::rotamer_set)   MMBondLengthEnergyCreator (core::scoring::methods)   ResidueName3Isnt (core::pack::task::operation)   SubroutineMover (protocols::protein_interface_design::movers)   
CentroidDisulfideEnergy (core::scoring::disulfides)   FlexbbRotamerSets (protocols::flexpack::rotamer_set)   MMBondLengthLibrary (core::scoring::mm)   ResidueName3IsntCreator (core::pack::task::operation)   SubroutineMoverCreator (protocols::protein_interface_design::movers)   
CentroidDisulfideEnergyComponents (core::scoring::disulfides)   FlexbbSimAnnealer (protocols::flexpack::annealer)   MMBondLengthScore (core::scoring::mm)   ResidueNblistData (core::scoring)   SubToFullInfo (protocols::swa::monte_carlo)   
CentroidDisulfideEnergyContainer (core::scoring::disulfides)   FlexbbSparseMatrixIndex (protocols::flexpack::interaction_graph)   MMEnergyTableAtom (core::scoring::mm::mmtrie)   ResidueNeighborConstIterator (core::scoring)   SuckerEnergy (core::scoring::methods)   
CentroidDisulfideEnergyCreator (core::scoring::disulfides)   FlexPacker (protocols::flexpack)   MMLJEnergyInter (core::scoring::methods)   ResidueNeighborIterator (core::scoring)   SuckerEnergyCreator (core::scoring::methods)   
CentroidDisulfideNeighborConstIterator (core::scoring::disulfides)   FlexPepDockingAbInitio (protocols::flexpep_docking)   MMLJEnergyInterCreator (core::scoring::methods)   ResiduePairJump (protocols::jumping)   SuggestValueMessage (protocols::topology_broker)   
CentroidDisulfideNeighborIterator (core::scoring::disulfides)   FlexPepDockingFlags (protocols::flexpep_docking)   MMLJEnergyIntra (core::scoring::methods)   ResiduePairJumpSetup (protocols::jumping)   suite_info (protocols::rna)   
CentroidDisulfidePotential (core::scoring::disulfides)   FlexPepDockingLowRes (protocols::flexpep_docking)   MMLJEnergyIntraCreator (core::scoring::methods)   ResiduePairJumpSingle (protocols::jumping)   SumFunc (core::scoring::constraints)   
CentroidRelax (protocols::relax)   FlexPepDockingPoseMetrics (protocols::flexpep_docking)   MMLJEnergyTable (core::scoring::mm)   ResiduePairNeighborList (core::scoring)   SuperimposeMover (protocols::simple_moves)   
CentroidRelaxMover (protocols::surface_docking)   FlexPepDockingProtocol (protocols::flexpep_docking)   MMLJLibrary (core::scoring::mm)   ResiduePairXYZ (core::scoring::constraints)   SuperimposeMoverCreator (protocols::simple_moves)   
ChainbreakDistFunc (core::scoring::constraints)   FlexPepDockingProtocolCreator (protocols::flexpep_docking)   MMLJScore (core::scoring::mm)   ResiduePDBIndexIs (core::pack::task::operation)   SurfaceBackgroundEdge (core::pack::interaction_graph)   
ChainbreakEnergy (core::scoring::methods)   NonPlaidFingerprint::float4 (protocols::pockets)   MMTorsionEnergy (core::scoring::methods)   ResiduePDBIndexIsCreator (core::pack::task::operation)   SurfaceBackgroundNode (core::pack::interaction_graph)   
ChainbreakEnergyCreator (core::scoring::methods)   FloatingBaseChainClosureJobParameter (protocols::swa::rna)   MMTorsionEnergyCreator (core::scoring::methods)   ResiduePDBIndexIsnt (core::pack::task::operation)   SurfaceCalculator (protocols::toolbox::pose_metric_calculators)   
ChainbreakUtil (core::util)   FloatingResonance (protocols::noesy_assign)   MMTorsionLibrary (core::scoring::mm)   ResiduePDBIndexIsntCreator (core::pack::task::operation)   SurfaceDockingProtocol (protocols::surface_docking)   
ChainExistsFilter (protocols::ligand_docking)   FloppyTailMover (protocols::floppy_tail)   MMTorsionScore (core::scoring::mm)   PDBInfo::ResidueRecord (core::pose)   SurfaceEdge (core::pack::interaction_graph)   
ChainExistsFilterCreator (protocols::ligand_docking)   FlxbbDesign (protocols::flxbb)   ModelCDRH3 (protocols::antibody2)   ResidueScoresFeatures (protocols::features)   SurfaceEnergies (core::scoring::solid_surface)   
ChainGroupDiscriminator (protocols::simple_moves)   FlxbbDesignCreator (protocols::flxbb)   ModifyAnnealer (protocols::toolbox::task_operations)   ResidueScoresFeaturesCreator (protocols::features)   SurfaceEnergy (core::pack::interaction_graph)   
ChainIs (core::pack::task::operation)   FlxbbDesignPack (protocols::flxbb)   ModifyAnnealerCreator (protocols::toolbox::task_operations)   ResidueSecondaryStructureFeatures (protocols::features)   SurfaceEnergyCreator (core::pack::interaction_graph)   
ChainIsCreator (core::pack::task::operation)   FoldandDockClaimer (protocols::topology_broker)   ModifyStoredRBConfs (protocols::enzdes)   ResidueSecondaryStructureFeaturesCreator (protocols::features)   SurfaceInteractionGraph (core::pack::interaction_graph)   
ChainIsnt (core::pack::task::operation)   FoldConstraints (protocols::abinitio)   ModifyVariantTypeMover (protocols::simple_moves)   ResidueSelector (core::chemical)   SurfaceNode (core::pack::interaction_graph)   
ChainIsntCreator (core::pack::task::operation)   FoldResonance (protocols::noesy_assign)   ModifyVariantTypeMoverCreator (protocols::simple_moves)   ResidueSelectorSingle (core::chemical)   SurfaceOrientMover (protocols::surface_docking)   
ResiduePDBIndexIs::ChainPos (core::pack::task::operation)   FoldTree (core::kinematics)   MolarMassFilter (protocols::ligand_docking)   ResidueSetChainEnergyFilter (protocols::simple_filters)   SurfaceParameters (protocols::surface_docking)   
ChangeFoldTreeMover (protocols::moves)   FoldTreeFromLoops (protocols::loops)   MolarMassFilterCreator (protocols::ligand_docking)   ResidueSetChainEnergyFilterCreator (protocols::simple_filters)   SurfacePotential (core::pack::interaction_graph)   
ChargeAtom (protocols::qsar::scoring_grid)   FoldTreeFromLoopsCreator (protocols::loops)   MolData (core::chemical::sdf)   ResiduesInInterfaceFilter (protocols::simple_filters)   SurfaceSearchPattern (protocols::hotspot_hashing)   
ChargeCalculator (protocols::toolbox::pose_metric_calculators)   FoldTreeHybridize (protocols::hybridization)   MolecularDynamics (protocols::cartesian)   ResiduesInInterfaceFilterCreator (protocols::simple_filters)   SurfEnergy (core::scoring::packing)   
ChargeChargeFeatures (protocols::features)   ForceDisulfidesMover (protocols::simple_moves)   MolecularMassFilter (protocols::ligand_docking)   ResidueTorsionRestraints (protocols::ligand_docking)   SurfEnergyCreator (core::scoring::packing)   
ChargeChargeFeaturesCreator (protocols::features)   ForceDisulfidesMoverCreator (protocols::simple_moves)   MolecularMassFilterCreator (protocols::ligand_docking)   ResidueTotalScoresFeatures (protocols::features)   SurfVol (core::scoring::packing)   
ChargeGrid (protocols::qsar::scoring_grid)   FormatStringOutputter (protocols::outputter)   MolecularSurfaceCalculator (core::scoring::sc)   ResidueTotalScoresFeaturesCreator (protocols::features)   SurfVolDeriv (core::scoring::packing)   
ChargeGridCreator (protocols::qsar::scoring_grid)   FormFactor (core::scoring::saxs)   MolFileParser (core::chemical::sdf)   ResidueType (core::chemical)   SurfVolEnergy (core::scoring::packing)   
CharmmPeriodicFunc (core::scoring::constraints)   FormFactorManager (core::scoring::saxs)   MolWriter (core::chemical::sdf)   ResidueTypeConstraint (core::scoring::constraints)   SurfVolEnergyCreator (core::scoring::packing)   
CheckPointer (protocols::checkpoint)   FourAtomsConstraintData (protocols::frag_picker::scores)   MonteCarlo (protocols::moves)   ResidueTypeFilter (core::pack::task::operation)   SurrogateVariableExpression (protocols::pack_daemon)   
ChemicalManager (core::chemical)   FourPointsFunc (core::scoring::constraints)   MonteCarloExceptionConverge (protocols::moves)   ResidueTypeFilterCreator (core::pack::task::operation)   SWAligner (core::sequence)   
ChemicalShiftAnisotropy (core::scoring)   FragCache (core::fragment)   MonteCarloLoader (protocols::jd2::parser)   ResidueTypeLinkingConstraint (core::scoring::constraints)   SwapSegment (protocols::seeded_abinitio)   
ChemicalShiftAnisotropyEnergy (core::scoring::methods)   FragData (core::fragment)   MonteCarloLoaderCreator (protocols::jd2::parser)   ResidueTypeSet (core::chemical)   SwapSegmentCreator (protocols::seeded_abinitio)   
ChemicalShiftAnisotropyEnergyCreator (core::scoring::methods)   FragFactory (core::fragment)   MonteCarloRecover (protocols::simple_moves)   ResidueTypesFeatures (protocols::features)   SwitchChainOrderMover (protocols::simple_moves)   
ChemicalShiftData (core::scoring::rna::chemical_shift)   FragID (core::fragment)   MonteCarloRecoverCreator (protocols::simple_moves)   ResidueTypesFeaturesCreator (protocols::features)   SwitchChainOrderMoverCreator (protocols::simple_moves)   
ChemicalShiftEvaluator (protocols::sparta)   FragID_Iterator (core::fragment)   MonteCarloTest (protocols::simple_moves)   ResidueVicinityCstGeneratorCreator (protocols::forge::remodel)   SwitchResidueTypeSetMover (protocols::simple_moves)   
ChemicalShiftEvaluatorCreator (protocols::sparta)   FragInsertAndAlignMover (protocols::rbsegment_relax)   MonteCarloTestCreator (protocols::simple_moves)   ResidueVicinityInfo (protocols::forge::remodel)   SwitchResidueTypeSetMoverCreator (protocols::simple_moves)   
ChemicalShiftScoringScheme (core::sequence)   FragmentAllAtomCrmsd (protocols::frag_picker::scores)   MonteCarloUtil (protocols::moves)   ResidueVicinityRCG (protocols::forge::remodel)   SymAtomTreeMinimizer (core::optimization::symmetry)   
ChemicalShiftSequence (core::sequence)   FragmentCandidate (protocols::frag_picker)   Motif (protocols::motifs)   ResidueXYZ (core::scoring::constraints)   SymAtomTreeMultifunc (core::optimization::symmetry)   
ChemicalShiftSequenceCreator (core::sequence)   FragmentClaimer (protocols::topology_broker)   MotifDnaPacker (protocols::motifs)   ResInteractions (protocols::toolbox::match_enzdes_util)   SymDockBaseProtocol (protocols::symmetric_docking)   
ChiralMover (protocols::simple_moves::chiral)   FragmentComparatorBase (protocols::frag_picker)   MotifDnaPackerCreator (protocols::motifs)   ResLvlTaskOperation (core::pack::task::operation)   SymDockingHiRes (protocols::symmetric_docking)   
ChiSet (core::pack::dunbrack)   FragmentCost (protocols::simple_moves)   MotifHit (protocols::motifs)   ResLvlTaskOperationCreator (core::pack::task::operation)   SymDockingInitialPerturbation (protocols::simple_moves::symmetry)   
ChiWellRmsdEvaluator (protocols::simple_filters)   FragmentCrmsd (protocols::frag_picker::scores)   MotifLibrary (protocols::motifs)   ResLvlTaskOperationFactory (core::pack::task::operation)   SymDockingLowRes (protocols::symmetric_docking)   
ChiWellRmsdEvaluatorCreator (protocols::simple_filters)   FragmentCrmsdResDepth (protocols::frag_picker::scores)   MotifSearch (protocols::motifs)   ResLvlTaskOperationRegistrator (core::pack::task::operation)   SymDockingSlideIntoContact (protocols::simple_moves::symmetry)   
Chunk (protocols::nonlocal)   FragmentDME (protocols::frag_picker::scores)   MoveBeforeFilter (protocols::filters)   DisulfideFile::ResNum (core::io::raw_data)   SymDockProtocol (protocols::symmetric_docking)   
ChunkSet (protocols::rna)   FragmentIO (core::fragment)   MoveBeforeFilterCreator (protocols::filters)   ResolutionSwitcher (protocols::abinitio)   SymDof (core::conformation::symmetry)   
ChunkTrialMover (protocols::hybridization)   FragmentLibrary (protocols::rna)   MoveMap (core::kinematics)   Resonance (protocols::noesy_assign)   symECreator (core::scoring::sym_e)   
Circle (core::scoring::packstat)   FragmentLibraryManager (core::fragment::picking_old)   MoveMapBuilder (protocols::ligand_docking)   ResonanceList (protocols::noesy_assign)   symEnergy (core::scoring::sym_e)   
CircularGeneral1D_Func (core::scoring::constraints)   FragmentMover (protocols::simple_moves)   MoveMapBuilderLoader (protocols::ligand_docking)   RespairInteractions (core::scoring::custom_pair_distance)   SymEnergyCutRotamerTrialsMover (protocols::simple_moves::symmetry)   
CircularHarmonicFunc (core::scoring::constraints)   FragmentPair (protocols::features::helixAssembly)   MoveMapBuilderLoaderCreator (protocols::ligand_docking)   ResPairMinimizationData (core::scoring)   SymFoldandDockMoveRbJumpMover (protocols::symmetric_docking)   
CircularPermutation (protocols::fldsgn)   FragmentPicker (protocols::frag_picker)   MovePoseToMembraneCenterMover (protocols::rigid)   ResRangePredicate (core::scoring)   SymFoldandDockRbTrialMover (protocols::symmetric_docking)   
CircularPermutationCreator (protocols::fldsgn)   FragmentReader (protocols::jd2::parser)   Mover (protocols::moves)   ResResEnergyInvoker (core::scoring::etable)   SymFoldandDockSlideTrialMover (protocols::symmetric_docking)   
CircularPowerFunc (core::scoring::constraints)   FragmentRmsd (core::fragment)   Mover_LoopHashRefine (protocols::loophash)   ResSingleMinimizationData (core::scoring)   SymInterfaceSidechainMinMover (protocols::symmetric_docking)   
CircularSigmoidalFunc (core::scoring::constraints)   FragmentSampler (protocols::abinitio)   MoverContainer (protocols::moves)   RestrictAbsentCanonicalAAS (core::pack::task::operation)   SymmData (core::conformation::symmetry)   
ClaimerMessage (protocols::topology_broker)   FragmentScoreManager (protocols::frag_picker::scores)   MoverCreator (protocols::moves)   RestrictAbsentCanonicalAASCreator (core::pack::task::operation)   SymmDataFactory (core::conformation::symmetry)   
ClashCountCalculator (protocols::toolbox::pose_metric_calculators)   FragmentScoreMap (protocols::frag_picker::scores)   MoverFactory (protocols::moves)   RestrictAbsentCanonicalAASRLT (core::pack::task::operation)   SymmDataLoader (core::conformation::symmetry)   
ClassicAbinitio (protocols::abinitio)   FragmentScoringMethod (protocols::frag_picker::scores)   MoverList (protocols::wum)   RestrictAbsentCanonicalAASRLTCreator (core::pack::task::operation)   SymmDataLoaderCreator (core::conformation::symmetry)   
ClassicFragmentMover (protocols::simple_moves)   FragmentSelectingRule (protocols::frag_picker)   MoverRegistrator (protocols::moves)   RestrictByCalculatorsOperation (protocols::toolbox::task_operations)   SymmDataOptions (core::conformation::symmetry)   
ClassicGrid (protocols::qsar::scoring_grid)   FragQualCalculator (protocols::toolbox::pose_metric_calculators)   MoverStatistics (protocols::moves)   RestrictByCalculatorsOperationCreator (protocols::toolbox::task_operations)   SymmDataOptionsCreator (core::conformation::symmetry)   
ClassicGridCreator (protocols::qsar::scoring_grid)   FragQualFilter (protocols::fldsgn::filters)   MPI_LoopHashRefine (protocols::loophash)   RestrictChainToRepackingOperation (protocols::toolbox::task_operations)   SymmetricConformation (core::conformation::symmetry)   
ClassicMatchAlgorithm (protocols::match::downstream)   FragQualFilterCreator (protocols::fldsgn::filters)   MPI_LoopHashRefine_Emperor (protocols::loophash)   RestrictChainToRepackingOperationCreator (protocols::toolbox::task_operations)   SymmetricEnergies (core::scoring::symmetry)   
ClassicRelax (protocols::relax)   FragSet (core::fragment)   MPI_LoopHashRefine_Master (protocols::loophash)   RestrictConservedLowDdgOperation (protocols::toolbox::task_operations)   SymmetricFragmentMover (protocols::simple_moves)   
ClassicRelaxCreator (protocols::relax)   FragSetCollection (core::fragment)   MPI_Relax (protocols::wum)   RestrictConservedLowDdgOperationCreator (protocols::toolbox::task_operations)   SymmetricLigandEnergy (core::scoring::methods)   
ClearConstraintsMover (protocols::simple_moves)   FragSetLoader (protocols::jd2::parser)   MPI_WorkUnitManager (protocols::wum)   RestrictDesignToProteinDNAInterface (protocols::dna)   SymmetricLigandEnergyCreator (core::scoring::methods)   
ClearConstraintsMoverCreator (protocols::simple_moves)   FragSetLoaderCreator (protocols::jd2::parser)   MPI_WorkUnitManager_Slave (protocols::wum)   RestrictDesignToProteinDNAInterfaceCreator (protocols::dna)   SymmetricMotifFilter (protocols::simple_filters)   
CloseFold (protocols::seeded_abinitio)   FragsToAtomDist (protocols::noesy_assign)   MPIArchiveJobDistributor (protocols::jd2::archive)   RestrictIdentitiesAtAlignedPositionsOperation (protocols::toolbox::task_operations)   SymmetricMotifFilterCreator (protocols::simple_filters)   
CloseFoldCreator (protocols::seeded_abinitio)   FragStore (core::fragment)   MPIBPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   RestrictIdentitiesAtAlignedPositionsOperationCreator (protocols::toolbox::task_operations)   SymmetricRmsdEvaluator (protocols::simple_filters)   
CloseOneCDRLoop (protocols::antibody2)   Frame (core::fragment)   MpiFileBuffer (protocols::jd2)   RestrictInterGroupVectorOperation (protocols::toolbox::task_operations)   SymmetricRMSMover (protocols::simple_moves::symmetry)   
CloseOneMover (protocols::antibody)   FrameIterator (core::fragment)   MPIFileBufJobDistributor (protocols::jd2)   RestrictInterGroupVectorOperationCreator (protocols::toolbox::task_operations)   SymmetricRotamerSet_ (core::pack::rotamer_set::symmetry)   
CloudPDBWriter (protocols::match::output)   FrameIteratorWorker_ (core::fragment)   MPIHPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   RestrictNativeResiduesOperation (protocols::toolbox::task_operations)   SymmetricRotamerSetFactory (core::pack::rotamer_set::symmetry)   
Cluster (protocols::cluster)   FrameList (core::fragment)   MPIMultiCommJobDistributor (protocols::jd2)   RestrictNativeResiduesOperationCreator (protocols::toolbox::task_operations)   SymmetricRotamerSets (core::pack::rotamer_set::symmetry)   
Cluster_Member (protocols::swa::rna)   FrameListIterator_ (core::fragment)   MPIMultistateFitnessFunction (protocols::pack_daemon)   RestrictNonSurfaceToRepackingOperation (protocols::toolbox::task_operations)   SymmetricScoreFunction (core::scoring::symmetry)   
ClusterBase (protocols::toolbox)   FrameWork (protocols::antibody2)   MPIPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   RestrictNonSurfaceToRepackingOperationCreator (protocols::toolbox::task_operations)   SymmetryInfo (core::conformation::symmetry)   
ClusterBase (protocols::cluster)   FullatomCustomPairDistanceEnergy (core::scoring::custom_pair_distance)   MPIWorkPartitionJobDistributor (protocols::jd2)   RestrictOperationsBase (protocols::toolbox::task_operations)   SymmetrySlider (protocols::simple_moves::symmetry)   
ClusterOptions (protocols::toolbox)   FullatomCustomPairDistanceEnergyCreator (core::scoring::custom_pair_distance)   MPIWorkPoolJobDistributor (protocols::jd2)   RestrictResiduesToRepackingOperation (protocols::toolbox::task_operations)   SymMinimizerMap (core::optimization::symmetry)   
ClusterPhilStyle (protocols::toolbox)   FullatomDisulfideEnergy (core::scoring::disulfides)   MultiConstraint (core::scoring::constraints)   RestrictResiduesToRepackingOperationCreator (protocols::toolbox::task_operations)   SymMinMover (protocols::simple_moves::symmetry)   
ClusterPhilStyle (protocols::cluster)   FullatomDisulfideEnergyComponents (core::scoring::disulfides)   MultiConstraintCreator (core::scoring::constraints)   RestrictResidueToRepacking (core::pack::task::operation)   SymMinMoverCreator (protocols::simple_moves::symmetry)   
ClusterPhilStyle_Loop (protocols::cluster)   FullatomDisulfideEnergyContainer (core::scoring::disulfides)   MultiCoolAnnealer (core::pack::annealer)   RestrictResidueToRepackingCreator (core::pack::task::operation)   SymmLinearMemEdge (core::pack::interaction_graph)   
RigidChunkClaimer::CM_SuggestFixResidue (protocols::topology_broker)   FullatomDisulfideEnergyCreator (core::scoring::disulfides)   Multifunc (core::optimization)   RestrictToAlignedSegmentsOperation (protocols::toolbox::task_operations)   SymmLinearMemNode (core::pack::interaction_graph)   
CmdLineData (protocols::topology_broker)   FullatomDisulfidePotential (core::scoring::disulfides)   MultipleDomainMover (protocols::rna)   RestrictToAlignedSegmentsOperationCreator (protocols::toolbox::task_operations)   SymmLinearMemoryInteractionGraph (core::pack::interaction_graph)   
CoarseEtable (core::coarse)   FullatomRelaxMover (protocols::surface_docking)   MultiProbePerSphereAccumulator (core::scoring::packstat)   RestrictToCDRH3Loop (protocols::toolbox::task_operations)   SymmMinimalistEdge (core::pack::interaction_graph)   
CoarseEtableEnergy (core::scoring::etable)   FullAtomRNA_Fragments (protocols::rna)   MultiProbePoseAccumulator (core::scoring::packstat)   RestrictToCDRH3LoopCreator (protocols::toolbox::task_operations)   SymmMinimalistInteractionGraph (core::pack::interaction_graph)   
CoarseEtableEnergyCreator (core::scoring::etable)   FullChiSampleSet (protocols::match::upstream)   MultistateAggregateFunction (protocols::pack_daemon)   RestrictToInterface (protocols::toolbox::task_operations)   SymmMinimalistNode (core::pack::interaction_graph)   
CoarseRNA_DeNovoProtocol (protocols::coarse_rna)   Func (core::scoring::constraints)   MultiStateAggregateFunction (protocols::multistate_design)   RestrictToInterface (core::pack::task::operation)   SymmOnTheFlyEdge (core::pack::interaction_graph)   
CoarseRNA_Fragments (protocols::coarse_rna)   func_1d (core::optimization)   MultiStateEntity (protocols::multistate_design)   RestrictToInterfaceCreator (protocols::toolbox::task_operations)   SymmOnTheFlyInteractionGraph (core::pack::interaction_graph)   
CoarseRNA_LoopCloser (protocols::coarse_rna)   FuncFactory (core::scoring::constraints)   MultistateFitnessFunction (protocols::pack_daemon)   RestrictToInterfaceOperation (protocols::toolbox::task_operations)   SymmOnTheFlyNode (core::pack::interaction_graph)   
CoarseRotamer (core::pack::dunbrack)   FunGroupTK (protocols::kinmatch)   MultiStateFitnessFunction (protocols::multistate_design)   RestrictToInterfaceOperationCreator (protocols::toolbox::task_operations)   SymPackRotamersMover (protocols::simple_moves::symmetry)   
CoarseRotamerSet (core::pack::dunbrack)   
  G  
MultiStatePacker (protocols::multistate_design)   RestrictToInterfaceVectorOperation (protocols::toolbox::task_operations)   SymPackRotamersMoverCreator (protocols::simple_moves::symmetry)   
CoarseSingleResidueLibrary (core::pack::dunbrack)   MultiTemperatureTrialCounter (protocols::canonical_sampling)   RestrictToInterfaceVectorOperationCreator (protocols::toolbox::task_operations)   SymRestrictTaskForDocking (protocols::symmetric_docking)   
COFilter (protocols::simple_filters)   G   MultiThreadingJob (protocols::jd2)   RestrictToLoopsAndNeighbors (protocols::toolbox::task_operations)   SymRotamerTrialsMover (protocols::simple_moves::symmetry)   
ColorGradient (protocols::qsar)   GA_Minimizer (core::optimization)   MultiThreadingMover (protocols::comparative_modeling)   RestrictToLoopsAndNeighborsCreator (protocols::toolbox::task_operations)   SymRotamerTrialsMoverCreator (protocols::simple_moves::symmetry)   
Combine_Tags_Info (protocols::swa::rna)   GatherPosesMover (protocols::cluster)   Mutant (protocols::pmut_scan)   RestrictToNeighborhoodOperation (protocols::toolbox::task_operations)   SymShakeStructureMover (protocols::simple_moves::symmetry)   
CombineChainsMover (protocols::domain_assembly)   Gaussian_parameter (core::scoring::rna)   MutateResidue (protocols::simple_moves)   RestrictToNeighborhoodOperationCreator (protocols::toolbox::task_operations)   SymSidechainMinMover (protocols::symmetric_docking)   
CombinedConstraintEvaluator (protocols::constraints_additional)   GaussianFunc (core::scoring::constraints)   MutateResidueCreator (protocols::simple_moves)   RestrictToRepacking (core::pack::task::operation)   SymSlideInfo (core::conformation::symmetry)   
CombinedConstraintEvaluatorCreator (protocols::constraints_additional)   GaussianOverlapEnergy (core::scoring::methods)   MutationData (protocols::pmut_scan)   RestrictToRepackingCreator (core::pack::task::operation)   
  T  
CombinedFilter (protocols::filters)   GaussianOverlapEnergyCreator (core::scoring::methods)   MyAtom (protocols::fldsgn)   RestrictToRepackingRLT (core::pack::task::operation)   
CombinedFilterCreator (protocols::filters)   GaussianRBSegmentMover (protocols::rbsegment_relax)   
  N  
RestrictToRepackingRLTCreator (core::pack::task::operation)   TableLookupEtableEnergy (core::scoring::etable)   
CombinedTaskOperation (protocols::flxbb)   GDB (protocols::sparta)   RestrictToTerminiOperation (protocols::toolbox::task_operations)   TableLookupEvaluator (core::scoring::etable)   
compare_base_bin (protocols::swa::rna)   GenBornEnergy (core::scoring::methods)   NamedAtomID (core::id)   RestrictToTerminiOperationCreator (protocols::toolbox::task_operations)   TabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
compare_int_pair (protocols::swa::rna)   GenBornEnergyCreator (core::scoring::methods)   NamedAtomPairConstraint (core::scoring::constraints)   RestrictYSDesign (core::pack::task::operation)   TailsScoreMover (protocols::simple_moves)   
compare_test (protocols::swa::rna)   GenBornPoseInfo (core::scoring)   NamedAtomPairConstraintCreator (protocols::constraints_additional)   RestrictYSDesignCreator (core::pack::task::operation)   TalosSSSimilarity (protocols::frag_picker::scores)   
CompareByScoreCombination (protocols::frag_picker)   GenBornPotential (core::scoring)   NamedStubID (core::id)   ResTypeSequence_lt (protocols::dna)   TARGET (core::pack::task)   
CompareQueryPosition (protocols::frag_picker)   GenBornResidueInfo (core::scoring)   NATAA (core::pack::task)   ReturnSidechainMover (protocols::simple_moves)   TargetRotamerCoords (protocols::match::downstream)   
CompareScoreComponent (protocols::frag_picker)   GenBornRotamerSetInfo (core::scoring)   NatbiasHelicesSheetPotential (protocols::fldsgn::potentials::sspot)   Reversion (protocols::dna)   TaskAwareCsts (protocols::protein_interface_design::movers)   
CompareTags (protocols::jd2)   GeneralEvent (core::conformation::signals)   NatbiasHelixPairPotential (protocols::fldsgn::potentials::sspot)   Revert (protocols::protein_interface_design)   TaskAwareCstsCreator (protocols::protein_interface_design::movers)   
CompareTotalScore (protocols::frag_picker)   GeneralEvent (core::pose::signals)   NatbiasSecondaryStructureEnergy (protocols::fldsgn::potentials::sspot)   RG_Energy (core::scoring::methods)   TaskAwareMinMover (protocols::simple_moves)   
CompassScoringScheme (core::sequence)   GenerateStoredRBConfs (protocols::enzdes)   NatbiasSecondaryStructureEnergyCreator (protocols::fldsgn::potentials::sspot)   RG_Energy_Fast (core::scoring::methods)   TaskAwareMinMoverCreator (protocols::simple_moves)   
CompleteConnectionsFilter (protocols::ligand_docking)   GenericJobInputter (protocols::comparative_modeling)   NatbiasSheetPotential (protocols::fldsgn::potentials::sspot)   RG_Energy_FastCreator (core::scoring::methods)   TaskFactory (core::pack::task)   
CompleteConnectionsFilterCreator (protocols::ligand_docking)   GenericJobInputterCreator (protocols::comparative_modeling)   NatbiasStrandPairPotential (protocols::fldsgn::potentials::sspot)   RG_Energy_RNA (core::scoring::rna)   TaskOperation (core::pack::task::operation)   
MPIArchiveJobDistributor::CompletionMessage (protocols::jd2::archive)   GenericMonteCarloMover (protocols::simple_moves)   NativeEvaluatorCreator (protocols::simple_filters)   RG_Energy_RNACreator (core::scoring::rna)   TaskOperationCreator (core::pack::task::operation)   
ComposeSearchPatterns (protocols::hotspot_hashing)   GenericMonteCarloMoverCreator (protocols::simple_moves)   NATRO (core::pack::task)   RG_MinData (core::scoring::methods)   TaskOperationFactory (core::pack::task::operation)   
CompositeFragmentSelector (protocols::frag_picker)   GenericResidueConnectionData (core::scoring::etable::etrie)   NBListCache (core::scoring::symmetry)   RGFilter (protocols::simple_filters)   TaskOperationLoader (protocols::jd2::parser)   
CompositeScoringScheme (core::sequence)   GenericRule (core::coarse)   NC (core::pack::task)   RigidBodyDeterministicSpinMover (protocols::rigid)   TaskOperationLoaderCreator (protocols::jd2::parser)   
CompositeSequence (core::sequence)   GeneticAlgorithm (protocols::genetic_algorithm)   NCAARotLibPath (core::chemical)   RigidBodyDofPerturbMover (protocols::rigid)   TaskOperationMPM (protocols::match)   
CompositeSequenceCreator (core::sequence)   GeometricFunc (protocols::moves)   NCaCaC_Dihedral_Func (core::scoring::disulfides)   RigidBodyDofRandomizeMover (protocols::rigid)   TaskOperationRegistrator (core::pack::task::operation)   
CompositionMover (protocols::moves)   GeometricSolEnergy (core::scoring::geometric_solvation)   NcontactsCalculator (protocols::fldsgn)   RigidBodyDofRandomTransMover (protocols::rigid)   TemperatureController (protocols::canonical_sampling)   
CompoundFilter (protocols::filters)   GeometricSolEnergyCreator (core::scoring::geometric_solvation)   NcontactsFilter (protocols::fldsgn::filters)   RigidBodyDofSeqPerturbMover (protocols::rigid)   TemperedDocking (protocols::docking)   
CompoundFilterCreator (protocols::filters)   GeometricSolvationFeatures (protocols::features)   NcontactsFilterCreator (protocols::fldsgn::filters)   RigidBodyDofSeqRandomizeMover (protocols::rigid)   TemperedDockingCreator (protocols::docking)   
CompoundTranslate (protocols::ligand_docking)   GeometricSolvationFeaturesCreator (protocols::features)   NegSpaceElement (core::graph)   RigidBodyDofSeqTransMover (protocols::rigid)   TemperingBase (protocols::canonical_sampling)   
CompoundTranslateCreator (protocols::ligand_docking)   GeometrySecMatchRPE (protocols::match::downstream)   NeighborDependentTabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   RigidBodyDofTransMover (protocols::rigid)   Template (protocols::abinitio)   
Computes   GeomSampleInfo (protocols::toolbox::match_enzdes_util)   NeighborDependentTorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   RigidBodyInfo (protocols::docking)   TemplateFragmentClaimer (protocols::topology_broker)   
ComputeTotalDistCst (protocols::abinitio)   GrabAllCollector (protocols::frag_picker)   NeighborhoodByDistanceCalculator (protocols::toolbox::pose_metric_calculators)   RigidBodyMotionMover (protocols::rigid)   TemplateHistory (protocols::hybridization)   
ConcurrencyTest (protocols::features::helixAssembly)   GraftCDRLoopsProtocol (protocols::antibody2)   NeighborList (core::scoring)   RigidBodyMoveBaseRSO (protocols::toolbox::rotamer_set_operations)   TemplateJumpClaimer (protocols::topology_broker)   
ConcurrencyTestCreator (protocols::features::helixAssembly)   GraftMover (protocols::antibody)   NeighborsByDistanceCalculator (protocols::toolbox::pose_metric_calculators)   RigidBodyMover (protocols::rigid)   TemplateJumpSetup (protocols::abinitio)   
Conformation (core::conformation)   GraftMoverBase (protocols::grafting)   NeighborTypeFilter (protocols::simple_filters)   RigidBodyMoveRSO (protocols::toolbox::rotamer_set_operations)   Templates (protocols::abinitio)   
ConformationEvent (core::pose::signals)   GraftOneCDRLoop (protocols::antibody2)   NeighborTypeFilterCreator (protocols::simple_filters)   RigidBodyPerturbMover (protocols::rigid)   TenANeighborEdge (core::scoring)   
ConformationKinWriter (core::conformation)   GraftOneMover (protocols::antibody)   NestedEnergyTermDDGMutationOptEData (protocols::optimize_weights)   RigidBodyPerturbNoCenterMover (protocols::rigid)   TenANeighborGraph (core::scoring)   
ConformationViewer (protocols::viewer)   Graph (core::graph)   NestedEnergyTermPNatAAOptEPositionData (protocols::optimize_weights)   RigidBodyPerturbNoCenterMoverCreator (protocols::rigid)   TenANeighborNode (core::scoring)   
ConformationXYZ (core::scoring::constraints)   GraphicsState (protocols::viewer)   NMerPSSMEnergy (core::scoring::methods)   RigidBodyRandomizeMover (protocols::rigid)   TensorsOptimizer (protocols::scoring::methods::pcs)   
ConformerSwitchMover (protocols::docking)   GreedyKCenter (protocols::toolbox)   NMerPSSMEnergyCreator (core::scoring::methods)   RigidBodySampler (protocols::swa)   TensorsOptimizer (protocols::scoring::methods::pcs2)   
ConformerSwitchMoverCreator (protocols::docking)   GreedyOptMutationMover (protocols::design_opt)   NMerPSSMEnergyFilter (protocols::simple_filters)   RigidBodySpinMover (protocols::rigid)   TensorsOptimizerFix (protocols::scoring::methods::pcs2)   
ConnectionEvent (core::conformation::signals)   GreedyOptMutationMoverCreator (protocols::design_opt)   NMerPSSMEnergyFilterCreator (protocols::simple_filters)   RigidBodyTransMover (protocols::rigid)   TensorsOptimizerSvd (protocols::scoring::methods::pcs2)   
ConnectRight (protocols::forge::build)   GreenPacker (protocols::simple_moves)   NMerRefEnergy (core::scoring::methods)   RigidChunkClaimer (protocols::topology_broker)   TerminusDistanceFilter (protocols::simple_filters)   
ConsensusDesignMover (protocols::simple_moves)   GridBase (protocols::qsar::scoring_grid)   NMerRefEnergyCreator (core::scoring::methods)   RigidLigandBuilder (protocols::match::downstream)   TerminusDistanceFilterCreator (protocols::simple_filters)   
ConsensusDesignMoverCreator (protocols::simple_moves)   GridCreator (protocols::qsar::scoring_grid)   NO_ADDUCTS (core::pack::task)   RigidScore (protocols::sic_dock)   TestPattern (protocols::hotspot_hashing)   
ConservedPosMutationFilter (protocols::simple_filters)   GridFactory (protocols::qsar::scoring_grid)   Node (core::kinematics)   RigidSearchMover (protocols::ligand_docking)   TetherLigand (protocols::ligand_docking)   
ConservedPosMutationFilterCreator (protocols::simple_filters)   GridInfo (core::scoring::geometric_solvation)   Node (core::graph)   RingConformationMover (protocols::simple_moves::carbohydrates)   TheozymeInvrotTree (protocols::toolbox::match_enzdes_util)   
SilentFileData::const_iterator (core::io::silent)   GridInitMover (protocols::qsar::scoring_grid)   NodeBase (core::pack::interaction_graph)   RingData (protocols::sparta)   ThermodynamicMover (protocols::canonical_sampling)   
RawFileData::const_iterator (core::io::raw_data)   GridInitMoverCreator (protocols::qsar::scoring_grid)   NoesyModule (protocols::noesy_assign)   RMS_Energy (core::scoring::methods)   ThermodynamicObserver (protocols::canonical_sampling)   
ConstAbinitioMoverWeight (protocols::topology_broker::weights)   GridManager (protocols::qsar::scoring_grid)   NonContinuousFrame (core::fragment)   RMS_EnergyCreator (core::scoring::methods)   ThreadingJob (protocols::comparative_modeling)   
ConstantConstraint (core::scoring::constraints)   GridRegistrator (protocols::qsar::scoring_grid)   NonlocalContactsCalculator (protocols::toolbox::pose_metric_calculators)   RmsdEvaluator (protocols::simple_filters)   ThreadingJobInputter (protocols::comparative_modeling)   
ConstantFunc (core::scoring::constraints)   GridSearchIterator (protocols::scoring::methods::pcs2)   NonlocalFrags (protocols::frag_picker::nonlocal)   RmsdEvaluatorCreator (protocols::simple_filters)   ThreadingJobInputterCreator (protocols::comparative_modeling)   
ConstantLengthFragSet (core::fragment)   GridSearchIterator (protocols::scoring::methods::pcs)   NonlocalPair (protocols::frag_picker::nonlocal)   RmsdFilter (protocols::protein_interface_design::filters)   ThreadingMover (protocols::comparative_modeling)   
ConstantLengthFragSetIterator_ (core::fragment)   GridSearchIteratorCA (protocols::scoring::methods::pcs2)   NonPlaidFingerprint (protocols::pockets)   RmsdFilterCreator (protocols::protein_interface_design::filters)   ThreadSequenceOperation (protocols::toolbox::task_operations)   
ConstPattern (protocols::hotspot_hashing)   GroupDiscriminator (protocols::simple_moves)   NonResidueTypeConstraint (core::scoring::constraints)   RmsdTargetEvaluatorCreator (protocols::simple_filters)   ThreadSequenceOperationCreator (protocols::toolbox::task_operations)   
Constraint (core::scoring::constraints)   GrowLeft (protocols::forge::build)   NonSequentialNeighborsFilter (protocols::simple_filters)   RMSVallData (protocols::frags)   TimeEvaluator (protocols::evaluation)   
ConstraintClaimer (protocols::topology_broker)   GrowLigand (protocols::ligand_docking)   NonSequentialNeighborsFilterCreator (protocols::simple_filters)   RNA_AddMover (protocols::swa::monte_carlo)   TimeFilter (protocols::filters)   
ConstraintCreator (core::scoring::constraints)   GrowLigandCreator (protocols::ligand_docking)   NoOutputJobOutputter (protocols::jd2)   RNA_AddOrDeleteMover (protocols::swa::monte_carlo)   TimeFilterCreator (protocols::filters)   
ConstraintEdge (core::scoring::constraints)   GrowPeptides (protocols::seeded_abinitio)   NoOutputJobOutputterCreator (protocols::jd2)   RNA_AnalyticLoopCloser (protocols::swa::rna)   Timer (protocols::checkpoint)   
ConstraintedOptimizationWeightFunc (protocols::optimize_weights)   GrowPeptidesCreator (protocols::seeded_abinitio)   NoRepackDisulfides (core::pack::task::operation)   RNA_AtomVDW (core::scoring::rna)   TMalign (protocols::hybridization)   
ConstraintEvaluator (protocols::constraints_additional)   GrowRight (protocols::forge::build)   NoRepackDisulfidesCreator (core::pack::task::operation)   RNA_BaseBaseEnergy (core::scoring::rna)   TopCountOfAllInputs (protocols::features)   
ConstraintEvaluatorCreator (protocols::constraints_additional)   GuardedLoopsFromFile (protocols::loops)   NoResFilter (core::pack::task::operation)   RNA_BulgeEnergy (core::scoring::rna)   TopCountOfEachInput (protocols::features)   
ConstraintEvaluatorWrapper (protocols::topology_broker)   GunnCost (protocols::simple_moves)   NoResFilterCreator (core::pack::task::operation)   RNA_BulgeEnergyCreator (core::scoring::rna)   TopologyBroker (protocols::topology_broker)   
ConstraintEvaluatorWrapperCreator (protocols::topology_broker)   GunnCost (protocols::frag_picker::scores)   NormalizedEvaluatedArchive (protocols::jd2::archive)   RNA_CentroidInfo (core::scoring::rna)   TopologyClaimer (protocols::topology_broker)   
ConstraintFactory (core::scoring::constraints)   GunnCostScore (protocols::frag_picker::scores)   NOTAA (core::pack::task)   RNA_ChemicalShiftEnergy (core::scoring::rna::chemical_shift)   TopologyClaimerFactory (protocols::topology_broker)   
ConstraintFileCstGeneratorCreator (protocols::forge::constraints)   GunnTuple (protocols::simple_moves)   NPDPropCalculator (protocols::pack_daemon)   RNA_ChemicalShiftEnergyCreator (core::scoring::rna::chemical_shift)   TopOutFunc (core::scoring::constraints)   
ConstraintFileRCG (protocols::forge::constraints)   GunnTuple (protocols::frag_picker::scores)   NPDPropCalculatorCreator (protocols::pack_daemon)   RNA_ChemicalShiftPotential (core::scoring::rna::chemical_shift)   TopPercentOfAllInputs (protocols::features)   
ConstraintFragmentMover (protocols::simple_moves)   
  H  
NtoC_RCG (protocols::forge::constraints)   RNA_ChunkLibrary (protocols::rna)   TopPercentOfEachInput (protocols::features)   
ConstraintFragmentSampler (protocols::abinitio)   NtoCCstGeneratorCreator (protocols::forge::constraints)   RNA_CS_parameters (core::scoring::rna::chemical_shift)   Torsion (protocols::protein_interface_design::filters)   
ConstraintGraph (core::scoring::constraints)   H3CterInsert (protocols::antibody2)   NullDesignMover (protocols::protein_interface_design::movers)   RNA_CS_residue_parameters (core::scoring::rna::chemical_shift)   Torsion_Info (protocols::swa::rna)   
ConstraintIO (core::scoring::constraints)   H3PerturbCCD (protocols::antibody2)   NullMover (protocols::moves)   RNA_DataBackboneEnergy (core::scoring::rna)   TorsionBinIO (protocols::frag_picker)   
ConstraintNode (core::scoring::constraints)   H3RefineCCD (protocols::antibody2)   NumberHBondsCalculator (protocols::toolbox::pose_metric_calculators)   RNA_DataBackboneEnergyCreator (core::scoring::rna)   TorsionBinPool (protocols::frag_picker::quota)   
ConstrainToIdealMover (protocols::simple_moves)   HackAroEnergy (core::scoring::hackaro)   NumDerivCheckData (core::optimization)   RNA_DataInfo (core::scoring::rna)   TorsionBinSimilarity (protocols::frag_picker::scores)   
ConstraintRegistrator (core::scoring::constraints)   HackAroEnergyCreator (core::scoring::hackaro)   NumericalDerivCheckResult (core::optimization)   RNA_DataReader (protocols::rna)   TorsionCreator (protocols::protein_interface_design::filters)   
Constraints (core::scoring::constraints)   HackElecEnergy (core::scoring::hackelec)   NumNeighborsMPM (protocols::match)   RNA_Datum (core::scoring::rna)   TorsionDOFMover (protocols::simple_moves)   
ConstraintScoreCutoffFilter (protocols::simple_filters)   HackElecEnergyAroAll (core::scoring::hackelec)   NVlookup (core::scoring::nv)   RNA_DeleteMover (protocols::swa::monte_carlo)   TorsionFeature (protocols::comparative_modeling::features)   
ConstraintScoreCutoffFilterCreator (protocols::simple_filters)   HackElecEnergyAroAllCreator (core::scoring::hackelec)   NVscore (core::scoring::nv)   RNA_DeNovoProtocol (protocols::rna)   TorsionFourierComponent (core::scoring::dna)   
ConstraintsEnergy (core::scoring::constraints)   HackElecEnergyAroAro (core::scoring::hackelec)   NVscoreCreator (core::scoring::nv)   RNA_FA_Stack (core::scoring::rna)   TorsionFragment (protocols::frags)   
ConstraintsEnergyCreator (core::scoring::constraints)   HackElecEnergyAroAroCreator (core::scoring::hackelec)   NWAligner (core::sequence)   RNA_FilteredBaseBaseInfo (core::scoring::rna)   TorsionFragmentLibrary (protocols::frags)   
ConstraintSet (core::scoring::constraints)   HackElecEnergyCreator (core::scoring::hackelec)   
  O  
RNA_FittedTorsionInfo (core::scoring::rna)   TorsionID (core::id)   
ConstraintSetMover (protocols::simple_moves)   Hairpin (core::scoring)   RNA_FragmentMover (protocols::rna)   TorsionID_Range (core::id)   
ConstraintSetMoverCreator (protocols::simple_moves)   Hairpins (core::scoring)   O2M_MutateMover (protocols::simple_moves)   RNA_Fragments (protocols::rna)   TorsionInfoSet (core::fragment)   
ConstScore (protocols::frag_picker::scores)   HamiltonianExchange (protocols::canonical_sampling)   ObserverCache (core::pose::datacache)   RNA_FullAtomStackingEnergy (core::scoring::rna)   TorsionRestrictedKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
Contact (protocols::contact_map)   HamiltonianExchangeCreator (protocols::canonical_sampling)   Obsolet_NamedAtomPairConstraint (core::scoring::constraints)   RNA_FullAtomStackingEnergyCreator (core::scoring::rna)   TorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
Contact (protocols::frag_picker)   HarmonicFunc (core::scoring::constraints)   OccludedHbondSolEnergy (core::scoring::geometric_solvation)   RNA_FullAtomVDW_BasePhosphate (core::scoring::rna)   TorsionSet (protocols::rna)   
ContactCounts (protocols::frag_picker)   hash_upstream_hit (protocols::match::downstream)   OccludedHbondSolEnergy_onebody (core::scoring::geometric_solvation)   RNA_FullAtomVDW_BasePhosphateCreator (core::scoring::rna)   TorsionSweepingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
ContactMap (protocols::contact_map)   HbaGrid (protocols::qsar::scoring_grid)   OccludedHbondSolEnergy_onebodyCreator (core::scoring::geometric_solvation)   RNA_HelixAssembler (protocols::rna)   trace (core::scoring::packstat)   
ContactMapCreator (protocols::contact_map)   HbaGridCreator (protocols::qsar::scoring_grid)   OccludedHbondSolEnergyCreator (core::scoring::geometric_solvation)   RNA_IdealCoord (protocols::rna)   TrajectoryRecorder (protocols::canonical_sampling)   
ContactMapEvaluator (protocols::simple_filters)   HBAtom (core::scoring::hbonds::hbtrie)   OccupiedSpaceHash (protocols::match)   RNA_JumpLibrary (protocols::rna)   TransferBuffer (protocols::canonical_sampling::mc_convergence_checks)   
ContactMapEvaluatorCreator (protocols::simple_filters)   HBCountPairFunction (core::scoring::hbonds::hbtrie)   Octree2D (core::scoring::packstat)   RNA_LJ_BaseEnergy (core::scoring::rna)   Transform (protocols::ligand_docking)   
ContactOrderEnergy (core::scoring::methods)   HBCPData (core::scoring::hbonds::hbtrie)   OffsetPeriodicBoundFunc (core::scoring::constraints)   RNA_LJ_BaseEnergyCreator (core::scoring::rna)   Transform_info (protocols::ligand_docking)   
ContactOrderEnergyCreator (core::scoring::methods)   HbdGrid (protocols::qsar::scoring_grid)   OmegaTether (core::scoring)   RNA_LoopCloser (protocols::rna)   Transformation   
ContactPartner (protocols::contact_map)   HbdGridCreator (protocols::qsar::scoring_grid)   OmegaTetherEnergy (core::scoring::methods)   RNA_LoopCloseSampler (protocols::swa::rna)   Transformation (protocols::protein_interface_design)   
ContextDependentLRTwoBodyEnergy (core::scoring::methods)   HBEvalTuple (core::scoring::hbonds)   OmegaTetherEnergyCreator (core::scoring::methods)   RNA_LowResolutionPotential (core::scoring::rna)   TransformCreator (protocols::ligand_docking)   
ContextDependentOneBodyEnergy (core::scoring::methods)   HBond (core::scoring::hbonds)   OneBodyEnergy (core::scoring::methods)   RNA_Mg_Energy (core::scoring::rna)   Translate (protocols::ligand_docking)   
ContextDependentTwoBodyEnergy (core::scoring::methods)   HBondAcceptorFilter (protocols::ligand_docking)   OneGaussianScattering (core::scoring::electron_density)   RNA_Mg_EnergyCreator (core::scoring::rna)   Translate_info (protocols::ligand_docking)   
ContextGraph (core::scoring)   HBondAcceptorFilterCreator (protocols::ligand_docking)   OneToAllEnergyContainer (core::scoring)   RNA_Mg_KnowledgeBasedPotential (core::scoring::rna)   TranslateCreator (protocols::ligand_docking)   
ContextGraphFactory (core::scoring)   HBondDatabase (core::scoring::hbonds)   OneToAllNeighborConstIterator (core::scoring)   RNA_Minimizer (protocols::rna)   Translator (core::coarse)   
ContextIndependentGeometricSolEnergy (core::scoring::geometric_solvation)   HBondDerivs (core::scoring::hbonds)   OneToAllNeighborIterator (core::scoring)   RNA_O2StarMover (protocols::swa::monte_carlo)   TranslatorSet (core::coarse)   
ContextIndependentGeometricSolEnergyCreator (core::scoring::geometric_solvation)   HBondDonorFilter (protocols::ligand_docking)   OnTheFlyEdge (core::pack::interaction_graph)   RNA_Pairing (protocols::rna)   TreeBuilder (protocols::nonlocal)   
ContextIndependentLRTwoBodyEnergy (core::scoring::methods)   HBondDonorFilterCreator (protocols::ligand_docking)   OnTheFlyInteractionGraph (core::pack::interaction_graph)   RNA_PairingTemplate (protocols::rna)   TreeBuilderFactory (protocols::nonlocal)   
ContextIndependentOneBodyEnergy (core::scoring::methods)   HBondEnergy (core::scoring::hbonds)   OnTheFlyNode (core::pack::interaction_graph)   RNA_PairwiseLowResolutionEnergy (core::scoring::rna)   TreeVizBuilder (core::kinematics)   
ContextIndependentTwoBodyEnergy (core::scoring::methods)   HBondEnergyCreator (core::scoring::hbonds)   OopDPuckMinusMover (protocols::simple_moves::oop)   RNA_PairwiseLowResolutionEnergyCreator (core::scoring::rna)   Trial   
ContingentFilter (protocols::filters)   HBondFeatures (protocols::features)   OopDPuckPlusMover (protocols::simple_moves::oop)   RNA_RawBaseBaseInfo (core::scoring::rna)   TrialCounter (protocols::moves)   
ContingentFilterCreator (protocols::filters)   HBondFeaturesCreator (protocols::features)   OopMover (protocols::simple_moves::oop)   RNA_Relaxer (protocols::rna)   TrialCounterObserver (protocols::canonical_sampling)   
ContinuousRotamerSet (core::pack::rotamer_set)   HBondOptions (core::scoring::hbonds)   OopPatcher (protocols::simple_moves::oop)   RNA_ResidueType (core::chemical::rna)   TrialCounterObserverCreator (protocols::canonical_sampling)   
ContinuousRotamerSets (core::pack::rotamer_set)   HBondParameterFeatures (protocols::features)   OopPuckMinusMover (protocols::simple_moves::oop)   RNA_ScoringInfo (core::scoring::rna)   TrialMover (protocols::moves)   
ConvergenceCheck (protocols::moves::mc_convergence_checks)   HBondParameterFeaturesCreator (protocols::features)   OopPuckPlusMover (protocols::simple_moves::oop)   RNA_SecStructInfo (protocols::rna)   triangle (protocols::viewer)   
ConvergenceTest (core::optimization)   HBondResidueMinData (core::scoring::hbonds)   OopRandomPuckMover (protocols::simple_moves::oop)   RNA_SilentStruct (core::io::silent)   triangleIterator (protocols::viewer)   
CoordConstraintClaimer (protocols::topology_broker)   HBondResPairMinData (core::scoring::hbonds)   OopRandomSmallMover (protocols::simple_moves::oop)   RNA_SilentStructCreator (core::io::silent)   TrieCollection (core::scoring::trie)   
CoordinateConstraint (core::scoring::constraints)   HBondSet (core::scoring::hbonds)   OP_const_iterator (protocols::toolbox)   RNA_StructureParameters (protocols::rna)   TrieCountPair1BC3 (core::scoring::etable::etrie)   
CoordinateConstraintCreator (core::scoring::constraints)   HbondsToResidueFilter (protocols::protein_interface_design::filters)   OperateOnCertainResidues (core::pack::task::operation)   RNA_SugarCloseEnergy (core::scoring::rna)   TrieCountPair1BC4 (core::scoring::etable::etrie)   
CoordinateConstraintKC (protocols::abinitio)   HbondsToResidueFilterCreator (protocols::protein_interface_design::filters)   OperateOnCertainResiduesCreator (core::pack::task::operation)   RNA_SugarCloseEnergyCreator (core::scoring::rna)   TrieCountPairAll (core::scoring::etable::etrie)   
CoordinateCst (protocols::seeded_abinitio)   HBondTypeManager (core::scoring::hbonds)   Operator (protocols::simple_filters)   RNA_suite_list (protocols::rna)   TrieCountPairBase (core::scoring::trie)   
CoordinateCstCreator (protocols::seeded_abinitio)   HbsPatcher (protocols::simple_moves::hbs)   OperatorFilterCreator (protocols::simple_filters)   RNA_SWA_MonteCarloMover (protocols::swa::monte_carlo)   TrieCountPairGeneric (core::scoring::etable::etrie)   
CORdata (protocols::sparta)   hConvergenceCheck (protocols::abinitio)   OptCysHG (core::pack::task::operation)   RNA_TorsionEnergy (core::scoring::rna)   TrieCountPairNone (core::scoring::etable::etrie)   
CoreDunbrackFilter (protocols::fldsgn::filters)   hConvergenceCheck (protocols::hybridization)   OptCysHGCreator (core::pack::task::operation)   RNA_TorsionEnergyCreator (core::scoring::rna)   TrieNode (core::scoring::trie)   
CoreDunbrackFilterCreator (protocols::fldsgn::filters)   HeaderInformation (core::io::pdb)   OptEData (protocols::optimize_weights)   RNA_TorsionMover (protocols::swa::monte_carlo)   TrueFilter (protocols::filters)   
CorrectionVisitor (protocols::sic_dock)   Heat_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks)   OptEMultifunc (protocols::optimize_weights)   RNA_TorsionPotential (core::scoring::rna)   TrueFilterCreator (protocols::filters)   
CountFromLeft (protocols::forge::build)   HeavyAtomFilter (protocols::filters)   OptEPositionData (protocols::optimize_weights)   RNA_VDW_Energy (core::scoring::rna)   TruncatedScoreEvaluator (protocols::simple_filters)   
CountPair1B (core::scoring::etable::count_pair)   HeavyAtomFilter (protocols::ligand_docking)   OptEPositionDataFactory (protocols::optimize_weights)   RNA_VDW_EnergyCreator (core::scoring::rna)   TryRotamers (protocols::protein_interface_design::movers)   
CountPairAll (core::scoring::etable::count_pair)   HeavyAtomFilterCreator (protocols::ligand_docking)   OptEVariableExpression (protocols::optimize_weights)   RNAHackElecEnergy (core::scoring::hackelec)   TryRotamersCreator (protocols::protein_interface_design::movers)   
CountPairCrossover3 (core::scoring::etable::count_pair)   HedgeArchive (protocols::abinitio)   OptH (core::pack::task::operation)   RNAHackElecEnergyCreator (core::scoring::hackelec)   TwelveANeighborEdge (core::scoring)   
CountPairCrossover4 (core::scoring::etable::count_pair)   HelicalFragment (protocols::features::helixAssembly)   OptHCreator (core::pack::task::operation)   RollMover (protocols::rigid)   TwelveANeighborGraph (core::scoring)   
CountPairData_1_1 (core::scoring::etable::etrie)   HelicalGaussianMover (protocols::rbsegment_relax)   Orbital (core::chemical)   RollMoverCreator (protocols::rigid)   TwelveANeighborNode (core::scoring)   
CountPairData_1_2 (core::scoring::etable::etrie)   HelicalPeptideLengthMover (protocols::simple_moves)   OrbitalsAssigned (core::scoring::orbitals)   RootClaim (protocols::topology_broker)   TwoBodyEnergy (core::scoring::methods)   
CountPairData_1_3 (core::scoring::etable::etrie)   Helices (core::scoring)   OrbitalsFeatures (protocols::features)   Rose (protocols::sic_dock)   
  U  
CountPairDataGeneric (core::scoring::etable::etrie)   Helix (protocols::fldsgn::topology)   OrbitalsFeaturesCreator (protocols::features)   RotamerAssigningAnnealer (core::pack::annealer)   
CountPairFactory (core::scoring::etable::count_pair)   HelixBundleFeatures (protocols::features::helixAssembly)   OrbitalsLookup (core::scoring::orbitals)   RotamerBoltzCalculator (protocols::toolbox::pose_metric_calculators)   ubi_e2c_modeler (protocols::ub_e2c)   
CountPairFunction (core::scoring::etable::count_pair)   HelixBundleFeaturesCreator (protocols::features::helixAssembly)   OrbitalsScore (core::scoring::orbitals)   RotamerBoltzmannWeight (protocols::simple_filters)   UDPSocketClient (protocols::moves)   
CountPairGeneric (core::scoring::etable::count_pair)   HelixKinkFilter (protocols::fldsgn::filters)   OrbitalsScoreCreator (core::scoring::orbitals)   RotamerBoltzmannWeightFeatures (protocols::features)   UEEdge (core::graph)   
CountPairIntraRes (core::scoring::etable::count_pair)   HelixKinkFilterCreator (protocols::fldsgn::filters)   OrbitalsStatistics (core::scoring::orbitals)   RotamerBoltzmannWeightFeaturesCreator (protocols::features)   UEVertex (core::graph)   
CountPairIntraResC3 (core::scoring::etable::count_pair)   HelixPairing (protocols::fldsgn::topology)   OrbitalType (core::chemical::orbitals)   RotamerBoltzmannWeightFilterCreator (protocols::simple_filters)   UnaryExpression (numeric::expression_parser)   
CountPairIntraResC4 (core::scoring::etable::count_pair)   HelixPairingFilter (protocols::fldsgn::filters)   OrbitalTypeMapper (core::chemical::orbitals)   RotamerBuildingData (core::pack::dunbrack)   UnboundRotamersOperation (core::pack::rotamer_set)   
CountPairNone (core::scoring::etable::count_pair)   HelixPairingFilterCreator (protocols::fldsgn::filters)   OrbitalTypeSet (core::chemical::orbitals)   RotamerConstraint (core::pack::dunbrack)   UnconstrainedTorsionsMover (protocols::ligand_docking)   
CountViolFunc (core::scoring::constraints)   HelixPairingSet (protocols::fldsgn::topology)   OrbitalXYZCoords (core::conformation::orbitals)   RotamerCouplings (core::pack::rotamer_set)   UnfoldedStateEnergy (core::scoring::methods)   
CovalentCompliance (protocols::noesy_assign)   HelixRotate (protocols::nonlocal)   OrderCavBallOnR (core::scoring::packstat)   RotamerDescriptor (core::scoring::trie)   UnfoldedStateEnergyCalculatorJobDistributor (protocols::unfolded_state_energy_calculator)   
CovalentConnectionReplaceInfo (protocols::toolbox::match_enzdes_util)   HelixScore (protocols::sic_dock)   OrderCavBallOnRmAnb (core::scoring::packstat)   RotamerDescriptorAtom (core::scoring::trie)   UnfoldedStateEnergyCalculatorMover (protocols::unfolded_state_energy_calculator)   
CPDataCorrespondence (core::scoring::trie)   HierarchicalLevel (protocols::canonical_sampling::mc_convergence_checks)   OrderCavBallOnRmE (core::scoring::packstat)   RotamerDNAHBondFilter (protocols::dna)   UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (protocols::unfolded_state_energy_calculator)   
CrossoverBehavior   HighResDocker (protocols::ligand_docking)   OrderCavBallOnX (core::scoring::packstat)   RotamerDots (core::pack::interaction_graph)   UnfoldedStateEnergyCreator (core::scoring::methods)   
CrossPeak (protocols::noesy_assign)   HighResDockerCreator (protocols::ligand_docking)   OrderCBC (core::scoring::packstat)   RotamerDotsCache (core::pack::interaction_graph)   UnfoldedStatePotential (core::scoring)   
CrossPeak3D (protocols::noesy_assign)   history_queue_struct (core::pack::interaction_graph)   OrderedFragSet (core::fragment)   RotamerDotsRadiusData (core::pack::interaction_graph)   UniformPolicy (protocols::nonlocal)   
CrossPeak4D (protocols::noesy_assign)   Hit (protocols::match)   OrderedFragSetIterator_ (core::fragment)   RotamerDumpMover (protocols::RotamerDump)   UniformSphereTransMover (protocols::rigid)   
CrossPeakInfo (protocols::noesy_assign)   HitHasher (protocols::match)   OrderedSequentialSymmetrySlider (protocols::simple_moves::symmetry)   RotamerExplosion (core::pack::task::operation)   unordered_object_pool (boost)   
CrossPeakList (protocols::noesy_assign)   HitNeighborFinder (protocols::match)   OrderSphereOnID (core::scoring::packstat)   RotamerExplosionCreator (core::pack::task::operation)   UnrecognizedAtomFeatures (protocols::features)   
CS2ndShift (protocols::frag_picker)   HolesEnergy (core::scoring::packing)   OrderSphereOnX (core::scoring::packstat)   RotamerFeatures (protocols::features)   UnrecognizedAtomFeaturesCreator (protocols::features)   
CSA (core::scoring)   HolesEnergyCreator (core::scoring::packing)   OriginalBackboneBuildPoint (protocols::match::upstream)   RotamerFeaturesCreator (protocols::features)   UnrecognizedAtomRecord (core::pose)   
CSD_TorsionEnergy (core::scoring::methods)   HolesEnergyRes (core::scoring::packing)   OTFFlexbbEdge (protocols::flexpack::interaction_graph)   RotamericData (core::pack::dunbrack)   UpJumpSRFD (core::fragment)   
CSDAtomType (core::chemical)   HolesFilter (protocols::simple_filters)   OTFFlexbbInteractionGraph (protocols::flexpack::interaction_graph)   RotamericSingleResidueDunbrackLibrary (core::pack::dunbrack)   UpperEdgeGraph (core::graph)   
CSDAtomTypeSet (core::chemical)   HolesFilterCreator (protocols::simple_filters)   OTFFlexbbNode (protocols::flexpack::interaction_graph)   RotamerInitializer (protocols::features)   upstream_hit (protocols::match)   
CSScore (protocols::frag_picker::scores)   HolesParams (core::scoring::packing)   OtherContextScoreFunction (protocols::flexpack)   RotamerLibrary (core::pack::dunbrack)   UpstreamBuilder (protocols::match::upstream)   
CSTalosIO (protocols::frag_picker)   HolesParamsRes (core::scoring::packing)   output_data_struct (protocols::swa::rna)   RotamerLibraryScratchSpace (core::pack::dunbrack)   UpstreamCollisionFilter (protocols::match::output)   
CstEnergyContainer (core::scoring::constraints)   HolesResult (core::scoring::packing)   RRReporterSQLite::OutputLevel (protocols::rotamer_recovery)   RotamerLinks (core::pack::rotamer_set)   UpstreamDownstreamCollisionFilter (protocols::match::output)   
CstMinimizationData (core::scoring::constraints)   HotspotDisjointedFoldTreeMover (protocols::protein_interface_design::movers)   Outputter (protocols::outputter)   RotamerOperation (core::pack::rotamer_set)   UpstreamHitCacher (protocols::match::output)   
CstResInteractions (protocols::toolbox::match_enzdes_util)   HotspotDisjointedFoldTreeMoverCreator (protocols::protein_interface_design::movers)   OutputWriter (protocols::match::output)   RotamerRecovery (protocols::rotamer_recovery)   UpstreamResidueProcessor (protocols::match::upstream)   
CstResNeighbConstIterator (core::scoring::constraints)   HotspotHasherMover (protocols::protein_interface_design::movers)   owning_ptr (utility::pointer)   RotamerRecovery (protocols::toolbox::pose_metric_calculators)   UpstreamResTypeGeometry (protocols::match::upstream)   
CstResNeighbIterator (core::scoring::constraints)   HotspotHasherMoverCreator (protocols::protein_interface_design::movers)   
  P  
RotamerRecoveryFactory (protocols::rotamer_recovery)   us_secmatch_hit_compare (protocols::match::downstream)   
CtabBase (core::chemical::sdf)   HotspotStub (protocols::hotspot_hashing)   RotamerRecoveryFeatures (protocols::features)   USE_INPUT_SC (core::pack::task)   
ctabV2000Parser (core::chemical::sdf)   HotspotStubSet (protocols::hotspot_hashing)   P_AA (core::scoring)   RotamerRecoveryFeaturesCreator (protocols::features)   UserDefinedGroupDiscriminator (protocols::simple_moves)   
ctabV3000Parser (core::chemical::sdf)   HPatchBackgroundEdge (core::pack::interaction_graph)   P_AA_Energy (core::scoring::methods)   RotamerRecoveryMover (protocols::rotamer_recovery)   USOGFunc (core::scoring::constraints)   
CustomAtomPairEnergy (core::scoring::methods)   HPatchBackgroundNode (core::pack::interaction_graph)   P_AA_EnergyCreator (core::scoring::methods)   RotamerRecoveryMoverCreator (protocols::rotamer_recovery)   UDPSocketClient::UUID (protocols::moves)   
CustomAtomPairEnergyCreator (core::scoring::methods)   HPatchCalculator (protocols::toolbox::pose_metric_calculators)   P_AA_pp_Energy (core::scoring::methods)   RotamerRecoveryRegistrator (protocols::rotamer_recovery)   
  V  
CustomScoreSelector (protocols::frag_picker)   HPatchEdge (core::pack::interaction_graph)   P_AA_pp_EnergyCreator (core::scoring::methods)   RotamerSet (core::pack::rotamer_set)   
CutBiasClaimer (protocols::topology_broker)   HPatchEnergy (core::pack::interaction_graph)   PackDaemon (protocols::pack_daemon)   RotamerSet_ (core::pack::rotamer_set)   V2Parser (core::chemical::sdf)   
CutChainMover (protocols::simple_moves)   HPatchEnergyCreator (core::pack::interaction_graph)   PackedDunbrackRotamer (core::pack::dunbrack)   RotamerSetBase (core::conformation)   V3Parser (core::chemical::sdf)   
CutChainMoverCreator (protocols::simple_moves)   HPatchInteractionGraph (core::pack::interaction_graph)   PackerNeighborGraphFilter (protocols::simple_filters)   RotamerSetFactory (core::pack::rotamer_set)   VallChunk (protocols::frag_picker)   
CutClaim (protocols::topology_broker)   HPatchNode (core::pack::interaction_graph)   PackerTask (core::pack::task)   RotamerSetOperation (core::pack::rotamer_set)   VallChunkFilter (protocols::frag_picker)   
PCluster::Cxyz (protocols::pockets)   HPool_RMSD (protocols::canonical_sampling::mc_convergence_checks)   PackerTask_ (core::pack::task)   RotamerSets (core::pack::rotamer_set)   VallData (protocols::frags)   
CycleMover (protocols::moves)   HSPairPotential (protocols::fldsgn::potentials::sspot)   PackingScore (core::scoring::packstat)   RotamerSetsBase (core::pack::rotamer_set)   VallFragmentEval (core::fragment::picking_old::vall::eval)   
CyclicMover (protocols::moves)   HSSTriplet (protocols::fldsgn::topology)   PackingScoreResData (core::scoring::packstat)   RotamerSubset (core::pack::rotamer_set)   VallFragmentGen (core::fragment::picking_old::vall::gen)   
  D  
HSSTripletFilter (protocols::fldsgn::filters)   PackingState (protocols::multistate_design)   RotamerSubsetRepacker (protocols::pack_daemon)   VallFragmentScore (core::fragment::picking_old::vall::scores)   
HSSTripletFilterCreator (protocols::fldsgn::filters)   PackRotamersMover (protocols::simple_moves)   RotamerSubsets (core::pack::rotamer_set)   VallLibrarian (core::fragment::picking_old::vall)   
DaemonSet (protocols::pack_daemon)   HSSTripletSet (protocols::fldsgn::topology)   PackRotamersMoverCreator (protocols::simple_moves)   RotamerTrialsMinMover (protocols::simple_moves)   VallLibrary (core::fragment::picking_old::vall)   
DarcElectrostaticsBase (protocols::pockets)   HTL_EventX (core::scoring::packstat)   PackRotamersMoverLazy (protocols::simple_moves)   RotamerTrialsMinMoverCreator (protocols::simple_moves)   VallProvider (protocols::frag_picker)   
DarcParticleSwarmMinimizer (protocols::pockets)   HybridizeFoldtreeDynamic (protocols::hybridization)   PackRotamersMoverLazyCreator (protocols::simple_moves)   RotamerTrialsMover (protocols::simple_moves)   VallResidue (protocols::frag_picker)   
data_struct (core::scoring)   HybridizeProtocol (protocols::hybridization)   PackRotamersMoverPartGreedy (protocols::enzdes)   RotamerTrialsMoverCreator (protocols::simple_moves)   VallResidue (core::fragment::picking_old::vall)   
data_structDa (core::scoring)   HybridizeProtocolCreator (protocols::hybridization)   PackRotamersMoverPartGreedyCreator (protocols::enzdes)   RotamerTrie (core::scoring::trie)   VallResidues (core::fragment::picking_old::vall)   
data_structDaR (core::scoring)   HybridVDW_Energy (core::scoring::methods)   PackstatCalculator (protocols::toolbox::pose_metric_calculators)   RotamerTrieBase (core::scoring::trie)   VallSection (core::fragment::picking_old::vall)   
data_structR (core::scoring)   HybridVDW_EnergyCreator (core::scoring::methods)   PackStatEnergy (core::scoring::methods)   Rotate (protocols::ligand_docking)   VallSections (core::fragment::picking_old::vall)   
DatabaseEntryWorkUnit (protocols::wum)   HydrophobicityProfileSimilarity (protocols::frag_picker::scores)   PackStatEnergyCreator (core::scoring::methods)   Rotate_info (protocols::ligand_docking)   ValueEvaluator (protocols::enzdes)   
DatabaseFilter (protocols::features)   HydrophobicitySimilarity (protocols::frag_picker::scores)   PackStatFilter (protocols::simple_filters)   RotateCreator (protocols::ligand_docking)   VariableExpression (numeric::expression_parser)   
DatabaseJobInputter (protocols::features)   
  I  
PackStatFilterCreator (protocols::simple_filters)   RotateJumpAxisMover (protocols::rigid)   VariableVectorExpression (protocols::pack_daemon)   
DatabaseJobInputterCreator (protocols::features)   PackStatMover (protocols::analysis)   Rotates (protocols::ligand_docking)   VarianceStatisticsArchive (protocols::jd2::archive)   
DatabaseJobOutputter (protocols::features)   APBSConfig::I_PARAM (core::scoring)   PairEnergy (core::scoring::methods)   RotatesCreator (protocols::ligand_docking)   VarLengthBuild (protocols::forge::components)   
DatabaseJobOutputterCreator (protocols::features)   ICoorAtomID (core::chemical)   PairEnergyCreator (core::scoring::methods)   RotationSearchPattern (protocols::hotspot_hashing)   VDW_Energy (core::scoring::methods)   
DatabaseOccSolEne (core::scoring::geometric_solvation)   ICoorOrbitalData (core::chemical::orbitals)   PairEPotential (core::scoring)   RotData (protocols::MakeRotLib)   VDW_EnergyCreator (core::scoring::methods)   
DatabaseQueryWorkUnitManager (protocols::wum)   IdealBondLengthSet (core::chemical)   PairFeatures (protocols::features)   RPF_ScoreEvaluator (protocols::simple_filters)   VDW_RepScreeninfo (protocols::swa::rna)   
DataBuffer (protocols::canonical_sampling::mc_convergence_checks)   IdealizeMover (protocols::idealize)   PairFeaturesCreator (protocols::features)   RRComparer (protocols::rotamer_recovery)   VdwGrid (protocols::qsar::scoring_grid)   
DataLoader (protocols::jd2::parser)   IdealizeMoverCreator (protocols::idealize)   Pairing (core::scoring::dssp)   RRComparerAutomorphicRMSD (protocols::rotamer_recovery)   VdwGridCreator (protocols::qsar::scoring_grid)   
DataLoaderCreator (protocols::jd2::parser)   IdealParametersDatabase (core::scoring::methods)   PairingLibrary (protocols::jumping)   RRComparerAutomorphicRMSDCreator (protocols::rotamer_recovery)   Vec1Hash (protocols::genetic_algorithm)   
DataLoaderFactory (protocols::jd2::parser)   IdentityEval (core::fragment::picking_old::vall::eval)   PairingStatEntry (protocols::abinitio)   RRComparerChiDiff (protocols::rotamer_recovery)   Vec3 (protocols::sic_dock)   
DataLoaderRegistrator (protocols::jd2::parser)   IdentityEvent (core::conformation::signals)   PairingStatistics (protocols::abinitio)   RRComparerChiDiffCreator (protocols::rotamer_recovery)   vector0 (utility)   
DataMap (protocols::moves)   IdentityFunc (core::scoring::constraints)   PairingTemplate (protocols::jumping)   RRComparerCreator (protocols::rotamer_recovery)   vector1 (utility)   
DataMapObj (protocols::moves)   IfMover (protocols::moves)   PairScoringScheme (core::sequence)   RRComparerRotBins (protocols::rotamer_recovery)   VectorCacheUnit (core::fragment)   
DataPoint (protocols::cluster)   IfMoverCreator (protocols::moves)   PalesEvaluator (protocols::simple_filters)   RRComparerRotBinsCreator (protocols::rotamer_recovery)   VectorExpression (protocols::pack_daemon)   
DC (core::scoring)   IfThenFilter (protocols::filters)   PalesEvaluatorCreator (protocols::simple_filters)   RRProtocol (protocols::rotamer_recovery)   VectorExpressionCreator (protocols::pack_daemon)   
ddG (protocols::simple_moves)   IfThenFilterCreator (protocols::filters)   ParallelBetaPairingPreferenceFilter (protocols::fldsgn::filters)   RRProtocolCreator (protocols::rotamer_recovery)   VectorFunction (protocols::pack_daemon)   
DDGBindOptEData (protocols::optimize_weights)   IGEdgeReweightContainer (core::pack::task)   ParallelBetaPairingPreferenceFilterCreator (protocols::fldsgn::filters)   RRProtocolMinPack (protocols::rotamer_recovery)   VectorFunction2 (protocols::pack_daemon)   
ddGCreator (protocols::simple_moves)   IGEdgeReweighter (core::pack::task)   ParallelTempering (protocols::canonical_sampling)   RRProtocolMinPackCreator (protocols::rotamer_recovery)   vectorL (utility)   
ddGData (protocols::ddG)   IGLigandDesignEdgeUpweighter (protocols::toolbox)   ParallelTemperingCreator (protocols::canonical_sampling)   RRProtocolMover (protocols::rotamer_recovery)   VectorPair (protocols::hotspot_hashing)   
DdgFilter (protocols::simple_filters)   IgnoreSubsetConstraintSet (protocols::comparative_modeling)   CentroidRelax::parameters (protocols::relax)   RRProtocolMoverCreator (protocols::rotamer_recovery)   VicinitySamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure)   
DdgFilterCreator (protocols::simple_filters)   Implements   ParetoOptMutationMover (protocols::design_opt)   RRProtocolPackRotamers (protocols::rotamer_recovery)   VIP_Mover (protocols::vip)   
ddGMover (protocols::ddg)   Implements   ParetoOptMutationMoverCreator (protocols::design_opt)   RRProtocolPackRotamersCreator (protocols::rotamer_recovery)   VIP_Report (protocols::vip)   
DDGMutationOptEData (protocols::optimize_weights)   ImplicitFastClashCheck (protocols::scoring)   ParsedProtocol (protocols::rosetta_scripts)   RRProtocolReferenceStructure (protocols::rotamer_recovery)   VirtualCoordinate (core::conformation::symmetry)   
DDomainParse (protocols::hybridization)   ImportPoseOptions (core::import_pose)   ParsedProtocolCreator (protocols::rosetta_scripts)   RRProtocolReferenceStructureCreator (protocols::rotamer_recovery)   VirtualCoordinates (core::conformation::symmetry)   
DDPlookup (core::scoring::interface)   ImportPoseOptionsCreator (core::import_pose)   Parser (protocols::jd2)   RRProtocolRotamerTrials (protocols::rotamer_recovery)   VLB (protocols::protein_interface_design::movers)   
DDPscore (core::scoring::interface)   IncludeCurrent (core::pack::task::operation)   ParserJobInputter (protocols::protein_interface_design)   RRProtocolRotamerTrialsCreator (protocols::rotamer_recovery)   VLBCreator (protocols::protein_interface_design::movers)   
DDPscoreCreator (core::scoring::interface)   IncludeCurrentCreator (core::pack::task::operation)   ParserJobInputterCreator (protocols::protein_interface_design)   RRProtocolRTMin (protocols::rotamer_recovery)   VMax (protocols::pack_daemon)   
DebugArchive (protocols::jd2::archive)   IndependentBBTorsionSRFD (core::fragment)   PartialSecondarySimilarity (protocols::frag_picker::scores)   RRProtocolRTMinCreator (protocols::rotamer_recovery)   VMaxBy (protocols::pack_daemon)   
DebuggingAnnealer (core::pack::annealer)   IndependentLoopMover (protocols::loops::loop_mover)   PartialThreadingMover (protocols::comparative_modeling)   RRReporter (protocols::rotamer_recovery)   VMin (protocols::pack_daemon)   
DebugOut_MpiFileBuffer (protocols::jd2)   InitializeExtraRotsFromCommandline (core::pack::task::operation)   Particle (core::optimization)   RRReporterCreator (protocols::rotamer_recovery)   VMinBy (protocols::pack_daemon)   
DecomposeAndReweightEnergiesCalculator (protocols::toolbox::pose_metric_calculators)   InitializeExtraRotsFromCommandlineCreator (core::pack::task::operation)   ParticleSwarmMinimizer (core::optimization)   RRReporterHuman (protocols::rotamer_recovery)   VoxelSetIterator (protocols::match)   
DecoyFileData (core::io::raw_data)   InitializeFromCommandline (core::pack::task::operation)   PartitionAggregateFunction (protocols::multistate_design)   RRReporterHumanCreator (protocols::rotamer_recovery)   
  W  
DecoySetEvaluation (protocols::toolbox)   InitializeFromCommandlineCreator (core::pack::task::operation)   PartitionedSearchPattern (protocols::hotspot_hashing)   RRReporterSimple (protocols::rotamer_recovery)   
DecoyStruct (core::io::raw_data)   InnerJob (protocols::jd2)   Patch (core::chemical)   RRReporterSimpleCreator (protocols::rotamer_recovery)   WaterAdductHBondEnergy (core::scoring::methods)   
DefaultCubeHash (core::conformation)   InnerMultiThreadingJob (protocols::jd2)   PatchCase (core::chemical)   RRReporterSQLite (protocols::rotamer_recovery)   WaterAdductHBondEnergyCreator (core::scoring::methods)   
DefineMovableLoops (protocols::seeded_abinitio)   InputStreamWithResidueInfo (protocols::swa)   PatchdockReader (protocols::protein_interface_design)   RRReporterSQLiteCreator (protocols::rotamer_recovery)   WaterAdductHBondPotential (core::scoring)   
DefineMovableLoopsCreator (protocols::seeded_abinitio)   Inputter (protocols::inputter)   PatchOperation (core::chemical)   RT (core::kinematics)   WaterAdductIntraEnergy (core::scoring::methods)   
DeleteAtom (core::chemical)   InputterStream (protocols::inputter)   PatchOperation (protocols::canonical_sampling)   RT_helper (core::scoring::disulfides)   WaterAdductIntraEnergyCreator (core::scoring::methods)   
DeleteProperty (core::chemical)   InsertChunkMover (protocols::hybridization)   PattersonCorrEnergy (core::scoring::electron_density)   RTMin (core::pack)   WaterAnchorInfo (core::pack::rotamer_set)   
DelphiElectrostatics (protocols::pockets)   InSetExpression (protocols::pack_daemon)   PattersonCorrEnergyCreator (core::scoring::electron_density)   Rule (core::coarse)   WaterBuilder (core::scoring::methods)   
DeltaFilter (protocols::simple_filters)   RemodelMover::instruction_flags (protocols::forge::remodel)   PBLifetimeCache (core::scoring::methods)   RuleSet (core::coarse)   WaterPackingInfo (core::pack::rotamer_set)   
DeltaFilterCreator (protocols::simple_filters)   InteractionGraphBase (core::pack::interaction_graph)   PCA (protocols::evaluation)   
  S  
WaterWeightGridSet (core::scoring::geometric_solvation)   
DenseEnergyContainer (core::scoring)   InteractionGraphFactory (core::pack::interaction_graph)   PcaEvaluator (protocols::abinitio)   WatsonCrickResidueMatcher (core::conformation)   
DenseIGRepacker (protocols::pack_daemon)   InteratomicVarianceMatrix (protocols::toolbox)   PCluster (protocols::pockets)   SA_Energy (core::scoring::methods)   WatsonCrickRotamerCouplings (protocols::dna)   
DenseNeighborConstIterator (core::scoring)   InterbondAngleScore (protocols::frag_picker::scores)   PClusterSet (protocols::pockets)   SA_EnergyCreator (core::scoring::methods)   WatsonCrickRotamerCouplingsCreator (protocols::dna)   
DenseNeighborIterator (core::scoring)   InterchainEnvEnergy (protocols::scoring::methods)   PCS_data (protocols::scoring::methods::pcs)   SaltBridgeCalculator (protocols::toolbox::pose_metric_calculators)   weight_triple (core::scoring::hackelec)   
DensePDEdge (core::pack::interaction_graph)   InterchainEnvEnergyCreator (protocols::scoring::methods)   PCS_data_input (protocols::scoring::methods::pcs)   SaltBridgeFeatures (protocols::features)   WeightedFragmentSmoothTrialMover (protocols::hybridization)   
DensePDInteractionGraph (core::pack::interaction_graph)   InterchainPairEnergy (protocols::scoring::methods)   PCS_data_input_manager (protocols::scoring::methods::pcs)   SaltBridgeFeaturesCreator (protocols::features)   WeightedFragmentTrialMover (protocols::hybridization)   
DensePDNode (core::pack::interaction_graph)   InterchainPairEnergyCreator (protocols::scoring::methods)   PCS_data_per_lanthanides (protocols::scoring::methods::pcs)   SameChiBinComboGrouper (protocols::match::output)   WeightRangeConstraint (protocols::optimize_weights)   
DensityScoringClaimer (protocols::topology_broker)   InterchainPotential (protocols::scoring)   PCS_Energy (protocols::scoring::methods::pcs)   SameRotamerComboGrouper (protocols::match::output)   WhileMover (protocols::moves)   
DenyPdbIdFilter (protocols::frag_picker)   Interface (protocols::scoring)   PCS_Energy_parameters_manager (protocols::scoring::methods::pcs)   SameSequenceAndDSPositionGrouper (protocols::match::output)   WholeBodyRotationMover (protocols::rigid)   
DerivCheckDataPoint (core::optimization)   Interface (protocols::ligand_docking::ligand_options)   PCS_file_data (protocols::scoring::methods::pcs)   SameSequenceGrouper (protocols::match::output)   WholeBodyTranslationMover (protocols::rigid)   
DerivedSequenceMapping (core::sequence)   InterfaceAnalyzerMover (protocols::analysis)   PCS_FragDistance (protocols::frag_picker::scores)   SameStrand (protocols::jumping)   WholeStructureEnergy (core::scoring::methods)   
DerivVectorPair (core::scoring)   InterfaceAnalyzerMoverCreator (protocols::analysis)   PCS_line_data (protocols::scoring::methods::pcs)   SampleStrategyData (protocols::match::upstream)   WholeWholeEnergyInvoker (core::scoring::etable)   
DescentDirectionAlgorithm (core::optimization)   InterfaceBindingEnergyDensityFilter (protocols::simple_filters)   PCS_tensor (protocols::scoring::methods::pcs)   SaneDockingProtocol (protocols::docking::stateless)   WidgetFactory (utility::factory)   
DesignableResiduesFilter (protocols::protein_interface_design::filters)   InterfaceBindingEnergyDensityFilterCreator (protocols::simple_filters)   PcsDataCenter (protocols::scoring::methods::pcs2)   SaneMinMover (protocols::simple_moves)   WidgetRegistrator (utility::factory)   
DesignableResiduesFilterCreator (protocols::protein_interface_design::filters)   InterfaceBuilder (protocols::ligand_docking)   PcsDataCenterManager (protocols::scoring::methods::pcs2)   SaneMinMoverCreator (protocols::simple_moves)   WidthFirstSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd)   
DesignAroundOperation (protocols::toolbox::task_operations)   InterfaceBuilderLoader (protocols::ligand_docking)   PcsDataCenterManagerSingleton (protocols::scoring::methods::pcs2)   SasaCalculator (core::pose::metrics::simple_calculators)   WobbleMover (protocols::simple_moves)   
DesignAroundOperationCreator (protocols::toolbox::task_operations)   InterfaceBuilderLoaderCreator (protocols::ligand_docking)   PcsDataLanthanide (protocols::scoring::methods::pcs2)   SasaOptions (core::scoring::packstat)   WorkingRemodelSet (protocols::forge::remodel)   
DesignContrast (core::io::sequence_comparation)   InterfaceDefinitionCalculator (core::pose::metrics::simple_calculators)   PcsEnergy (protocols::scoring::methods::pcs2)   SasaResult (core::scoring::packstat)   WorkUnit (protocols::wum2)   
DesignMinimizeHbonds (protocols::protein_interface_design::movers)   InterfaceDeltaEnergeticsCalculator (core::pose::metrics::simple_calculators)   PcsEnergyController (protocols::topology_broker)   SaveAndRetrieveSidechains (protocols::protein_interface_design::movers)   WorkUnit_BatchRelax (protocols::relax)   
DesignMinimizeHbondsCreator (protocols::protein_interface_design::movers)   InterfaceHolesFilter (protocols::protein_interface_design::filters)   PcsEnergyCreator (protocols::scoring::methods::pcs2)   SaveAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers)   WorkUnit_BatchRelax_and_PostRescore (protocols::relax)   
DesignProteinBackboneAroundDNA (protocols::dna)   InterfaceHolesFilterCreator (protocols::protein_interface_design::filters)   PcsEnergyParameter (protocols::scoring::methods::pcs2)   SavePoseMover (protocols::rosetta_scripts)   WorkUnit_ElScripts (protocols::wum2)   
DesignProteinBackboneAroundDNACreator (protocols::dna)   InterfaceInfo (protocols::scoring)   PcsEnergyParameterManager (protocols::scoring::methods::pcs2)   SavePoseMoverCreator (protocols::rosetta_scripts)   WorkUnit_LoopHash (protocols::loophash)   
DesignRepackMover (protocols::simple_moves)   InterfaceInfo (protocols::ligand_docking::ligand_options)   PcsGridSearchParameter (protocols::scoring::methods::pcs2)   SAXSEnergy (core::scoring::saxs)   WorkUnit_MoverWrapper (protocols::wum)   
DesignTask (protocols::flxbb)   InterfaceNeighborDefinitionCalculator (core::pose::metrics::simple_calculators)   PcsGridSearchParameterManager (protocols::scoring::methods::pcs2)   SAXSEnergyCEN (core::scoring::saxs)   WorkUnit_SilentStructStore (protocols::wum)   
DesignTask_Layer (protocols::flxbb)   InterfaceRecapitulationMover (protocols::protein_interface_design::movers)   PcsInputCenter (protocols::scoring::methods::pcs2)   SAXSEnergyCreator (core::scoring::saxs)   WorkUnit_Wait (protocols::wum2)   
DesignTask_Normal (protocols::flxbb)   InterfaceRecapitulationMoverCreator (protocols::protein_interface_design::movers)   PcsInputCenterManager (protocols::scoring::methods::pcs2)   SAXSEnergyCreatorCEN (core::scoring::saxs)   WorkUnit_Wait (protocols::wum)   
DesignVsNativeComparison (protocols::enzdes)   InterfaceSasaDefinitionCalculator (core::pose::metrics::simple_calculators)   PcsInputFile (protocols::scoring::methods::pcs2)   SAXSEnergyCreatorFA (core::scoring::saxs)   WorkUnitBase (protocols::wum)   
DestructionEvent (core::pose::signals)   InterfaceSasaFilter (protocols::simple_filters)   PcsInputLine (protocols::scoring::methods::pcs2)   SAXSEnergyFA (core::scoring::saxs)   WorkUnitList (protocols::wum)   
DetectProteinLigandInterface (protocols::enzdes)   InterfaceSasaFilterCreator (protocols::simple_filters)   PcsTensor (protocols::scoring::methods::pcs2)   SAXSScoreFilter (protocols::simple_filters)   WorkUnitManager (protocols::wum)   
DetectProteinLigandInterfaceOperationCreator (protocols::enzdes)   InterfaceScoreCalculator (protocols::ligand_docking)   PDB (protocols::sparta)   SC_BB_EnergyInvoker (core::scoring::etable)   WorkUnitQueue (protocols::wum)   
DetectSymmetry (protocols::simple_moves::symmetry)   InterfaceScoreCalculatorCreator (protocols::ligand_docking)   PDB_DReader (core::io::pdb)   SC_SC_EnergyInvoker (core::scoring::etable)   WorkUnitQueue_Swapped (protocols::wum)   
DetectSymmetryMoverCreator (protocols::simple_moves::symmetry)   InterfaceSidechainMinMover (protocols::docking)   PDB_DReaderOptions (core::io::pdb)   SC_Whole_EnergyInvoker (core::scoring::etable)   WrappedOptEExpressionCreator (protocols::optimize_weights)   
DFIRE_Energy (core::scoring::methods::dfire)   InterfaceTaskOperation (protocols::toolbox::task_operations)   PdbDataFeatures (protocols::features)   ScaffoldBuildPoint (protocols::match::upstream)   WrapperOptEMultifunc (protocols::optimize_weights)   
DFIRE_EnergyCreator (core::scoring::methods::dfire)   InterGroupNeighborsCalculator (protocols::toolbox::pose_metric_calculators)   PdbDataFeaturesCreator (protocols::features)   ScalarWeightedFunc (core::scoring::constraints)   WriteFileSFB (protocols::jd2)   
DFIRE_Potential (core::scoring::methods::dfire)   InterlockAroma (protocols::flxbb)   PDBDumpMover (protocols::moves)   ScaleAnnealerTemperatureOperation (protocols::optimize_weights)   WriteKinemageOutputter (protocols::match::output)   
DFPMinConvergedAbsolute (core::optimization)   InterlockAromaCreator (protocols::flxbb)   PdbIdChunkFilter (protocols::frag_picker)   SCAN (core::pack::task)   WriteOut_MpiFileBuffer (protocols::jd2)   
DFPMinConvergedFractional (core::optimization)   InterlockingAromaFilter (protocols::fldsgn::filters)   PDBInfo (core::pose)   SCMinMinimizerMap (core::pack::scmin)   WriteUpstreamCoordinateKinemage (protocols::match::output)   
DGBindOptEData (protocols::optimize_weights)   InterlockingAromaFilterCreator (protocols::fldsgn::filters)   PDBInputter (protocols::inputter)   SCMinMultifunc (core::pack::scmin)   WriteUpstreamHitKinemage (protocols::match::output)   
DiffAtomSasaFilter (protocols::enzdes)   InternalWorkingResidueParameter (protocols::swa::rna)   PDBJobInputter (protocols::jd2)   ScoreCutoffFilter (protocols::simple_filters)   WorkUnitBase::WU_Header (protocols::wum)   
DiffAtomSasaFilterCreator (protocols::enzdes)   Interval (protocols::jumping)   PDBJobInputterCreator (protocols::jd2)   ScoreCutoffFilterCreator (protocols::simple_filters)   WUQueue (protocols::wum2)   
DihedralConstraint (core::scoring::constraints)   Interval (protocols::forge::build)   PDBJobOutputter (protocols::jd2)   ScoreEValuator (protocols::frag_picker::scores)   
  X  
DihedralConstraintCreator (core::scoring::constraints)   InverseRotamersCstGeneratorCreator (protocols::forge::constraints)   PDBJobOutputterCreator (protocols::jd2)   ScoreEvaluator (protocols::simple_filters)   
DihedralConstraintsScore (protocols::frag_picker::scores)   InverseRotamersRCG (protocols::forge::constraints)   PDBOutput (protocols::dna)   ScoreFileData (core::io::raw_data)   XfoxmScore (protocols::sic_dock)   
DihedralPairConstraint (core::scoring::constraints)   InvGeometricFunc (protocols::moves)   PDBOutputter (protocols::outputter)   ScoreFileSilentStruct (core::io::silent)   XYZ_Func (core::scoring::constraints)   
DihedralPairConstraintCreator (core::scoring::constraints)   Invoker (core::scoring::etable::count_pair)   PDBPoseInputStream (core::import_pose::pose_stream)   ScoreFileSilentStructCreator (core::io::silent)   XYZEvent (core::conformation::signals)   
DimerPairing (protocols::fldsgn::topology)   InvRotamerDots (core::pack::interaction_graph)   PDBPoseMap (core::pose)   ScoreFunction (core::scoring)   xyzMatrix (numeric)   
DimerPairing (core::scoring)   InvrotCollector (protocols::toolbox::match_enzdes_util)   PDBReloadMover (protocols::simple_moves)   ScoreFunctionFactory (core::scoring)   xyzStripeHashPose (protocols::sic_dock)   
DimerPairings (protocols::fldsgn::topology)   InvrotTarget (protocols::toolbox::match_enzdes_util)   PDBReloadMoverCreator (protocols::simple_moves)   ScoreFunctionFeatures (protocols::features)   xyzStripeHashPoseWithMeta (protocols::sic_dock)   
DipolarCoupling (core::scoring)   InvrotTree (protocols::toolbox::match_enzdes_util)   PDBSilentStruct (core::import_pose)   ScoreFunctionFeaturesCreator (protocols::features)   xyzVector (numeric)   
DipolarCouplingEnergy (core::scoring::methods)   InvrotTreeCstGeneratorCreator (protocols::forge::constraints)   PDBSilentStructCreator (core::import_pose)   ScoreFunctionInfo (core::scoring)   
  Y  
DipolarCouplingEnergyCreator (core::scoring::methods)   InvrotTreeNode (protocols::toolbox::match_enzdes_util)   PDBTrajectoryRecorder (protocols::canonical_sampling)   ScoreFunctionLoader (protocols::jd2::parser)   
DirectReadoutEnergy (core::scoring::methods)   InvrotTreeNodeBase (protocols::toolbox::match_enzdes_util)   PDBTrajectoryRecorderCreator (protocols::canonical_sampling)   ScoreFunctionLoaderCreator (protocols::jd2::parser)   YHHPlanarityEnergy (core::scoring::methods)   
DirectReadoutEnergyCreator (core::scoring::methods)   InvrotTreeRCG (protocols::forge::constraints)   PDBWriter (protocols::match::output)   ScoreLessThanComparator (core::import_pose::atom_tree_diffs)   YHHPlanarityEnergyCreator (core::scoring::methods)   
DirectReadoutPotential (core::scoring::dna)   IRCollection (protocols::motifs)   PDDFEnergy (protocols::scoring::methods::saxs)   ScoreMap (protocols::jd2)   
  _  
DisallowIfNonnative (core::pack::task::operation)   IsProteinCAPredicate (core::scoring)   PDDFEnergyCreator (protocols::scoring::methods::saxs)   ScoreMover (protocols::simple_moves)   
DisallowIfNonnativeCreator (core::pack::task::operation)   LoggedFragmentMover::Item (protocols::simple_moves)   PDDFScoreFilter (protocols::simple_filters)   ScoreMoverCreator (protocols::simple_moves)   _ATOM_RADIUS (core::scoring::sc)   
DisallowIfNonnativeRLT (core::pack::task::operation)   IteratedConvergenceMover (protocols::moves)   PDEdge (core::pack::interaction_graph)   ScoreOnlyJobOutputter (protocols::jd2)   _BoolMover (protocols::moves)   
DisallowIfNonnativeRLTCreator (core::pack::task::operation)   IteratedConvergenceMoverCreator (protocols::moves)   PDInteractionGraph (core::pack::interaction_graph)   ScoreOnlyJobOutputterCreator (protocols::jd2)   _DOT (core::scoring::sc)   
DiscreteRandomizer (protocols::genetic_algorithm)   IterativeAbrelax (protocols::abinitio)   PDNode (core::pack::interaction_graph)   ScoreStruct (core::io::raw_data)   _HashEntry (protocols::abinitio)   
DisjointSets (core::graph)   IterativeBase (protocols::abinitio)   PeakAssignment (protocols::noesy_assign)   ScoreTypeFeatures (protocols::features)   _MergableEntries (protocols::abinitio)   
DistanceChainbreakEnergy (core::scoring::methods)   IterativeCentroid (protocols::abinitio)   PeakAssignmentParameters (protocols::noesy_assign)   ScoreTypeFeaturesCreator (protocols::features)   _PROBE (core::scoring::sc)   
DistanceChainbreakEnergyCreator (core::scoring::methods)   IterativeFullatom (protocols::abinitio)   PeakAssignmentResidueMap (protocols::noesy_assign)   ScoreTypeFilter (protocols::simple_filters)   _RESULTS (core::scoring::sc)   
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