A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | _

A: A; A3BHbsPatcher (protocols::simple_moves::a3b_hbs); AACompositionConstraint (core::scoring::aa_composition_energy); AACompositionEnergy (core::energy_methods); AACompositionEnergy (protocols::fldsgn::potentials); AACompositionEnergyCreator (core::energy_methods); AACompositionEnergyCreator (protocols::fldsgn::potentials); AACompositionEnergySetup (core::scoring::aa_composition_energy); AACompositionPropertiesSet (core::scoring::aa_composition_energy); AAFrequencies (protocols::denovo_design::task_operations); AAFrequency (protocols::denovo_design::task_operations); AAMatrix (protocols::mean_field); AAProb (protocols::mean_field); AARepeatEnergy (core::energy_methods); AARepeatEnergyCreator (core::energy_methods); AASynthesisFitnessCost (protocols::evolution); AASynthesisFitnessCostFilterCreator (protocols::evolution); Ab_TemplateInfo (protocols::antibody); Abego (core::energy_methods); ABEGO (core::sequence); ABEGO_SS_Config (protocols::frag_picker::quota); ABEGO_SS_Map (protocols::frag_picker::quota); ABEGO_SS_Pool (protocols::frag_picker::quota); ABEGO_SS_Score (protocols::frag_picker::scores); AbegoEnergyCreator (core::energy_methods); ABEGOEval (core::fragment::picking_old::vall::eval); ABEGOManager (core::sequence); AbinitioBaseFilter (protocols::simple_filters); AbinitioMoverWeight (protocols::topology_broker::weights); AbrelaxApplication (protocols::abinitio); AbrelaxMover (protocols::abinitio); AbscriptLoopCloserCM (protocols::abinitio::abscript); AbscriptLoopCloserCMCreator (protocols::abinitio::abscript); AbscriptMover (protocols::abinitio::abscript); AbscriptMoverCreator (protocols::abinitio::abscript); AbscriptStageMover (protocols::abinitio::abscript); AbstractArchiveBase (protocols::jd2::archive); AbstractRotamerTrie (core::conformation); AcceptanceCheck (protocols::loop_modeling::utilities); AcceptedScores (protocols::monte_carlo); AcceptorAtomFilter (core::chemical); AcceptToBestMover (protocols::relax); AcceptToBestMoverCreator (protocols::relax); Accumulator (core::scoring::packstat); ActiveSiteGrid (protocols::match::downstream); AdaptiveScoreHistogram (protocols::frag_picker::scores); AddAllPositionsMPM (protocols::match); AddAssemblyConstraints (protocols::domain_assembly); AddAtom (core::chemical); AddAtomAlias (core::chemical); AddAtomAliasCreator (core::chemical); AddAtomCreator (core::chemical); AddBehaviorRLT (core::pack::task::operation); AddBehaviorRLTCreator (core::pack::task::operation); AddBond (core::chemical); AddBondCreator (core::chemical); AddBondType (core::chemical); AddBondTypeCreator (core::chemical); AddCavitiesMover (protocols::simple_moves); AddCDRProfileSetsOperation (protocols::antibody::task_operations); AddCDRProfileSetsOperationCreator (protocols::antibody::task_operations); AddCDRProfilesOperation (protocols::antibody::task_operations); AddCDRProfilesOperationCreator (protocols::antibody::task_operations); AddChainBreak (protocols::protein_interface_design::movers); AddChainBreakCreator (protocols::protein_interface_design::movers); AddChainMover (protocols::simple_moves); AddChainMoverCreator (protocols::simple_moves); AddChi (core::chemical); AddChiCreator (core::chemical); AddChiRotamer (core::chemical); AddChiRotamerCreator (core::chemical); AddCompositionConstraintMover (protocols::aa_composition); AddCompositionConstraintMoverCreator (protocols::aa_composition); AddConnect (core::chemical); AddConnectAndDeleteChildProtonCreator (core::chemical); AddConnectAndTrackingVirt (core::chemical); AddConnectAndTrackingVirtCreator (core::chemical); AddConnectCreator (core::chemical); AddConnectDeleteChildProton (core::chemical); AddConstraints (protocols::constraint_generator); AddConstraintsCreator (protocols::constraint_generator); AddConstraintsToCurrentConformationMover (protocols::constraint_movers); AddConstraintsToCurrentConformationMoverCreator (protocols::constraint_movers); AddEdgeVisitor (core::conformation); AddFlankingVirtualResiduesMover (protocols::pose_sewing::movers); AddFlankingVirtualResiduesMoverCreator (protocols::pose_sewing::movers); AddGood2BPairEnergyRotamers (protocols::toolbox::rotamer_set_operations); AddHelixSequenceConstraintsMover (protocols::aa_composition); AddHelixSequenceConstraintsMoverCreator (protocols::aa_composition); AddHydrogen (protocols::ligand_docking); AddHydrogens (protocols::ligand_docking); AddHydrogensCreator (protocols::ligand_docking); AdditionalBackgroundNodesInteractionGraph (core::pack::interaction_graph); AdditionalOutputWrapper (protocols::rosetta_scripts); AdditionalOutputWrapperCreator (protocols::rosetta_scripts); AddJobPairData (protocols::simple_moves); AddJobPairDataCreator (protocols::simple_moves); AddLigandMotifRotamers (protocols::enzdes); AddLigandMotifRotamersOperationCreator (protocols::enzdes); AddMembraneMover (protocols::membrane); AddMembraneMoverCreator (protocols::membrane); AddMembraneSpanConstraint (protocols::membrane); AddMembraneSpanConstraintCreator (protocols::membrane); AddMembraneSpanTermZConstraint (protocols::membrane); AddMembraneSpanTermZConstraintCreator (protocols::membrane); AddMHCEpitopeConstraintMover (protocols::aa_composition); AddMHCEpitopeConstraintMoverCreator (protocols::aa_composition); AddMover (protocols::stepwise::monte_carlo::mover); AddMoverCreator (protocols::stepwise::monte_carlo::mover); AddMPLigandMover (protocols::membrane); AddMPLigandMoverCreator (protocols::membrane); AddNetChargeConstraintMover (protocols::aa_composition); AddNetChargeConstraintMoverCreator (protocols::aa_composition); AddOrDeleteMover (protocols::stepwise::monte_carlo::mover); AddOrRemoveMatchCsts (protocols::enzdes); AddOrRemoveMatchCstsCreator (protocols::enzdes); AddPDBInfoMover (protocols::simple_moves); AddPDBInfoMoverCreator (protocols::simple_moves); AddProperty (core::chemical); AddPropertyCreator (core::chemical); AddProtonChi (core::chemical); AddProtonChiCreator (core::chemical); AddResidueCouplingConstraint (protocols::simple_moves); AddResidueCouplingConstraintCreator (protocols::simple_moves); AddResidueLabelMover (protocols::simple_moves); AddResidueLabelMoverCreator (protocols::simple_moves); AddResiduesRotamerSetOperation (core::pack::rotamer_set); AddRigidBodyLigandConfs (protocols::enzdes); AddRigidBodyLigandConfsCreator (protocols::enzdes); AddSapConstraintMover (protocols::simple_moves); AddSapConstraintMoverCreator (protocols::simple_moves); AddSapMathConstraintMover (protocols::simple_moves); AddSapMathConstraintMoverCreator (protocols::simple_moves); AddSearchPatternRotSetOp (protocols::hotspot_hashing); AddSegmentDataMover (protocols::denovo_design::movers); AddSegmentDataMoverCreator (protocols::denovo_design::movers); AddSidechainConstraintsToHotspots (protocols::protein_interface_design::movers); AddSidechainConstraintsToHotspotsCreator (protocols::protein_interface_design::movers); Adduct (core::chemical); AddZincSiteConstraints (protocols::metal_interface); AdjacentList (protocols::cluster::calibur); ai_cmp (core::io::mmtf); AlaScan (protocols::simple_ddg); AlaScanFilterCreator (protocols::simple_ddg); Alias (protocols::denovo_design::components); Align_RmsdEvaluator (protocols::comparative_modeling); Align_RotamerEvaluator (protocols::comparative_modeling); AlignByResidueSelectorMover (protocols::fold_from_loops::movers); AlignByResidueSelectorMoverCreator (protocols::fold_from_loops::movers); AlignChainMover (protocols::simple_moves); AlignChainMoverCreator (protocols::simple_moves); AlignedThreadOperation (protocols::task_operations); AlignedThreadOperationCreator (protocols::task_operations); AlignEndsMover (protocols::splice); AlignEndsMoverCreator (protocols::splice); Aligner (core::sequence); AlignerFactory (core::sequence); AlignEvaluator (protocols::evaluation); AlignmentAAFinder (protocols::evolution); AlignmentAAFinderFilterCreator (protocols::evolution); AlignmentAtom (core::kinematics::inverse); AlignmentAtomArray (core::kinematics::inverse); AlignmentCluster (protocols::comparative_modeling); AlignmentClustering (protocols::comparative_modeling); AlignmentEnergy (protocols::rna); AlignmentEnergyCreator (protocols::rna); AlignmentFGMSettings (protocols::sewing::hashing); AlignmentFileGeneratorMover (protocols::sewing::hashing); AlignmentFileGeneratorMoverCreator (protocols::sewing::hashing); AlignmentGapInserter (protocols::evolution); AlignmentGapInserterFilterCreator (protocols::evolution); AlignmentGenerator (protocols::sewing::hashing); AlignmentSet (protocols::comparative_modeling); AlignmentSettings (protocols::sewing::hashing); AlignPDBInfoToSequences (protocols::pdbinfo_manipulations); AlignPDBInfoToSequencesCreator (protocols::pdbinfo_manipulations); AlignPoseToInvrotTreeMover (protocols::toolbox::match_enzdes_util); AlignResiduesMover (protocols::denovo_design::movers); AlignResiduesMoverCreator (protocols::denovo_design::movers); AlignRMSD_Screener (protocols::stepwise::screener); AlignRmsdTargetEvaluatorCreator (protocols::comparative_modeling); ALLAA (core::pack::task); ALLAAwc (core::pack::task); ALLAAxc (core::pack::task); AllAtomNormalization (protocols::qsar::scoring_grid); AlleleMatrix (core::scoring::mhc_epitope_energy); AllowedSeqposForGeomCst (protocols::toolbox::match_enzdes_util); AllowPdbIdFilter (protocols::frag_picker); AllResFilter (core::pack::task::operation); AllResFilterCreator (core::pack::task::operation); AllResiduesChanged (protocols::abinitio); AllResiduesChanged (protocols::hybridization); Alternating; AlternativePairings (protocols::abinitio); AlterSpecDisruptionDriver (protocols::pmut_scan); AmberPeriodicFunc (core::scoring::func); AmbigCSScore (protocols::frag_picker::scores); AmbiguousConstraint (core::scoring::constraints); AmbiguousConstraintCreator (core::scoring::constraints); AmbiguousMultiConstraint (protocols::constraints_additional); AmbiguousNMRConstraint (core::scoring::constraints); AmbiguousNMRConstraintCreator (core::scoring::constraints); AmbiguousNMRDistanceConstraint (core::scoring::constraints); AmbiguousNMRDistanceConstraintCreator (core::scoring::constraints); AminoAcidNeighborSparseMatrix (core::pack::interaction_graph); An; AnalyticEtableEnergy (core::scoring::etable); AnalyticEtableEvaluator (core::scoring::etable); AnalyzeLoopModeling (protocols::pose_length_moves); AnalyzeLoopModelingCreator (protocols::pose_length_moves); Anchor (protocols::anchored_design); AnchoredDesignMover (protocols::anchored_design); AnchoredGraftMover (protocols::grafting); AnchoredGraftMoverCreator (protocols::grafting); AnchoredPerturbMover (protocols::anchored_design); AnchoredRefineMover (protocols::anchored_design); AnchorMoversData (protocols::anchored_design); AnchorSugarScreener (protocols::stepwise::screener); AndJumpSelector (core::select::jump_selector); AndJumpSelectorCreator (core::select::jump_selector); AndResidueSelector (core::select::residue_selector); AndResidueSelectorCreator (core::select::residue_selector); AndSelector (protocols::pose_selectors); AndSelectorCreator (protocols::pose_selectors); AngleConstraint (core::scoring::constraints); AngleConstraintCreator (core::scoring::constraints); AngleToVector (protocols::simple_filters); AngleToVectorFilterCreator (protocols::simple_filters); ANN (protocols::sparta); AnnealableGraphBase (core::pack::interaction_graph); AnnealerFactory (core::pack::annealer); AnnealerObserver (core::pack::annealer); AnnotatedFragData (core::fragment); AnnotatedSequence (core::sequence); Antibody (protocols::antibody_legacy); AntibodyCDRGrafter (protocols::antibody); AntibodyCDRGrafterCreator (protocols::antibody); AntibodyDatabaseManager (protocols::antibody); AntibodyDesignEnumManager (protocols::antibody::design); AntibodyDesignMover (protocols::antibody::design); AntibodyDesignMoverCreator (protocols::antibody::design); AntibodyEnumManager (protocols::antibody); AntibodyFeatures (protocols::antibody); AntibodyFeaturesCreator (protocols::antibody); AntibodyInfo (protocols::antibody); AntibodyModeler (protocols::antibody_legacy); AntibodyModelerProtocol (protocols::antibody); AntibodyNumbering (protocols::antibody); AntibodyNumberingConverterMover (protocols::antibody); AntibodyNumberingConverterMoverCreator (protocols::antibody); AntibodyNumberingParser (protocols::antibody); AntibodyRegionSelector (protocols::antibody::residue_selector); AntibodyRegionSelectorCreator (protocols::antibody::residue_selector); AntibodySeqDesignTFCreator (protocols::antibody::design); AnyResFilter (core::pack::task::operation); AnyResFilterCreator (core::pack::task::operation); APBSConfig (core::scoring); APBSResult (core::scoring); APBSWrapper (core::scoring); APCluster (protocols::cluster); APOLA (core::pack::task); APOLAR (core::pack::task); APolarHydrogenFilter (core::chemical); AppendAssemblyMover (protocols::sewing::movers); AppendAssemblyMoverCreator (protocols::sewing::movers); AppendMainchainAtom (core::chemical); AppendMainchainAtomCreator (core::chemical); AppendResidueRotamerSet (core::pack::task::operation); AppendResidueRotamerSetCreator (core::pack::task::operation); AppendRotamer (core::pack::task::operation); AppendRotamerCreator (core::pack::task::operation); AppendRotamerSet (core::pack::task::operation); AppendRotamerSetCreator (core::pack::task::operation); ApplyChemistryMover (protocols::drug_design); ApplyChemistryMoverCreator (protocols::drug_design); ApplyRandomStoredRBConf (protocols::enzdes); ApproximateBuriedUnsatPenalty (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty); ApproximateBuriedUnsatPenaltyCreator (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty); AqueousPoreFinder (protocols::membrane); AqueousPoreFinderCreator (protocols::membrane); AqueousPoreParameters (core::conformation::membrane); ArchiveBase (protocols::jd2::archive); ArchiveManager (protocols::jd2::archive); AreaAccumulator (core::scoring::packstat); AreConnectablePredicate (protocols::denovo_design::connection); ArgCationPiEnergy (core::energy_methods); ArgCationPiEnergyCreator (core::energy_methods); ArmijoLineMinimization (core::optimization); AROMATIC (core::pack::task); AromaticAtomFilter (core::chemical); AromaticBackboneRestraintEnergy (core::energy_methods); AromaticBackboneRestraintEnergyCreator (core::energy_methods); Array2D (core::scoring::packstat); AspartimidePenaltyEnergy (core::energy_methods); AspartimidePenaltyEnergyCreator (core::energy_methods); AssembleLinkerMover (protocols::domain_assembly); Assembly (protocols::legacy_sewing); AssemblyFactory (protocols::legacy_sewing); AssemblyMover (protocols::sewing::movers); AssemblyMoverCreator (protocols::sewing::movers); AssemblyRequirement (protocols::sewing::requirements); AssemblyRequirementCreator (protocols::sewing::requirements); AssemblyRequirementFactory (protocols::sewing::requirements); AssemblyRequirementRegistrator (protocols::sewing::requirements); AssemblyScorer (protocols::sewing::scoring); AssemblyScorerCreator (protocols::sewing::scoring); AssemblyScorerFactory (protocols::sewing::scoring); AssemblyScorerRegistrator (protocols::sewing::scoring); AssignmentScaleAndDerivVectID (core::scoring::hbonds); AssignOrbitals (core::chemical::orbitals); AssignToClustersMover (protocols::cluster); ASTVisitor (numeric::expression_parser); AsymFoldandDockClaimer (protocols::topology_broker); AsymFoldandDockMoveRbJumpMover (protocols::simple_moves::asym_fold_and_dock); AsymFoldandDockMoveRbJumpMoverCreator (protocols::simple_moves::asym_fold_and_dock); AsymFoldandDockRbTrialMover (protocols::simple_moves::asym_fold_and_dock); AsymFoldandDockRbTrialMoverCreator (protocols::simple_moves::asym_fold_and_dock); AsymmetricUnitSelector (core::select::residue_selector); AsymmetricUnitSelectorCreator (core::select::residue_selector); AsyncMPITemperingBase (protocols::canonical_sampling); atmInfo (protocols::ligand_docking::ga_ligand_dock); Atom (core::chemical); Atom (core::scoring::sc); Atom (core::conformation); Atom (core::kinematics::tree); Atom_ (core::kinematics::tree); Atom_Bin (core::pose::rna); AtomAngleSecMatchRPE (protocols::match::downstream); AtomAtomPairFeatures (protocols::features); AtomAtomPairFeaturesCreator (protocols::features); AtomBasedConstraintsScore (protocols::frag_picker::scores); AtomCoordinateCstMover (protocols::relax); AtomCoordinateCstMoverCreator (protocols::relax); AtomCountFilter (protocols::ligand_docking); AtomCountFilterCreator (protocols::ligand_docking); AtomDihedralSecMatchRPE (protocols::match::downstream); AtomDistanceSecMatchRPE (protocols::match::downstream); AtomExistsFilter (protocols::drug_design); AtomExistsFilterCreator (protocols::drug_design); AtomGeometrySecMatchRPE (protocols::match::downstream); AtomGraphEdgeData (core::conformation); AtomGraphVertexData (core::conformation); AtomGrid (protocols::nmr::pcs); AtomGridPoint (protocols::nmr::pcs); AtomHash (protocols::simple_moves); AtomHashNode (protocols::simple_moves); AtomicContactCountFilter (protocols::protein_interface_design::filters); AtomicContactCountFilterCreator (protocols::protein_interface_design::filters); AtomicContactFilter (protocols::simple_filters); AtomicContactFilterCreator (protocols::simple_filters); AtomicDepth (core::scoring::atomic_depth); AtomicDistanceFilter (protocols::simple_filters); AtomicDistanceFilterCreator (protocols::simple_filters); AtomICoor (core::chemical); AtomID (core::id); AtomID_Map (core::id); AtomID_Map_AtomID (core::id); AtomID_Map_bool (core::id); AtomID_Map_Real (core::id); AtomID_Mapper (core::pose::toolbox); AtomIDHashFunction (protocols::sic_dock); AtomInfo (core::scoring::hbonds::graph); AtomInformation (core::io); AtomInfoSet (core::scoring::hbonds::graph); AtomInResidueAtomInResiduePairFeatures (protocols::features); AtomInResidueAtomInResiduePairFeaturesCreator (protocols::features); AtomLevelDomainMap (core::pose::toolbox); AtomNeighbor (core::scoring); AtomPack (protocols::abinitio::abscript); AtomPairConstraint (core::scoring::constraints); AtomPairConstraintCreator (core::scoring::constraints); AtomPairConstraintGenerator (protocols::constraint_generator); AtomPairConstraintGeneratorCreator (protocols::constraint_generator); AtomPairConstraintsData (protocols::frag_picker::scores); AtomPairConstraintsScore (protocols::frag_picker::scores); AtomPairData (protocols::ligand_docking::rdf); AtomPairEnergy (core::scoring::etable); AtomPairFuncList (core::scoring::custom_pair_distance); AtomProperties (core::chemical); AtomProperties (protocols::ligand_docking::ga_ligand_dock); AtomPropertiesManager (core::chemical); AtomRadiusMap (core::scoring::packstat); PDBInfo::AtomRecord (core::pose); AtomRefMapping (core::chemical); atoms_and_func_struct (core::scoring::custom_pair_distance); AtomSelection (core::io::nmr); AtomSubstitution (protocols::drug_design); AtomToAxisConstraint (core::scoring::constraints); AtomTree (core::kinematics); AtomTreeCollection (core::pack::scmin); AtomTreeDiff (core::import_pose::atom_tree_diffs); AtomTreeDiffJobDistributor (protocols::jobdist); AtomTreeDiffJobInputter (protocols::jd2); AtomTreeDiffJobInputterCreator (protocols::jd2); AtomTreeDiffJobOutputter (protocols::jd2); AtomTreeDiffJobOutputterCreator (protocols::jd2); AtomTreeMinimizer (core::optimization); AtomTreeMultifunc (core::optimization); AtomTreeSCMinMinimizerMap (core::pack::scmin); AtomType (core::chemical); AtomTypeData; AtomTypeDatabaseIO (core::chemical); AtomTypeSet (core::chemical); AtomTypesFeatures (protocols::features); AtomTypesFeaturesCreator (protocols::features); AtomVDW (core::scoring); AtomWithDOFChange (core::kinematics); AtrGrid (protocols::qsar::scoring_grid); AtrGridCreator (protocols::qsar::scoring_grid); Attachment (protocols::stepwise::monte_carlo::mover); AUTO (core::pack::task); AutoCutData (protocols::environment); AutoCutDataCreator (protocols::environment); AutomaticSheetConstraintGenerator (protocols::fold_from_loops::constraint_generator); AutomaticSheetConstraintGeneratorCreator (protocols::fold_from_loops::constraint_generator); AutomorphismIterator (core::chemical); AutoRBMover (protocols::rbsegment_relax); AverageDegreeFilter (protocols::protein_interface_design::filters); AverageDegreeFilterCreator (protocols::protein_interface_design::filters); AveragePathLengthFilter (protocols::simple_filters); AveragePathLengthFilterCreator (protocols::simple_filters); AverageProbabilitiesMetric (core::simple_metrics::metrics); AverageProbabilitiesMetricCreator (core::simple_metrics::metrics)

B: BackboneDB (protocols::loophash); BackboneGridSampler (protocols::helical_bundle); BackboneGridSamplerCreator (protocols::helical_bundle); BackboneGridSamplerHelper (protocols::helical_bundle); BackboneMover (protocols::simple_moves); BackboneSampler (protocols::enzdes); BackboneSamplerCreator (protocols::enzdes); BackboneSegment (protocols::loophash); BackboneStub (protocols::indexed_structure_store); BackboneStubConstraint (core::scoring::constraints); BackboneStubLinearConstraint (core::scoring::constraints); BackboneStubRMSDComparator (protocols::pose_length_moves); BackboneStubVectorRMSDComparator (protocols::indexed_structure_store); BackboneTorsionPerturbation (protocols::hybridization); BackboneTorsionPerturbationCreator (protocols::hybridization); BackboneTorsionSampler (protocols::hybridization); BackboneTorsionSamplerCreator (protocols::hybridization); BackgroundNode (core::pack::interaction_graph); BackgroundToFirstClassEdge (core::pack::interaction_graph); BackrubDDMover (protocols::protein_interface_design::movers); BackrubDDMoverCreator (protocols::protein_interface_design::movers); BackrubMover (protocols::backrub); BackrubMoverCreator (protocols::backrub); BackrubProtocol (protocols::backrub); BackrubProtocolCreator (protocols::backrub); BackrubSegment (protocols::backrub); BackrubSidechainMover (protocols::backrub); BackrubSidechainMoverCreator (protocols::backrub); BadInput (utility::excn); BalancedKicMover (protocols::kinematic_closure); BalancedKicMoverCreator (protocols::kinematic_closure); Ball (core::scoring::packing); BareMinimumPDEdge (core::pack::hbonds); Base (protocols::toolbox::py_inheritance_test); BaseArchiveManager (protocols::jd2::archive); BaseBin (protocols::stepwise::modeler::rna::rigid_body); BaseBinMapUpdater (protocols::stepwise::screener); BaseCacheUnit (core::fragment); BaseCentroidScreener (protocols::stepwise::screener); BaseDisulfPairingLibrary (protocols::jumping); BaseEtableEnergy (core::scoring::etable); BaseJobDistributor (protocols::jobdist); BaseJumpSetup (protocols::jumping); BasePair (core::pose::rna); BasePairConstraint (core::scoring::constraints); BasePairConstraintCreator (core::scoring::constraints); BasePairingLibrary (protocols::jumping); BasePairStep (core::pose::rna); BasePairStepLibrary (core::import_pose::libraries); BasePairStepSequence (core::import_pose::libraries); BasePairType (core::import_pose::libraries); BasePartner (core::scoring::dna); BaseStack (core::pose::rna); BaseTabooPerturber (protocols::loops::loop_closure::kinematic_closure); BaseTypeList (core::pack::palette); BasicCDRClusterSet (protocols::antibody::clusters); BasicCmdLineInit (protocols::rpc); BasicInit (protocols::rpc); BasicJob (protocols::jobdist); BasicJumpClaimer (protocols::topology_broker); BasicRotamerLibrarySpecification (core::chemical::rotamers); BasicRotamerLibrarySpecificationCreator (core::chemical::rotamers); BasicSimAnnealerRepacker (protocols::pack_daemon); Basis (protocols::legacy_sewing); Basis (protocols::sewing::data_storage); basis_pair_equal_to (protocols::legacy_sewing); basis_pair_hash (protocols::legacy_sewing); BasisMapGenerator (protocols::sewing::hashing); Batch (protocols::jd2::archive); BatchEvaluator (protocols::simple_filters); BatchFeatures (protocols::features); BatchJobInputter (protocols::jd2); BatchNrEvaluator (protocols::simple_filters); BB_BB_EnergyInvoker (core::scoring::etable); BB_Pos (core::scoring); BB_Pos (protocols::fldsgn::topology); BBClaim (protocols::topology_broker::claims); BBConRotMover (protocols::simple_moves); BBData (protocols::loophash); BBDepCartBondedParameters (core::scoring::methods); BBDepNRChiSample (core::pack::dunbrack); BBDepScoreInterpData (core::pack::dunbrack); BBDepSemiRotamericData (core::pack::dunbrack); BBDihedralSampler (protocols::simple_moves::bb_sampler); BBDihedralSampler2D (protocols::simple_moves::bb_sampler); BBDihedralSampler3D (protocols::simple_moves::bb_sampler); BBDihedralSamplerBase (protocols::simple_moves::bb_sampler); BBDihedralSamplerMover (protocols::simple_moves); BBDihedralSamplerMoverCreator (protocols::simple_moves); BBDihedralSamplerND (protocols::simple_moves::bb_sampler); BBDofs (protocols::splice); BBExtraData (protocols::loophash); BBG8T3AMover (protocols::simple_moves); BBGaussianMover (protocols::simple_moves); BBGaussianMoverCreator (protocols::simple_moves); BBIndepCartBondedParameters (core::scoring::methods); BBIndNRChiSample (core::pack::dunbrack); BBIndSemiRotamericData (core::pack::dunbrack); BBMatching (protocols::splice); BBTorsionAndAnglesSRFD (core::fragment); BBTorsionSRFD (core::fragment); BCLFragmentBaseMover (protocols::drug_design::bcl); BCLFragmentHandler (core::chemical::bcl); BCLFragmentMutateMover (protocols::drug_design::bcl); BCLFragmentMutateMoverCreator (protocols::drug_design::bcl); BCLReferenceSDFilesManager (protocols::drug_design::bcl); BCLSampleConfsManager (protocols::drug_design::bcl); BDR (protocols::forge::components); BenchmarkBuildRotamersMover (protocols::testing); BenchmarkBuildRotamersMoverCreator (protocols::testing); BestHotspotCstMover (protocols::protein_interface_design::movers); BestHotspotCstMoverCreator (protocols::protein_interface_design::movers); BestMatchesCollection (protocols::match::output); BestMutationsFromProbabilitiesMetric (core::simple_metrics::composite_metrics); BestMutationsFromProbabilitiesMetricCreator (core::simple_metrics::composite_metrics); BestTotalScoreSelector (protocols::frag_picker); BetaAlphaBetaMotif (protocols::fldsgn::topology); BetaAlphaBetaMotifSet (protocols::fldsgn::topology); BetaSheetArchitect (protocols::denovo_design::architects); BetaSheetArchitectCreator (protocols::denovo_design::architects); BetaTurnDetection (protocols::features); BetaTurnDetectionFeatures (protocols::features); BetaTurnDetectionFeaturesCreator (protocols::features); BFactor (protocols::frag_picker::scores); BfactorFittingMover (protocols::electron_density); BfactorFittingMoverCreator (protocols::electron_density); BfactorMPM (protocols::match); BfactorMultifunc (protocols::electron_density); BFactorSelector (core::select::residue_selector); BFactorSelectorCreator (core::select::residue_selector); BiasedFragmentMover (protocols::nonlocal); BiasedMonteCarlo (protocols::canonical_sampling); BiasEnergy (protocols::canonical_sampling); Bicelle (core::conformation::membrane::membrane_geometry); BigBinConstraint (core::scoring::constraints); BigBinConstraintCreator (core::scoring::constraints); BinaryExpression (numeric::expression_parser); BinaryFragmentStoreBackend (protocols::indexed_structure_store); BinarySilentStruct (core::io::silent); BinarySilentStructCreator (core::io::silent); BindingSiteConstraint (protocols::constraints_additional); BindingSiteConstraintCreator (protocols::constraints_additional); BindingStrainFilter (protocols::protein_interface_design::filters); BindingStrainFilterCreator (protocols::protein_interface_design::filters); BinSelector (core::select::residue_selector); BinSelectorCreator (core::select::residue_selector); BinTransitionCalculator (core::scoring::bin_transitions); BinTransitionCalculatorManager (core::scoring::bin_transitions); BinTransitionData (core::scoring::bin_transitions); BlockParam (core::pack::guidance_scoreterms::sap); BlockSelector (core::select::residue_selector); BlockSelectorCreator (core::select::residue_selector); BlockwiseAnalysisMover (protocols::pose_sewing::movers); BlockwiseAnalysisMoverCreator (protocols::pose_sewing::movers); BlockwisePoseCompMotifMetric (protocols::pose_sewing::simple_metrics); BlockwisePoseCompMotifMetricCreator (protocols::pose_sewing::simple_metrics); BlockwiseShapeCompMetric (protocols::pose_sewing::simple_metrics); BlockwiseShapeCompMetricCreator (protocols::pose_sewing::simple_metrics); Blosum62Map (core::sequence); BluePrint (protocols::parser); BlueprintArchitect (protocols::denovo_design::architects); BlueprintArchitectCreator (protocols::denovo_design::architects); BluePrintBDR (protocols::fldsgn); BluePrintBDRCreator (protocols::fldsgn); Boinc (protocols::boinc); BoincCurrentPoseObserver (protocols::boinc); BOINCJobDistributor (protocols::jd2); BoincSharedMemory (protocols::boinc); BoltzmannFilter (protocols::protein_interface_design::filters); BoltzmannFilterCreator (protocols::protein_interface_design::filters); BoltzmannRotamerMover (protocols::minimization_packing); BoltzmannRotamerMoverCreator (protocols::minimization_packing); Bond (core::chemical); BondAnglePerturber (protocols::kinematic_closure::perturbers); BondData (core::chemical::sdf); BondedAtom (core::kinematics::tree); BondedResidueSelector (core::select::residue_selector); BondedResidueSelectorCreator (core::select::residue_selector); BondID (core::id); BondInfo (protocols::denovo_design::components); BondOrderParser (core::scoring); Book (core::fragment::picking_old::concepts); Book_VallResidues (core::fragment::picking_old::concepts); Bool3DGrid (protocols::match); Bool3DGridKinemageWriter (protocols::match); BooleanValuedParameter (core::conformation::parametric); BoundedCollector (protocols::frag_picker); BoundedCollector_CompareTotalScore (protocols::frag_picker); BoundedPriorityQueue (protocols::frag_picker); BoundFunc (core::scoring::constraints); BranchAngleOptimizer (protocols::branch_angle); BranchCoef1 (protocols::branch_angle); BranchCoef2 (protocols::branch_angle); BranchEnergy (core::energy_methods); BranchEnergyCreator (core::energy_methods); BranchParam1 (protocols::branch_angle); BranchParam2 (protocols::branch_angle); BrentLineMinimization (core::optimization); Bridge (protocols::forge::build); BridgeChainsCreator (protocols::denovo_design::movers); BridgeChainsMover (protocols::denovo_design::movers); BridgeChainsMoverCreator (protocols::denovo_design::movers); EnvClaimBroker::BrokeredJumpData (protocols::environment); EnvClaimBroker::BrokerResult (protocols::environment); BruteFunGroupTK (protocols::kinmatch); BUFFER (core::io::serialization); BuildAlaPose (protocols::protein_interface_design::movers); BuildAlaPoseCreator (protocols::protein_interface_design::movers); BuildDeNovoBackboneMover (protocols::denovo_design::movers); BuildDeNovoBackboneMoverCreator (protocols::denovo_design::movers); BuildingBlockInterfaceOperation (protocols::matdes); BuildingBlockInterfaceOperationCreator (protocols::matdes); BuildInstruction (protocols::forge::build); BuildManager (protocols::forge::build); BuildPhases (protocols::denovo_design::components); BuildPosition (protocols::motifs); BuildSet (protocols::match::upstream); BulgeApplier (protocols::stepwise::screener); BulgeApplyMover (protocols::stepwise::modeler::rna::bulge); BulgeUnApplyMover (protocols::stepwise::modeler::rna::bulge); BumpGrid (protocols::match); BumpSelector (core::pack::rotamer_set); BundleGridSampler (protocols::helical_bundle); BundleGridSamplerCreator (protocols::helical_bundle); BundleGridSamplerHelper (protocols::helical_bundle); BundleParameters (protocols::helical_bundle::parameters); BundleParametersSet (protocols::helical_bundle::parameters); BundleParametrizationCalculator (protocols::helical_bundle); BundleReporterFilter (protocols::helical_bundle); BundleReporterFilterCreator (protocols::helical_bundle); Burial_v2Energy (core::energy_methods); Burial_v2EnergyCreator (core::energy_methods); BurialEnergy (core::energy_methods); BurialEnergyCreator (core::energy_methods); BuriedPolarScore (protocols::sic_dock); BuriedSurfaceAreaFilter (protocols::simple_filters); BuriedSurfaceAreaFilterCreator (protocols::simple_filters); BuriedUnsatHbondFilter (protocols::simple_filters); BuriedUnsatHbondFilter2 (protocols::buns); BuriedUnsatHbondFilter2Creator (protocols::buns); BuriedUnsatHbondFilterCreator (protocols::simple_filters); BuriedUnsatisfiedPolarsCalculator (protocols::simple_pose_metric_calculators); BuriedUnsatisfiedPolarsCalculator2 (protocols::buns); BuriedUnsatPenalty (core::pack::guidance_scoreterms::buried_unsat_penalty); BuriedUnsatPenaltyCreator (core::pack::guidance_scoreterms::buried_unsat_penalty); BuriedUnsatPenaltyEdge (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyEdgeData (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyGraph (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyGraphContainer (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyGraphHbond (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyGraphOptions (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyNode (core::pack::guidance_scoreterms::buried_unsat_penalty::graph); BuriedUnsatPenaltyNodeData (core::pack::guidance_scoreterms::buried_unsat_penalty::graph)

C: CaCbCb_Angle_Func (core::scoring::disulfides); CaCbCbCa_Dihedral_Func (core::scoring::disulfides); CacheableAtomID_MapVector (core::id); CacheableDataType (core::pose::datacache); CacheableObserver (core::pose::datacache); CacheablePoseRawPtr (core::pose::datacache); CacheableResidueTypeSets (core::chemical); CacheableSasaVector (core::energy_methods); CachedResidueSubset (core::select::residue_selector); CacheWrapper (core::fragment); CachingScoringMethod (protocols::frag_picker::scores); CAcstGenerator (protocols::seeded_abinitio); CAcstGeneratorCreator (protocols::seeded_abinitio); CalcInterNeighborGroup (protocols::toolbox); CalculatorFactory (core::pose::metrics); CalculatorFilter (protocols::filters); CalculatorFilterCreator (protocols::filters); CalculatorMetric (core::simple_metrics::metrics); CalculatorMetricCreator (core::simple_metrics::metrics); CamShiftEvaluator (protocols::simple_filters); CamShiftEvaluatorCreator (protocols::simple_filters); SmoothPolicy::Candidate (protocols::nonlocal); CandidatesCollector (protocols::frag_picker); CanonicalSamplingMover (protocols::canonical_sampling); CarbohydrateInfo (core::chemical::carbohydrates); CarbohydrateInfoManager (core::chemical::carbohydrates); CarbonHBondEnergy (core::scoring::carbon_hbonds); CarbonHBondEnergyCreator (core::scoring::carbon_hbonds); CarbonHBondPotential (core::scoring::carbon_hbonds); CartBondedParameters (core::scoring::methods); CartesianAtom (protocols::cartesian); CartesianBondedEnergy (core::energy_methods); CartesianBondedEnergyCreator (core::energy_methods); CartesianHybridize (protocols::hybridization); CartesianMD (protocols::md); CartesianMDCreator (protocols::md); CartesianMinimizer (core::optimization); CartesianMinimizerMap (core::optimization); CartesianMultifunc (core::optimization); CartesianSampler (protocols::hybridization); CartesianSamplerCreator (protocols::hybridization); CartesianSearchPattern (protocols::hotspot_hashing); CartGrid (core::grid); CartSCMinMinimizerMap (core::pack::scmin); CartSCMinMultifunc (core::pack::scmin); CatPiCalculator (protocols::pose_metric_calculators); CavityBall (core::scoring::packstat); CavityBallCluster (core::scoring::packstat); CavityCalculator (protocols::denovo_design::calculators); CavityVolumeFilter (protocols::denovo_design::filters); CavityVolumeFilterCreator (protocols::denovo_design::filters); CB_Angle_Func (core::scoring::disulfides); Cb_Distance_Func (core::scoring::disulfides); CBScore (protocols::sic_dock); CBScoreVisitor (protocols::sic_dock); CBSG_Dihedral_Func (core::scoring::disulfides); CCDEndsGraftMover (protocols::grafting); CCDEndsGraftMoverCreator (protocols::grafting); CCDLoopClosureMover (protocols::loops::loop_closure::ccd); CCDLoopClosureMoverCreator (protocols::loops::loop_closure::ccd); CCDMoveWrapper (protocols::rbsegment_relax); CCluster (protocols::pockets); CClusterSet (protocols::pockets); CCS_IMMSEnergy (core::energy_methods); CCS_IMMSEnergyCreator (core::energy_methods); CDRCluster (protocols::antibody::clusters); CDRClusterEnumManager (protocols::antibody::clusters); CDRClusterFeatures (protocols::antibody::clusters); CDRClusterFeaturesCreator (protocols::antibody::clusters); CDRClusterMatcher (protocols::antibody::clusters); CDRClusterSet (protocols::antibody::clusters); CDRDBPose (protocols::antibody); CDRDBSequence (protocols::antibody); CDRDihedralConstraintMover (protocols::antibody::constraints); CDRDihedralConstraintMoverCreator (protocols::antibody::constraints); CDRGraftDesignOptions (protocols::antibody::design); CDRGraftDesignOptionsParser (protocols::antibody::design); CDRH3Modeler (protocols::antibody_legacy); CDRResidueSelector (protocols::antibody::residue_selector); CDRResidueSelectorCreator (protocols::antibody::residue_selector); CDRSeqDesignOptions (protocols::antibody::design); CDRSeqDesignOptionsParser (protocols::antibody::design); CDRSetOptions (protocols::antibody); CDRSetOptionsParser (protocols::antibody); CDRsMinPackMin (protocols::antibody); Cell (core::sequence); Cen_Distance_Func (core::scoring::disulfides); CenHBEnergy (core::energy_methods); CenHBEnergyCreator (core::energy_methods); CenHBPotential (core::scoring); CenListInfo (core::scoring); CenPairEnergy (core::energy_methods); CenPairEnergyCreator (core::energy_methods); CenPairMotifDegreeEnergy (core::energy_methods); CenPairMotifDegreeEnergyCreator (core::energy_methods); CenPairMotifEnergy (core::energy_methods); CenPairMotifEnergyCreator (core::energy_methods); CenRotDunEnergy (core::pack::dunbrack::cenrot); CenRotDunEnergyCreator (core::pack::dunbrack::cenrot); CenRotEnvEnergy (core::energy_methods); CenRotEnvEnergyCreator (core::energy_methods); CenRotEnvPairPotential (core::scoring); CenrotLibrary (core::pack::dunbrack::cenrot); CenRotPairEnergy (core::energy_methods); CenRotPairEnergyCreator (core::energy_methods); CenrotRotamerLibrarySpecification (core::chemical::rotamers); CenrotRotamerLibrarySpecificationCreator (core::chemical::rotamers); CentroidDistanceScreener (protocols::stepwise::screener); CentroidDisulfideEnergy (core::energy_methods); CentroidDisulfideEnergyComponents (core::scoring::disulfides); CentroidDisulfideEnergyContainer (core::scoring::disulfides); CentroidDisulfideEnergyCreator (core::energy_methods); CentroidDisulfideNeighborConstIterator (core::scoring::disulfides); CentroidDisulfideNeighborIterator (core::scoring::disulfides); CentroidDisulfidePotential (core::scoring::disulfides); CentroidRelax (protocols::relax); CentroidRelaxMover (protocols::surface_docking); CentroidRotamerSampleData (core::pack::dunbrack::cenrot); CentroidRotNum (protocols::make_rot_lib); CentroidScatter (core::scoring::fiber_diffraction); Chain (protocols::pose_length_moves); chain_lt (protocols::pose_length_moves); ChainBreak (protocols::simple_filters); ChainbreakDistFunc (protocols::jumping); ChainbreakEnergy (core::energy_methods); ChainbreakEnergyCreator (core::energy_methods); ChainBreakFilterCreator (protocols::simple_filters); ChainbreakUtil (core::util); ChainCountFilter (protocols::simple_filters); ChainCountFilterCreator (protocols::simple_filters); ChainExistsFilter (protocols::ligand_docking); ChainExistsFilterCreator (protocols::ligand_docking); ChainGroupDiscriminator (protocols::minimization_packing); ChainIs (core::pack::task::operation); ChainIsCreator (core::pack::task::operation); ChainIsnt (core::pack::task::operation); ChainIsntCreator (core::pack::task::operation); ResiduePDBIndexIs::ChainPos (core::pack::task::operation); ChainSelector (core::select::residue_selector); ChainSelectorCreator (core::select::residue_selector); ChainSplitMover (protocols::simple_moves); ChainTerm (protocols::constel); ChangeAncestory (core::chemical); ChangeAndResetFoldTreeMover (protocols::simple_moves); ChangeAndResetFoldTreeMoverCreator (protocols::simple_moves); ChangeBondType (core::chemical); ChangeBondTypeCreator (core::chemical); ChangeFoldTreeMover (protocols::moves); ChargeAtom (protocols::qsar::scoring_grid); ChargeCalculator (protocols::pose_metric_calculators); ChargeChargeFeatures (protocols::features); ChargeChargeFeaturesCreator (protocols::features); CHARGED (core::pack::task); ChargeGrid (protocols::qsar::scoring_grid); ChargeGridCreator (protocols::qsar::scoring_grid); CharmmPeriodicFunc (core::scoring::func); CharPairHash (core::sequence); CheckPointer (protocols::checkpoint); ChemicalManager (core::chemical); ChemicalReaction (protocols::drug_design); ChemicalShiftAnisotropy (core::scoring); ChemicalShiftAnisotropyEnergy (core::energy_methods); ChemicalShiftAnisotropyEnergyCreator (core::energy_methods); ChemicalShiftData (core::scoring::rna::chemical_shift); ChemicalShiftEvaluator (protocols::sparta); ChemicalShiftEvaluatorCreator (protocols::sparta); ChemicalShiftScoringScheme (core::sequence); ChemicalShiftSequence (core::sequence); ChemicalShiftSequenceCreator (core::sequence); Chemistry (protocols::chemistries); ChemistryBase (core::chemical::modifications); ChemistryCreator (protocols::chemistries); ChemistryFactory (protocols::chemistries); ChemistryLoader (protocols::chemistries); ChemistryLoaderCreator (protocols::chemistries); ChemistryRegistrator (protocols::chemistries); CheshireCell (protocols::cryst); ChiAngleNormalization (protocols::qsar::scoring_grid); CHIDihedralSamplingData (core::scoring::carbohydrates); CHIEnergyFunction (core::scoring::carbohydrates); ChiInfo (protocols::ligand_docking::ga_ligand_dock); ChiralFlipAtoms (core::chemical); ChiralFlipAtomsCreator (core::chemical); ChiralFlipNaming (core::chemical); ChiralFlipNamingCreator (core::chemical); ChiralMover (protocols::simple_moves::chiral); ChiSet (core::pack::dunbrack); ChiWellRmsdEvaluator (protocols::simple_filters); ChiWellRmsdEvaluatorCreator (protocols::simple_filters); ChromophoreDataReader (protocols::chromophore); SliceToMiniProteinMover::Chunk (protocols::pose_creation); Chunk (protocols::nonlocal); ChunkLibraryInnerLarvalJob (protocols::jd3::chunk_library); ChunkLibraryInputSource (protocols::jd3::chunk_library_inputters); ChunkLibraryInputter (protocols::jd3::chunk_library_inputters); ChunkLibraryInputterCreator (protocols::jd3::chunk_library_inputters); ChunkLibraryInputterFactory (protocols::jd3::chunk_library_inputters); ChunkLibraryInputterRegistrator (protocols::jd3::chunk_library_inputters); ChunkLibraryJobQueen (protocols::jd3::chunk_library); ChunkLibraryJobResult (protocols::jd3::chunk_library); ChunkLibraryPreliminaryLarvalJob (protocols::jd3::chunk_library); ChunkSet (core::import_pose::libraries); ChunkTrialMover (protocols::hybridization); Circle (core::scoring::packstat); CircularGeneral1D_Func (core::scoring::func); CircularHarmonicFunc (core::scoring::func); CircularPermutation (protocols::fldsgn); CircularPermutationCreator (protocols::fldsgn); CircularPermuteFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers); CircularPowerFunc (core::scoring::func); CircularSigmoidalFunc (core::scoring::func); CircularSplineFunc (core::scoring::func); CisPeptideInformation (core::io); ClaimerMessage (protocols::topology_broker); ClaimStrength (protocols::environment::claims); ClashBasedRepackShell (core::pack::task::operation); ClashBasedRepackShellCreator (core::pack::task::operation); ClashBasedShellSelector (core::pack::task::residue_selector); ClashBasedShellSelectorCreator (core::pack::task::residue_selector); ClashCheckFilter (protocols::matdes); ClashCheckFilterCreator (protocols::matdes); ClashCountCalculator (protocols::pose_metric_calculators); ClashRequirement (protocols::sewing::requirements); ClashRequirementCreator (protocols::sewing::requirements); ClashWithTargetFilter (protocols::protein_interface_design::filters); ClashWithTargetFilterCreator (protocols::protein_interface_design::filters); ClassicAbinitio (protocols::abinitio); ClassicFragmentMover (protocols::simple_moves); ClassicGrid (protocols::qsar::scoring_grid); ClassicGridCreator (protocols::qsar::scoring_grid); ClassicMatchAlgorithm (protocols::match::downstream); ClassicRelax (protocols::relax); ClassicRelaxCreator (protocols::relax); ClearChiRotamers (core::chemical); ClearChiRotamersCreator (core::chemical); ClearCompositionConstraintsMover (protocols::aa_composition); ClearCompositionConstraintsMoverCreator (protocols::aa_composition); ClearConstraintsMover (protocols::constraint_movers); ClearConstraintsMoverCreator (protocols::constraint_movers); ClientMover (protocols::environment); clique_saver (protocols::features); CloseContactResidueSelector (core::select::residue_selector); CloseContactResidueSelectorCreator (core::select::residue_selector); CloseFold (protocols::seeded_abinitio); CloseFoldCreator (protocols::seeded_abinitio); CloseOneCDRLoop (protocols::antibody); CloseOneMover (protocols::antibody_legacy); CloserToAtom (core::scoring::sc); ClosureProblem (protocols::kinematic_closure); ClosureSolution (protocols::kinematic_closure); CloudPDBWriter (protocols::match::output); Cluster (protocols::cluster); Cluster_Member (protocols::stepwise::legacy::modeler::rna); ClusterBase (protocols::cluster); ClusterBase (protocols::toolbox); ClusterData (protocols::antibody::clusters); Clusterer (protocols::mpi_refinement); Clustering (protocols::cluster::calibur); ClusterMetric (protocols::multistage_rosetta_scripts::cluster); ClusterMetricCreator (protocols::multistage_rosetta_scripts::cluster); ClusterMetricFactory (protocols::multistage_rosetta_scripts::cluster); ClusterMetricRegistrator (protocols::multistage_rosetta_scripts::cluster); ClusterOptions (protocols::toolbox); ClusterPhilStyle (protocols::cluster); ClusterPhilStyle (protocols::toolbox); ClusterPhilStyle_Loop (protocols::cluster); ClusterPhilStyle_PoseReporter (protocols::cluster); ClusterPoseSelector (protocols::pose_selectors); ClusterPoseSelectorCreator (protocols::pose_selectors); RigidChunkClaimer::CM_SuggestFixResidue (protocols::topology_broker); CMAES_Minimizer (core::optimization); CmdLineData (protocols::topology_broker); CoarseRNA_Fragments (protocols::rna::denovo::coarse); CoarseRNA_LoopCloser (protocols::rna::denovo::coarse); COFilter (protocols::simple_filters); ColorGradient (protocols::qsar); Combine_Tags_Info (protocols::stepwise::modeler::rna); CombineChainsMover (protocols::domain_assembly); CombinedConstraintEvaluator (protocols::constraints_additional); CombinedConstraintEvaluatorCreator (protocols::constraints_additional); CombinedFilter (protocols::filters); CombinedFilterCreator (protocols::filters); CombinedTaskOperation (protocols::flxbb); CombinePoseMover (protocols::simple_moves); COMCoordinateConstraint (protocols::constraints_additional); comparator; Comparator (protocols::environment); compare_base_bin (protocols::stepwise::modeler::rna::rigid_body); compare_by_x (protocols::hbnet); compare_hbond_residues (protocols::hbnet); compare_hbond_resnums (protocols::hbnet); compare_int_pair (protocols::stepwise::modeler::rna::rigid_body); compare_job_nodes (protocols::jd3); compare_net_vec (protocols::hbnet); CompareByScoreCombination (protocols::frag_picker); CompareQueryPosition (protocols::frag_picker); CompareScoreComponent (protocols::frag_picker); CompareTags (protocols::jd2); CompareTotalScore (protocols::frag_picker); ComparisonGrid (protocols::pockets); CompassScoringScheme (core::sequence); CompleteConnectionsFilter (protocols::ligand_docking); CompleteConnectionsFilterCreator (protocols::ligand_docking); CompletedJobOutput (protocols::jd3); MPIArchiveJobDistributor::CompletionMessage (protocols::jd2::archive); ComposeSearchPatterns (protocols::hotspot_hashing); CompositeEnergyMetric (core::simple_metrics::composite_metrics); CompositeEnergyMetricCreator (core::simple_metrics::composite_metrics); CompositeFragmentSelector (protocols::frag_picker); CompositeRealMetric (core::simple_metrics); CompositeScoringScheme (core::sequence); CompositeSequence (core::sequence); CompositeSequenceCreator (core::sequence); CompositeStringMetric (core::simple_metrics); CompositionMover (protocols::moves); CompoundArchitect (protocols::denovo_design::architects); CompoundArchitectCreator (protocols::denovo_design::architects); CompoundFilter (protocols::filters); CompoundFilterCreator (protocols::filters); CompoundPerturber (protocols::denovo_design::components); CompoundTranslate (protocols::ligand_docking); CompoundTranslateCreator (protocols::ligand_docking); ComputeLigandRDF (protocols::ligand_docking); ComputeLigandRDFCreator (protocols::ligand_docking); Computes; ComputeTotalDistCst (protocols::abinitio); CoMTrackerCM (protocols::environment); CoMTrackerCMCreator (protocols::environment); ConcatenatePosesMover (protocols::simple_moves); ConcatenatePosesMoverCreator (protocols::simple_moves); ConcurrencyTest (protocols::features::helixAssembly); ConcurrencyTestCreator (protocols::features::helixAssembly); ConfChangeMover (protocols::rbsegment_relax); ConfChangeMoverCreator (protocols::rbsegment_relax); ConfluentSelector (core::select::residue_selector); ConfluentSelectorCreator (core::select::residue_selector); Conformation (core::conformation); ConformationEvent (core::pose::signals); ConformationKinWriter (core::conformation); ConformationSelectionToRDMol (protocols::drug_design); ConformationXYZ (core::scoring::func); ConformerSwitchMover (protocols::docking); ConformerSwitchMoverCreator (protocols::docking); ConnectChainsMover (protocols::pose_length_moves); ConnectChainsMoverCreator (protocols::pose_length_moves); ConnectionArchitect (protocols::denovo_design::connection); ConnectionEvent (core::conformation::signals); ConnectionPerturber (protocols::denovo_design::components); ConnectRight (protocols::forge::build); ConnectSulfurAndMakeVirtualProton (core::chemical); ConnectSulfurAndMakeVirtualProtonCreator (core::chemical); ConsensusDesignMover (protocols::calc_taskop_movers); ConsensusDesignMoverCreator (protocols::calc_taskop_movers); ConsensusLoopDatabase (protocols::denovo_design::task_operations); ConsensusLoopDesignOperation (protocols::denovo_design::task_operations); ConsensusLoopDesignOperationCreator (protocols::denovo_design::task_operations); ConservativeDesignOperation (protocols::task_operations); ConservativeDesignOperationCreator (protocols::task_operations); ConservativeDesignOperation::ConservedMutationData (protocols::task_operations); ConservedPosMutationFilter (protocols::calc_taskop_filters); ConservedPosMutationFilterCreator (protocols::calc_taskop_filters); RawFileData::const_iterator (core::io::raw_data); SilentFileData::const_iterator (core::io::silent); ConstAbinitioMoverWeight (protocols::topology_broker::weights); ConstantConstraint (core::scoring::constraints); ConstantFunc (core::scoring::func); ConstantLengthFragSet (core::fragment); ConstantLengthFragSetIterator_ (core::fragment); ConstantScoreBase (protocols::qsar::scoring_grid); ConstFrameIterator (core::fragment); ConstPattern (protocols::hotspot_hashing); ConstrainHBondNetwork (protocols::hbnet); ConstrainHBondNetworkCreator (protocols::hbnet); Constraint (core::scoring::constraints); Constraint (protocols::md); ConstraintClaimer (protocols::topology_broker); ConstraintConditions (protocols::fold_from_loops::constraint_generator); ConstraintCreator (core::scoring::constraints); ConstraintEdge (core::scoring::constraints); ConstraintedOptimizationWeightFunc (protocols::optimize_weights); ConstraintEvaluator (protocols::constraints_additional); ConstraintEvaluatorCreator (protocols::constraints_additional); ConstraintEvaluatorWrapper (protocols::topology_broker); ConstraintEvaluatorWrapperCreator (protocols::topology_broker); ConstraintFactory (core::scoring::constraints); ConstraintFragmentSampler (protocols::abinitio); ConstraintFulfilmentFilter (protocols::fold_from_loops::filters); ConstraintFulfilmentFilterCreator (protocols::fold_from_loops::filters); ConstraintGenerator (protocols::constraint_generator); ConstraintGeneratorCreator (protocols::constraint_generator); ConstraintGeneratorFactory (protocols::constraint_generator); ConstraintGeneratorLoader (protocols::parser); ConstraintGeneratorLoaderCreator (protocols::parser); ConstraintGeneratorRegistrator (protocols::constraint_generator); ConstraintGraph (core::scoring::constraints); ConstraintInfo (protocols::ligand_docking::ga_ligand_dock); ConstraintIO (core::scoring::constraints); ConstraintNode (core::scoring::constraints); ConstrainToIdealMover (protocols::simple_moves); ConstraintPreparer (protocols::abinitio::abscript); ConstraintPreparerCreator (protocols::abinitio::abscript); ConstraintRegistrator (core::scoring::constraints); ConstraintResidueSelector (protocols::fold_from_loops::selectors); ConstraintResidueSelectorCreator (protocols::fold_from_loops::selectors); Constraints (core::scoring::constraints); ConstraintScoreCutoffFilter (protocols::constraint_filters); ConstraintScoreCutoffFilterCreator (protocols::constraint_filters); ConstraintScoreFilter (protocols::constraint_filters); ConstraintScoreFilterCreator (protocols::constraint_filters); ConstraintsEnergy (core::scoring::constraints); ConstraintsEnergyCreator (core::scoring::constraints); ConstraintSet (core::scoring::constraints); ConstraintSetMover (protocols::constraint_movers); ConstraintSetMoverCreator (protocols::constraint_movers); ConstraintSetScore (protocols::sic_dock); ConstraintsManager (protocols::constraint_generator); ConstraintsMap (protocols::constraint_generator); ConstraintsMetric (protocols::analysis::simple_metrics); ConstraintsMetricCreator (protocols::analysis::simple_metrics); ConstScore (protocols::frag_picker::scores); Contact (protocols::frag_picker); Contact (protocols::contact_map); ContactCounts (protocols::frag_picker); ContactDescription (protocols::sewing::data_storage); ContactMap (protocols::contact_map); ContactMapCreator (protocols::contact_map); ContactMapEvaluator (protocols::simple_filters); ContactMapEvaluatorCreator (protocols::simple_filters); ContactMolecularSurfaceCalculator (core::scoring::sc); ContactMolecularSurfaceFilter (protocols::simple_filters); ContactMolecularSurfaceFilterCreator (protocols::simple_filters); ContactOrderEnergy (core::energy_methods); ContactOrderEnergyCreator (core::energy_methods); ContactPartner (protocols::contact_map); ContactStruct (protocols::normalmode); ContextDependentGeometricSolEnergy (core::energy_methods); ContextDependentGeometricSolEnergyCreator (core::energy_methods); ContextDependentLRTwoBodyEnergy (core::scoring::methods); ContextDependentOneBodyEnergy (core::scoring::methods); ContextDependentTwoBodyEnergy (core::scoring::methods); ContextGraph (core::scoring); ContextGraphFactory (core::scoring); ContextIndependentGeometricSolEnergy (core::energy_methods); ContextIndependentGeometricSolEnergyCreator (core::energy_methods); ContextIndependentLRTwoBodyEnergy (core::scoring::methods); ContextIndependentOneBodyEnergy (core::scoring::methods); ContextIndependentTwoBodyEnergy (core::scoring::methods); ContingentAcceptMover (protocols::simple_moves); ContingentAcceptMoverCreator (protocols::simple_moves); ContingentFilter (protocols::filters); ContingentFilterCreator (protocols::filters); ContinuousAssembly (protocols::legacy_sewing); ContinuousRotamerSet (core::pack::rotamer_set); ContinuousRotamerSets (core::pack::rotamer_set); ConvergenceTest (core::optimization); ConvertRealToVirtualMover (protocols::simple_moves); ConvertRealToVirtualMoverCreator (protocols::simple_moves); ConvertVirtualToRealMover (protocols::simple_moves); ConvertVirtualToRealMoverCreator (protocols::simple_moves); coord_equal_to (protocols::legacy_sewing); coord_equal_to (protocols::sewing::hashing); coord_hash (protocols::legacy_sewing); coord_hash (protocols::sewing::hashing); CoordConstraintClaimer (protocols::topology_broker); CoordinateConstraint (core::scoring::constraints); CoordinateConstraintCreator (core::scoring::constraints); CoordinateConstraintGenerator (protocols::constraint_generator); CoordinateConstraintGeneratorCreator (protocols::constraint_generator); CoordinateConstraintKC (protocols::abinitio); CoordinateConstraintStack (protocols::protein_interface_design::movers); CoordinateCst (protocols::seeded_abinitio); CoordinateCstCreator (protocols::seeded_abinitio); CopyDofMover (protocols::simple_moves); CopyDofs (core::pose::copydofs); CopyDofsInfo (core::pose::copydofs); CopyDofStepWiseSampler (protocols::stepwise::sampler::copy_dofs); CopyEdge (core::chemical); CopyRotamerMover (protocols::simple_moves); CopyRotamerMoverCreator (protocols::simple_moves); CopyVertex (core::chemical); CoreDunbrackFilter (protocols::fldsgn::filters); CoreDunbrackFilterCreator (protocols::fldsgn::filters); CoreScorer (protocols::pose_sewing::filters); CoreScorerCreator (protocols::pose_sewing::filters); CorrectionVisitor (protocols::sic_dock); Coulomb (core::scoring::etable::coulomb); CountFromLeft (protocols::forge::build); CountPair1B (core::scoring::etable::count_pair); CountPair2B (core::scoring::etable::count_pair); CountPairAll (core::scoring::etable::count_pair); CountPairCrossover3 (core::scoring::etable::count_pair); CountPairCrossover34 (core::scoring::etable::count_pair); CountPairCrossover3full (core::scoring::etable::count_pair); CountPairCrossover4 (core::scoring::etable::count_pair); CountPairData_1_1 (core::scoring::etable::etrie); CountPairData_1_2 (core::scoring::etable::etrie); CountPairData_1_3 (core::scoring::etable::etrie); CountPairDataGeneric (core::scoring::etable::etrie); CountPairFactory (core::scoring::etable::count_pair); CountPairFunction (core::scoring::etable::count_pair); CountPairGeneric (core::scoring::etable::count_pair); CountPairIntraRes (core::scoring::etable::count_pair); CountPairNone (core::scoring::etable::count_pair); CountPairRepMap (core::scoring::elec); CountPairRepresentative (core::scoring::elec); CountViolFunc (core::scoring::func); CoupledMover (protocols::simple_moves); CoupledMoverCreator (protocols::simple_moves); CoupledMovesProtocol (protocols::coupled_moves); CoupledMovesProtocolCreator (protocols::coupled_moves); CovalentCompliance (protocols::noesy_assign); CovalentConnectionReplaceInfo (protocols::toolbox::match_enzdes_util); CovalentLabelingEnergy (core::energy_methods); CovalentLabelingEnergyCreator (core::energy_methods); CovalentLabelingFAEnergy (core::energy_methods); CovalentLabelingFAEnergyCreator (core::energy_methods); CovalentResidueNetwork (protocols::toolbox); CPDataCorrespondence (core::scoring::trie); CrankshaftFlipMover (protocols::cyclic_peptide); CrankshaftFlipMoverCreator (protocols::cyclic_peptide); CreateAngleConstraint (protocols::cyclic_peptide); CreateAngleConstraintCreator (protocols::cyclic_peptide); CreateDistanceConstraint (protocols::cyclic_peptide); CreateDistanceConstraintCreator (protocols::cyclic_peptide); CreateGlycanSequonMover (protocols::carbohydrates); CreateGlycanSequonMoverCreator (protocols::carbohydrates); CreateSequenceMotifMover (protocols::calc_taskop_movers); CreateSequenceMotifMoverCreator (protocols::calc_taskop_movers); CreateTorsionConstraint (protocols::cyclic_peptide); CreateTorsionConstraintCreator (protocols::cyclic_peptide); CrosslinkerMover (protocols::cyclic_peptide); CrosslinkerMoverCreator (protocols::cyclic_peptide); CrosslinkerMoverHelper (protocols::cyclic_peptide::crosslinker); Crossover (protocols::ligand_evolution); CrossoverBehavior; CrossPeak (protocols::noesy_assign); CrossPeak3D (protocols::noesy_assign); CrossPeak4D (protocols::noesy_assign); CrossPeakInfo (protocols::noesy_assign); CrossPeakList (protocols::noesy_assign); CrystalContactsOperation (protocols::task_operations); CrystalContactsOperationCreator (protocols::task_operations); CrystInfo (core::io); CrystRMS (protocols::cryst); CrystRMSCreator (protocols::cryst); CS2ndShift (protocols::frag_picker); CSA (core::scoring); CSScore (protocols::frag_picker::scores); CSSettings (protocols::pose_sewing::filters); CSTalosIO (protocols::frag_picker); CstEnergyContainer (core::scoring::constraints); CstInfoMover (protocols::constraint_movers); CstInfoMoverCreator (protocols::constraint_movers); CstMinimizationData (core::scoring::constraints); CstResInteractions (protocols::toolbox::match_enzdes_util); CstResNeighbConstIterator (core::scoring::constraints); CstResNeighbIterator (core::scoring::constraints); CtabParserBase (core::chemical::sdf); CtabV2000Parser (core::chemical::sdf); CtabV3000Parser (core::chemical::sdf); CurrentProbabilityMetric (core::simple_metrics::per_residue_metrics); CurrentProbabilityMetricCreator (core::simple_metrics::per_residue_metrics); CustomAtomPairEnergy (core::energy_methods); CustomAtomPairEnergyCreator (core::energy_methods); CustomBaseTypePackerPalette (core::pack::palette); CustomBaseTypePackerPaletteCreator (core::pack::palette); CustomRealValueMetric (core::simple_metrics::metrics); CustomRealValueMetricCreator (core::simple_metrics::metrics); CustomScoreSelector (protocols::frag_picker); CustomStringValueMetric (core::simple_metrics::metrics); CustomStringValueMetricCreator (core::simple_metrics::metrics); CutAndJump (protocols::denovo_design::movers); CutBiasClaim (protocols::environment::claims); CutBiasClaimer (protocols::topology_broker); CutBiasElement (protocols::environment::claims); CutChainMover (protocols::simple_moves); CutChainMoverCreator (protocols::simple_moves); CutClaim (protocols::topology_broker::claims); CutElement (protocols::environment::claims); CutOutDomain (protocols::cutoutdomain); CutOutDomainCreator (protocols::cutoutdomain); CutpointResidueSelector (protocols::fold_from_loops::selectors); CutpointResidueSelectorCreator (protocols::fold_from_loops::selectors); CCluster::Cxyz (protocols::pockets); PCluster::Cxyz (protocols::pockets); cycle_printer (core::scoring::loop_graph); CycleMover (protocols::moves); CyclicMover (protocols::moves); CyclizationMover (protocols::simple_moves); CyclizedPeptideInfo (protocols::peptide_deriver); PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo (protocols::peptide_deriver); CycpepRigidBodyPermutationMover (protocols::cyclic_peptide); CycpepRigidBodyPermutationMoverCreator (protocols::cyclic_peptide); CycpepSymmetryFilter (protocols::cyclic_peptide); CycpepSymmetryFilterCreator (protocols::cyclic_peptide)

D: D2H_SA_Energy (core::energy_methods); D2H_SA_EnergyCreator (core::energy_methods); DaemonSet (protocols::pack_daemon); DarcParticleSwarmMinimizer (protocols::pockets); data_struct (core::scoring); DatabaseEntryWorkUnit (protocols::wum); DatabaseFilter (protocols::features); DatabaseJobInputter (protocols::features); DatabaseJobInputterCreator (protocols::features); DatabaseJobOutputter (protocols::features); DatabaseJobOutputterCreator (protocols::features); DatabaseOccSolEne (core::scoring::geometric_solvation); DatabaseRelaxScript (protocols::relax); DatabaseSessionLoader (protocols::parser); DatabaseSessionLoaderCreator (protocols::parser); DatabaseThread (protocols::task_operations); DatabaseThreadCreator (protocols::task_operations); DataBuffer (protocols::canonical_sampling::mc_convergence_checks); DataCache (basic::datacache); DataLoader (protocols::parser); DataLoaderCreator (protocols::parser); DataLoaderFactory (protocols::parser); DataLoaderRegistrator (protocols::parser); DataMap (basic::datacache); DataPoint (protocols::cluster); DbTrajectoryReader (protocols::trajectory); DbTrajectoryRecorder (protocols::canonical_sampling); DbTrajectoryRecorderCreator (protocols::canonical_sampling); DbTrajectoryWriter (protocols::trajectory); DC (core::scoring); ddG (protocols::simple_ddg); DDGBindOptEData (protocols::optimize_weights); ddGCreator (protocols::simple_ddg); ddGData (protocols::ddG); DdGFeatures (protocols::features); DdGFeaturesCreator (protocols::features); DdgFilter (protocols::simple_ddg); DdgFilterCreator (protocols::simple_ddg); ddGMover (protocols::ddg); DDGMutationOptEData (protocols::optimize_weights); DdGScan (protocols::simple_ddg); DdGScanCreator (protocols::simple_ddg); DDomainParse (protocols::hybridization); DDPlookup (core::scoring::interface_); DDPscore (core::scoring::interface_); DDPscoreCreator (core::scoring::interface_); DeallocationMessage (protocols::jd3::deallocation); DebuggingAnnealer (core::pack::annealer); DebugOut_MpiFileBuffer (protocols::jd2); DeclareBond (protocols::simple_moves); DeclareBondCreator (protocols::simple_moves); DeclareStructureDataCovalentBondMover (protocols::denovo_design::movers); DeclareStructureDataCovalentBondMoverCreator (protocols::denovo_design::movers); DecomposeAndReweightEnergiesCalculator (protocols::pose_metric_calculators); DecoratedNetworkState (protocols::hbnet); DecoyFileData (core::io::raw_data); DecoySetEvaluation (protocols::toolbox); DecoyStruct (core::io::raw_data); DEERChiSqMethod (core::scoring::epr_deer::metrics); DEERData (core::scoring::epr_deer::metrics); DEERDataCache (core::scoring::epr_deer); DEERDecayData (core::scoring::epr_deer::metrics); DEERDistanceBounds (core::scoring::epr_deer::metrics); DEERDistanceDistribution (core::scoring::epr_deer::metrics); DEEREnergy (core::energy_methods); DEEREnergyCreator (core::energy_methods); DEERIO (core::scoring::epr_deer); DEERJaccardMethod (core::scoring::epr_deer::metrics); DEERJSMethod (core::scoring::epr_deer::metrics); DEERMiscMethod (core::scoring::epr_deer::metrics); DEEROptimizeCoordsMover (protocols::simple_moves); DEEROptimizeCoordsMoverCreator (protocols::simple_moves); DEEROverlapMethod (core::scoring::epr_deer::metrics); DefaultCubeHash (core::conformation); DefaultPackerPalette (core::pack::palette); DefaultPackerPaletteCreator (core::pack::palette); DefineMovableLoops (protocols::seeded_abinitio); DefineMovableLoopsCreator (protocols::seeded_abinitio); DeleteActCoordAtom (core::chemical); DeleteActCoordAtomCreator (core::chemical); DeleteAllRotamerSetOperation (core::pack::rotamer_set); DeleteAtom (core::chemical); DeleteAtomCreator (core::chemical); DeleteChainMover (protocols::simple_moves); DeleteChainMoverCreator (protocols::simple_moves); DeleteChainsMover (protocols::simple_moves); DeleteChainsMoverCreator (protocols::simple_moves); DeleteChildProton (core::chemical); DeleteChildProtonCreator (core::chemical); DeleteMetalbindingAtom (core::chemical); DeleteMetalBindingAtomCreator (core::chemical); DeleteMover (protocols::stepwise::monte_carlo::mover); DeleteMoverCreator (protocols::stepwise::monte_carlo::mover); DeleteProperty (core::chemical); DeletePropertyCreator (core::chemical); DeleteRegionMover (protocols::grafting::simple_movers); DeleteRegionMoverCreator (protocols::grafting::simple_movers); DeleteTerminalChi (core::chemical); DeleteTerminalChiCreator (core::chemical); DeleteVariantType (core::chemical); DeleteVariantTypeCreator (core::chemical); DeltaFilter (protocols::simple_filters); DeltaFilterCreator (protocols::simple_filters); DeNovoArchitect (protocols::denovo_design::architects); DeNovoArchitectCreator (protocols::denovo_design::architects); DeNovoArchitectFactory (protocols::denovo_design::architects); DeNovoSilentFilePoseOutputter (protocols::jd3::pose_outputters); DeNovoSilentFilePoseOutputterCreator (protocols::jd3::pose_outputters); DenseEnergyContainer (core::scoring); DenseIGRepacker (protocols::pack_daemon); DenseNeighborConstIterator (core::scoring); DenseNeighborIterator (core::scoring); DensePDEdge (core::pack::interaction_graph); DensePDInteractionGraph (core::pack::interaction_graph); DensePDNode (core::pack::interaction_graph); DensityFitResidueSelector (core::select::residue_selector); DensityFitResidueSelectorCreator (core::select::residue_selector); DensityGridSearchOptions (protocols::electron_density); DensityScoringClaimer (protocols::topology_broker); DensitySymmInfo (protocols::electron_density); DensityZscores (protocols::electron_density); DensityZscoresCreator (protocols::electron_density); DensityZscoresStatsSetup (core::scoring); DensSkeleton (protocols::loop_grower); DenyPdbIdFilter (protocols::frag_picker); DEPC_MS_Energy (core::energy_methods); DEPC_MS_EnergyCreator (core::energy_methods); DerivativeFinder (core::scoring::lkball); DerivativeFinderWadj (core::scoring::lkball); DerivCheckDataPoint (core::optimization); DerivedPeptideEntry (protocols::peptide_deriver); DerivedSequenceMapping (core::sequence); DerivVectorPair (core::scoring); DescentDirectionAlgorithm (core::optimization); MakeJunctionsMover::Design (protocols::pose_creation); DesignableResiduesFilter (protocols::protein_interface_design::filters); DesignableResiduesFilterCreator (protocols::protein_interface_design::filters); DesignAroundOperation (protocols::task_operations); DesignAroundOperationCreator (protocols::task_operations); DesignContrast (core::io::sequence_comparation); DesignInterfacesOperation (protocols::splice); DesignInterfacesOperationCreator (protocols::splice); DesignMeanField (protocols::mean_field); DesignMinimizeHbonds (protocols::protein_interface_design::movers); DesignMinimizeHbondsCreator (protocols::protein_interface_design::movers); DesignProteinBackboneAroundDNA (protocols::dna); DesignProteinBackboneAroundDNACreator (protocols::dna); DesignRepackMover (protocols::calc_taskop_movers); DesignRestrictions (core::pack::task::operation); DesignRestrictionsCreator (core::pack::task::operation); DesignTask (protocols::flxbb); DesignTask_Layer (protocols::flxbb); DesignTask_Normal (protocols::flxbb); DesignVsNativeComparison (protocols::enzdes); DestructionEvent (core::pose::signals); detailedControlsTagSetting (protocols::hybridization); DetectProteinLigandInterface (protocols::enzdes); DetectProteinLigandInterfaceOperationCreator (protocols::enzdes); DetectSymmetry (protocols::symmetry); DetectSymmetryMoverCreator (protocols::symmetry); DFIRE_Energy (core::energy_methods::dfire); DFIRE_EnergyCreator (core::energy_methods::dfire); DFIRE_Potential (core::scoring::methods::dfire); DFPMinConvergedAbsolute (core::optimization); DFPMinConvergedFractional (core::optimization); DGBindOptEData (protocols::optimize_weights); DiffAtomSasaFilter (protocols::enzdes); DiffAtomSasaFilterCreator (protocols::enzdes); Digraph (utility::graph); DihedralConstraint (core::scoring::constraints); DihedralConstraintCreator (core::scoring::constraints); DihedralConstraintGenerator (protocols::constraint_generator); DihedralConstraintGeneratorCreator (protocols::constraint_generator); DihedralConstraintsScore (protocols::frag_picker::scores); DihedralDistanceMetric (core::simple_metrics::metrics); DihedralDistanceMetricCreator (core::simple_metrics::metrics); DihedralPairConstraint (core::scoring::constraints); DihedralPairConstraintCreator (core::scoring::constraints); DimerPairing (core::scoring); DimerPairing (protocols::fldsgn::topology); DimerPairings (protocols::fldsgn::topology); DipolarCoupling (core::scoring); DipolarCouplingEnergy (core::energy_methods); DipolarCouplingEnergyCreator (core::energy_methods); DirectedEdge (utility::graph); DirectedNode (utility::graph); DirectReadoutEnergy (core::energy_methods); DirectReadoutEnergyCreator (core::energy_methods); DirectReadoutPotential (core::scoring::dna); DirectSegmentLookup (protocols::indexed_structure_store); DirectSegmentLookupConfig (protocols::indexed_structure_store); DirectSegmentLookupMover (protocols::indexed_structure_store::movers); DirectSegmentLookupMoverCreator (protocols::indexed_structure_store::movers); DirectSegmentLookupResult (protocols::indexed_structure_store); DirStructureStoreBackend (protocols::indexed_structure_store); DisableAntibodyRegionOperation (protocols::antibody::task_operations); DisableAntibodyRegionOperationCreator (protocols::antibody::task_operations); DisableCDRsOperation (protocols::antibody::task_operations); DisableCDRsOperationCreator (protocols::antibody::task_operations); DisallowIfNonnative (core::pack::task::operation); DisallowIfNonnativeCreator (core::pack::task::operation); DisallowIfNonnativeRLT (core::pack::task::operation); DisallowIfNonnativeRLTCreator (core::pack::task::operation); DiscreteRandomizer (protocols::genetic_algorithm); DisembodiedAssembly (protocols::legacy_sewing); DisplayPoseLabelsMover (protocols::fold_from_loops::movers); DisplayPoseLabelsMoverCreator (protocols::fold_from_loops::movers); DistanceChainbreakEnergy (core::energy_methods); DistanceChainbreakEnergyCreator (core::energy_methods); DistanceConstraintGenerator (protocols::constraint_generator); DistanceConstraintGeneratorCreator (protocols::constraint_generator); DistanceFunc (core::scoring::custom_pair_distance); DistanceHistogram (core::scoring::saxs); DistancePairConstraint (core::scoring::constraints); FragsToAtomDist::DistanceRecord (protocols::noesy_assign); DistanceResidueNetwork (protocols::toolbox); DistanceScoreMover (protocols::noesy_assign); DistributionMap (protocols::ligand_docking); DisulfideAtomIndices (core::scoring::disulfides); DisulfideDistance (protocols::frag_picker::scores); DisulfideEntropyFilter (protocols::simple_filters); DisulfideEntropyFilterCreator (protocols::simple_filters); DisulfideFile (core::io::raw_data); DisulfideFilter (protocols::protein_interface_design::filters); DisulfideFilterCreator (protocols::protein_interface_design::filters); DisulfideIdentity (protocols::frag_picker::scores); DisulfideInsertionMover (protocols::simple_moves); DisulfideInsertionMoverCreator (protocols::simple_moves); DisulfideMatchingDatabase (core::scoring::disulfides); DisulfideMatchingEnergy (core::energy_methods); DisulfideMatchingEnergyComponents (core::scoring::disulfides); DisulfideMatchingEnergyContainer (core::scoring::disulfides); DisulfideMatchingEnergyCreator (core::energy_methods); DisulfideMatchingNeighborConstIterator (core::scoring::disulfides); DisulfideMatchingNeighborIterator (core::scoring::disulfides); DisulfideMatchingPotential (core::scoring::disulfides); DisulfideMover (protocols::protein_interface_design::movers); DisulfideMoverCreator (protocols::protein_interface_design::movers); DisulfideOptimizationMover (protocols::minimization_packing); DisulfideOptimizationMoverCreator (protocols::minimization_packing); DisulfidizeMover (protocols::denovo_design); DisulfidizeMoverCreator (protocols::denovo_design); DisulfJumpClaimer (protocols::topology_broker); DisulfMinData (core::energy_methods); DisulfPairing (protocols::jumping); DisulfPairingLibrary (protocols::jumping); DisulfResNeighbConstIterator (core::scoring::disulfides); DisulfResNeighbIterator (core::scoring::disulfides); DisulfTemplate (protocols::jumping); DiversifyCrmsdByClustering (protocols::frag_picker); DiversifyCrmsdSelector (protocols::frag_picker); DiversifyDihedralsSelector (protocols::frag_picker); DiversifyStoredRBConfs (protocols::enzdes); DivideAndConqueror (protocols::denovo_design::components); DME_FilterMover (protocols::simple_moves); DNA_BaseEnergy (core::energy_methods); DNA_BaseEnergyCreator (core::energy_methods); DNA_BasePotential (core::scoring::dna); DNA_DihedralEnergy (core::energy_methods); DNA_DihedralEnergyCreator (core::energy_methods); DNA_DihedralPotential (core::scoring::dna); DNA_EnvPairEnergy (core::energy_methods); DNA_EnvPairEnergyCreator (core::energy_methods); DNA_EnvPairPotential (core::scoring::dna); DNA_ReferenceEnergy (core::energy_methods); DNA_ReferenceEnergyCreator (core::energy_methods); DNABase (protocols::dna); DNABasepair (protocols::dna); DNABasestep (protocols::dna); DNABFormPotential (core::scoring::dna); DnaChains (protocols::dna); DNAChiEnergy (core::energy_methods); DNAChiEnergyCreator (core::energy_methods); DNAClashCheckFilter (protocols::dna_dock); DNAClashCheckFilterCreator (protocols::dna_dock); DnaDesignDef (protocols::dna); DnaInterfaceFinder (protocols::dna); DnaInterfaceMinMover (protocols::dna); DnaInterfaceMinMoverCreator (protocols::dna); DnaInterfaceMultiStateDesign (protocols::dna); DnaInterfaceMultiStateDesignCreator (protocols::dna); DnaInterfacePacker (protocols::dna); DnaInterfacePackerCreator (protocols::dna); DNAMethyltransferaseMover (protocols::enzymatic_movers); DNAMethyltransferaseMoverCreator (protocols::enzymatic_movers); DnaNeighbor (protocols::dna); DNAParameters (protocols::dna); DnaPosition (protocols::dna); DNATorsionEnergy (core::energy_methods); DNATorsionEnergyCreator (core::energy_methods); DNATorsionPotential (core::scoring::dna); DockAndRetrieveSidechains (protocols::protein_interface_design::movers); DockAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers); DockFragmentsIntoDensityMover (protocols::electron_density); DockingEnsemble (protocols::docking); DockingEnsemblePrepackProtocol (protocols::docking); DockingHighRes (protocols::docking); DockingHighResFactory (protocols::docking); DockingHighResFilter (protocols::docking); DockingHighResLegacy (protocols::docking); DockingHighResLegacyCreator (protocols::docking); DockingInitialPerturbation (protocols::docking); DockingInitialPerturbationCreator (protocols::docking); DockingLowRes (protocols::docking); DockingLowResEnsemble (protocols::docking); DockingLowResFilter (protocols::docking); DockingNoRepack1 (protocols::simple_task_operations); DockingNoRepack2 (protocols::simple_task_operations); DockingPrepackProtocol (protocols::docking); DockingPrepackProtocolCreator (protocols::docking); DockingProtocol (protocols::docking); DockingProtocolCreator (protocols::docking); DockingScoreFunction (core::scoring); DockingSlideIntoContact (protocols::docking); DockingSlideIntoContactCreator (protocols::docking); DockLatticeMover (protocols::cryst); DockLatticeMoverCreator (protocols::cryst); DockMCMCycle (protocols::docking); DockMCMProtocol (protocols::docking); DockMCMProtocolCreator (protocols::docking); DockMinMover (protocols::docking); DockMinMoverCreator (protocols::docking); DockPDBIntoDensityMover (protocols::electron_density); DockSetupMover (protocols::docking); DockSetupMoverCreator (protocols::docking); DockTaskFactory (protocols::docking); DockWithHotspotMover (protocols::protein_interface_design::movers); DockWithHotspotMoverCreator (protocols::protein_interface_design::movers); DOF_Constraint (core::scoring::constraints); DOF_DataPoint (core::optimization); DOF_ID (core::id); DOF_ID_Map (core::id); DOF_ID_Range (core::id); DOF_Node (core::optimization); DofClaim (protocols::topology_broker::claims); DOFElement (protocols::environment::claims); DOFHistogramRecorder (protocols::simple_moves); DofPassport (core::environment); DofUnlock (protocols::environment); DomainAssembly (protocols::abinitio); DomainAssembly (protocols::hybridization); DomainAssemblyCreator (protocols::abinitio); DomainInterfaceFilter (protocols::simple_filters); MultiConstraint::dont_copy_constraints (core::scoring::constraints); DotSphere (core::pack::interaction_graph); DoubleDenseIGRepacker (protocols::pack_daemon); DoubleDensePDEdge (core::pack::interaction_graph); DoubleDensePDInteractionGraph (core::pack::interaction_graph); DoubleDensePDNode (core::pack::interaction_graph); DoubleLayerKinematicAbinitio (protocols::abinitio); DoubleLazyEdge (core::pack::interaction_graph); DoubleLazyInteractionGraph (core::pack::interaction_graph); DoubleLazyNode (core::pack::interaction_graph); DoubleVesicle (core::conformation::membrane::membrane_geometry); DownJumpSRFD (core::fragment); downstream_hit (protocols::match); DownstreamAlgorithm (protocols::match::downstream); DownstreamBuilder (protocols::match::downstream); DownstreamCoordinateKinemageWriter (protocols::match::output); DownstreamRMSEvaluator (protocols::match::output); DP_Matrix (core::sequence); DPScoringScheme (core::sequence); DrugDesignMover (protocols::drug_design); DrugDesignMoverCreator (protocols::drug_design); DrugPolishMover (protocols::drug_design); DrugPolishMoverCreator (protocols::drug_design); Dssp (core::scoring::dssp); DsspDesignOperation (protocols::task_operations); DsspDesignOperationCreator (protocols::task_operations); DsspMover (protocols::moves); DsspMoverCreator (protocols::moves); DsspShiftArray (protocols::pose_sewing::data_storage); DsspSpecificLengthRequirement (protocols::sewing::requirements); DsspSpecificLengthRequirementCreator (protocols::sewing::requirements); DualMonteCarlo (protocols::moves); DummyClass (protocols::toolbox); DumpPdb (protocols::simple_moves); DumpPdbCreator (protocols::simple_moves); DumpSingleResidueRotamers (protocols::simple_moves); DumpSingleResidueRotamersCreator (protocols::simple_moves); DumpTrajectoryEnergy (core::energy_methods); DumpTrajectoryEnergyCreator (core::energy_methods); DunbrackAAParameterSet (core::pack::dunbrack); DunbrackConstraint (core::pack::dunbrack); DunbrackConstraintCreator (core::pack::dunbrack); DunbrackEnergy (core::pack::dunbrack); DunbrackEnergyCreator (core::pack::dunbrack); DunbrackRotamer (core::pack::dunbrack); DunbrackRotamerLibrarySpecification (core::chemical::rotamers); DunbrackRotamerLibrarySpecificationCreator (core::chemical::rotamers); DunbrackRotamerMeanSD (core::pack::dunbrack); DunbrackRotamerSampleData (core::pack::dunbrack); DunbrackSCSampler (protocols::match::upstream); DynamicAggregateFunction (protocols::pack_daemon); DynamicAggregateFunctionDriver (protocols::pack_daemon)

E: E; Edge (core::kinematics); Edge (utility::graph); EdgeBase (core::pack::interaction_graph); EdgeMapGenerator (protocols::sewing::hashing); EdgeStandScore (protocols::sic_dock); EggshellGrid (protocols::pockets); EItem (core::optimization); ElecAtom (core::scoring::elec::electrie); ElecDensAllAtomCenEnergy (core::energy_methods); ElecDensAllAtomCenEnergyCreator (core::energy_methods); ElecDensAtomwiseEnergy (core::energy_methods); ElecDensAtomwiseEnergyCreator (core::energy_methods); ElecDensCenEnergy (core::energy_methods); ElecDensCenEnergyCreator (core::energy_methods); ElecDensEnergy (core::energy_methods); ElecDensEnergyCreator (core::energy_methods); ElecGroup (core::scoring::elec); ElectricfieldLipidlayer (protocols::membrane::scoring); ElectricfieldLipidlayerCreator (protocols::membrane::scoring); ElecTrieEvaluator (core::scoring::elec::electrie); ElectronConfiguration (core::chemical); ElectronDensity (core::scoring::electron_density); ElectronDensityAtomwise (core::scoring::electron_density_atomwise); ElectrostaticComplementarityCalculator (core::scoring::sc); ElectrostaticComplementarityMetric (core::simple_metrics::composite_metrics); ElectrostaticComplementarityMetricCreator (core::simple_metrics::composite_metrics); ElectrostaticComplementarityResults (core::scoring::sc); ElectrostaticpotentialGrid (protocols::pockets); ElectrostaticSimilarityCalculator (core::scoring::sc); ElectrostaticSimilarityMetric (core::simple_metrics::composite_metrics); ElectrostaticSimilarityMetricCreator (core::simple_metrics::composite_metrics); ElectrostaticSimilarityResults (core::scoring::sc); Element (core::chemical); ElementSet (core::chemical); ElitistSelector (protocols::ligand_evolution); EllipsoidalRandomizationMover (protocols::docking); EMapVector (core::scoring); Embedding (protocols::membrane::geometry); EmbeddingDef (protocols::membrane::geometry); EmptyPoseJobInputter (protocols::jd2); EmptyPoseJobInputterCreator (protocols::jd2); EmptyVertexData (protocols::pose_metric_calculators); enable_shared_from_this (utility::pointer); EnableMultiCoolAnnealer (core::pack::task::operation); EnableMultiCoolAnnealerCreator (core::pack::task::operation); EnableSmartAnnealer (core::pack::task::operation); EnableSmartAnnealerCreator (core::pack::task::operation); EndToEndPivots (protocols::kinematic_closure::pivot_pickers); Energies (core::scoring); EnergiesByTaskCalculator (protocols::mean_field); EnergiesData (protocols::pose_metric_calculators); EnergyBasedClusteringOptions (protocols::energy_based_clustering); EnergyBasedClusteringProtocol (protocols::energy_based_clustering); EnergyCutRotamerTrialsMinMover (protocols::minimization_packing); EnergyCutRotamerTrialsMover (protocols::minimization_packing); EnergyDependentCalculator (core::pose::metrics); EnergyEdge (core::scoring); EnergyEval (core::fragment::picking_old::vall::eval); EnergyEvent (core::pose::signals); EnergyGraph (core::scoring); EnergyJobSummary (protocols::jd3::job_summaries); EnergyLandscapeEvaluator (protocols::toolbox); EnergyMapContainer (protocols::relax); EnergyMethod (core::scoring::methods); EnergyMethodCreator (core::scoring::methods); EnergyMethodOptions (core::scoring::methods); EnergyMethodRegistrator (core::scoring::methods); EnergyNames (core::io::silent); EnergyNode (core::scoring); EnergyPerResidueFilter (protocols::simple_filters); EnergyPerResidueFilterCreator (protocols::simple_filters); EnergyReporter (protocols::pose_reporters); EnergyReporterCreator (protocols::pose_reporters); EnsembleConstraints (protocols::cluster); EnsembleConstraints_Simple (protocols::cluster); EnsembleEnergy (protocols::scoring::methods); EnsembleEnergyCreator (protocols::scoring::methods); EnsembleJobInputter (protocols::jd2); EnsembleJobInputterCreator (protocols::jd2); EnsureExclusivelySharedJumpMover (protocols::docking); EnsureExclusivelySharedJumpMoverCreator (protocols::docking); Entity (protocols::genetic_algorithm); EntityCorrespondence (protocols::pack_daemon); EntityElement (protocols::genetic_algorithm); EntityElementCreator (protocols::genetic_algorithm); EntityElementFactory (protocols::genetic_algorithm); EntityElementRegistrator (protocols::genetic_algorithm); EntityElementsEqual (protocols::genetic_algorithm); EntityFunc (protocols::pack_daemon); EntityFuncExpressionCreator (protocols::pack_daemon); EntityHistoryLT (protocols::pack_daemon); EntityRandomizer (protocols::genetic_algorithm); EntropyEstimator (protocols::ligand_docking::ga_ligand_dock); Enumerate1WithSelector (core::select); EnumeratedVectorSelector (protocols::denovo_design::components); EnumInfo (update_ResidueType_enum_files); EnvClaim (protocols::environment::claims); EnvClaimBroker (protocols::environment); EnvCore (core::environment); EnvEnergy (core::energy_methods); EnvEnergyCreator (core::energy_methods); Environment (protocols::environment); EnvLabelSelector (protocols::environment::claims); EnvMover (protocols::environment); EnvMoverCreator (protocols::environment); EnvPairPotential (core::scoring); EnvSmoothEnergy (core::energy_methods); EnvSmoothEnergyCreator (core::energy_methods); EnzConstraintIO (protocols::toolbox::match_enzdes_util); EnzConstraintParameters (protocols::toolbox::match_enzdes_util); EnzCstTemplateRes (protocols::toolbox::match_enzdes_util); EnzCstTemplateResAtoms (protocols::toolbox::match_enzdes_util); EnzCstTemplateResCache (protocols::toolbox::match_enzdes_util); EnzdesBaseProtocol (protocols::enzdes); EnzdesCacheableObserver (protocols::toolbox::match_enzdes_util); EnzdesConstraintReporter (protocols::enzdes); EnzdesCstCache (protocols::toolbox::match_enzdes_util); EnzdesCstParamCache (protocols::toolbox::match_enzdes_util); EnzdesFixBBProtocol (protocols::enzdes); EnzdesFlexBBProtocol (protocols::enzdes); EnzdesFlexibleRegion (protocols::enzdes); EnzdesJobInputter (protocols::enzdes); EnzdesJobInputterCreator (protocols::enzdes); EnzdesJobOutputter (protocols::enzdes); EnzdesJobOutputterCreator (protocols::enzdes); EnzdesLoopInfo (protocols::toolbox::match_enzdes_util); EnzdesLoopsFile (protocols::toolbox::match_enzdes_util); EnzdesScorefileFilter (protocols::enzdes); EnzdesScorefileFilterCreator (protocols::enzdes); EnzdesSeqRecoveryCache (protocols::toolbox::match_enzdes_util); EnzRepackMinimize (protocols::enzdes); EnzRepackMinimizeCreator (protocols::enzdes); EnzScoreFilter (protocols::enzdes); EnzScoreFilterCreator (protocols::enzdes); EnzymaticMover (protocols::enzymatic_movers); EnzymeData (core::enzymes); EnzymeManager (core::enzymes); EPRSpinLabel (core::scoring::epr_deer); ERRASER2Protocol (protocols::rna::movers); ERRASER2ProtocolCreator (protocols::rna::movers); ErraserMinimizerMover (protocols::rna::movers); ErraserMinimizerMoverCreator (protocols::rna::movers); EsmPerplexityTensorflowProtocol (protocols::esm_perplexity); Etable (core::scoring::etable); EtableAtom (core::scoring::etable::etrie); EtableClassicIntraEnergyCreator (core::scoring::etable); EtableEnergyCreator (core::scoring::etable); EtableEvaluator (core::scoring::etable); EtableFunc (core::scoring::func); EtableOptions (core::scoring::etable); EtableParamsOnePair (core::scoring::etable); EulerAngles (protocols::stepwise::sampler::rigid_body); EvaluatedArchive (protocols::jd2::archive); EvaluatedTrialMover (protocols::simple_filters); EvaluatorCreator (protocols::evaluation); EvaluatorFactory (protocols::evaluation); EvaluatorRegistrator (protocols::evaluation); EvenlyPartitionedNodeManager (protocols::jd3::dag_node_managers); Event (core::scoring::packstat); EvolutionaryDynamicsMover (protocols::evolution); EvolutionaryDynamicsMoverCreator (protocols::evolution); EvolutionManager (protocols::ligand_evolution); EvolutionOptions (protocols::ligand_evolution); EX (core::pack::task); EX_CUTOFF (core::pack::task); ExactOccludedHbondSolEnergy (core::energy_methods); ExactOccludedHbondSolEnergyCreator (core::energy_methods); ExactResidueMatcher (core::conformation); Exception (utility::excn); AsyncMPITemperingBase::ExchangeRequest (protocols::canonical_sampling); ExcludedFilter (protocols::constel); ExcludedResPredicate (core::scoring); ExclusivelySharedJumpSelector (core::select::jump_selector); ExclusivelySharedJumpSelectorCreator (core::select::jump_selector); EXCN_Archive (protocols::jd2::archive); EXCN_AssignmentNotFound (protocols::noesy_assign); EXCN_AtomNotFound (core::id); EXCN_bbdb_Merge_Failed (protocols::loophash); EXCN_CalcFailed (core::simple_metrics::composite_metrics); EXCN_CalcFailed (core::simple_metrics::metrics); EXCN_CalcFailed (protocols::simple_filters); EXCN_ConnectionSetupFailed (protocols::denovo_design::connection); EXCN_Converged (protocols::moves); EXCN_DB_IO_Failed (protocols::loophash); EXCN_Env_Exception (core::environment); EXCN_Env_Passport (protocols::environment); EXCN_Env_Security_Exception (protocols::environment); EXCN_FailedBroking (protocols::topology_broker); EXCN_FileFormat (protocols::noesy_assign); EXCN_FilterFailed (protocols::denovo_design::movers); EXCN_FilterFailed (protocols::topology_broker); EXCN_Fold (protocols::denovo_design::components); EXCN_FTSketchGraph (core::environment); EXCN_Heat_Converged (protocols::canonical_sampling::mc_convergence_checks); EXCN_Illegal_Arguments (core::conformation::membrane); EXCN_InitFailed (core::simple_metrics::composite_metrics); EXCN_InitFailed (core::simple_metrics::metrics); EXCN_InitFailed (protocols::simple_filters); EXCN_Input (protocols::topology_broker); EXCN_Invalid_Hashmap (protocols::loophash); EXCN_InvalidFoldTree (core::kinematics); EXCN_Loop_not_closed (protocols::loops); EXCN_Membrane (core::conformation::membrane); EXCN_Membrane_Bounds (core::conformation::membrane); EXCN_MembraneFoldTree (core::conformation::membrane); EXCN_No_Extra_Data_To_Write (protocols::loophash); EXCN_NoesyAssign (protocols::noesy_assign); EXCN_NonMembrane (core::conformation::membrane); EXCN_NothingToFold (protocols::denovo_design::movers); EXCN_Pool_Converged (protocols::canonical_sampling::mc_convergence_checks); EXCN_PoseInconsistent (protocols::denovo_design::components); EXCN_PreFilterFailed (protocols::denovo_design::architects); EXCN_RemarksNotPresent (protocols::denovo_design::components); EXCN_RemoveCstsFailed (protocols::constraint_generator); EXCN_RemoveCstsFailed (protocols::forge::remodel); EXCN_Resource_Definition (core::conformation::membrane); EXCN_TopologyBroker (protocols::topology_broker); EXCN_Unknown (protocols::topology_broker); EXCN_UnknownAtomname (protocols::noesy_assign); EXCN_UnknownResonance (protocols::noesy_assign); EXCN_VirtualRsd (core::conformation::membrane); EXCN_Wrong_DB_Format (protocols::loophash); Exemplar (protocols::cluster); ExpExpression (protocols::pack_daemon); ExpiryFilter (protocols::simple_filters); ExpiryFilterCreator (protocols::simple_filters); ExplicitWaterMover (protocols::simple_moves); ExplicitWaterMoverCreator (protocols::simple_moves); exposed_hydrophobic_data (core::pack::interaction_graph); ExposedHydrophobicsFilter (protocols::denovo_design::filters); ExposedHydrophobicsFilterCreator (protocols::denovo_design::filters); Expression (numeric::expression_parser); ExpressionCreator (numeric::expression_parser); ExtendChainMover (protocols::denovo_design::movers); ExtendChainMoverCreator (protocols::denovo_design::movers); ExtendedPoseBuilder (protocols::denovo_design::components); ExtendedPoseInputStream (core::import_pose::pose_stream); ExtendedPoseMover (protocols::pose_creation); ExtendedPoseMoverCreator (protocols::pose_creation); Extender (protocols::star); Extent (core::fragment::picking_old::concepts); ExternalEvaluator (protocols::simple_filters); ExternalGeomSampler (protocols::toolbox::match_enzdes_util); ExternalPackerResultLoader (protocols::quantum_annealing); ExternalPackerResultLoaderCreator (protocols::quantum_annealing); ExtraChiCutoff (core::pack::task::operation); ExtraChiCutoffCreator (core::pack::task::operation); ExtraChiCutoffRLT (core::pack::task::operation); ExtraChiCutoffRLTCreator (core::pack::task::operation); ExtractAsymmetricPoseMover (protocols::symmetry); ExtractAsymmetricPoseMoverCreator (protocols::symmetry); ExtractAsymmetricUnitMover (protocols::symmetry); ExtractAsymmetricUnitMoverCreator (protocols::symmetry); ExtractSubposeMover (protocols::matdes); ExtractSubposeMoverCreator (protocols::matdes); ExtraDataEnumManager (core::io::mmtf); ExtraQuadraticRepulsion (core::scoring::etable); ExtraRotamers (core::pack::task::operation); ExtraRotamerSamplingData (core::pack::task::operation); ExtraRotamersCreator (core::pack::task::operation); ExtraRotamersGeneric (core::pack::task::operation); ExtraRotamersGenericCreator (core::pack::task::operation); ExtraRotamersGenericRLT (core::pack::task::operation); ExtraRotamersGenericRLTCreator (core::pack::task::operation); ExtraScoreEvaluatorCreator (protocols::simple_filters); ExtraThreadingMover (protocols::comparative_modeling)

F: FA_ElecEnergy (core::scoring::elec); FA_ElecEnergyAroAll (core::energy_methods); FA_ElecEnergyAroAllCreator (core::energy_methods); FA_ElecEnergyAroAro (core::energy_methods); FA_ElecEnergyAroAroCreator (core::energy_methods); FA_ElecEnergyCreator (core::scoring::elec); FA_GrpElecEnergy (core::energy_methods); FA_GrpElecEnergyCreator (core::energy_methods); Fa_MbenvEnergy (core::energy_methods); Fa_MbenvEnergyCreator (core::energy_methods); Fa_MbsolvEnergy (core::energy_methods); Fa_MbsolvEnergyCreator (core::energy_methods); FabConstraint (core::scoring::constraints); FabConstraintCreator (core::scoring::constraints); FACTSEnergy (core::energy_methods); FACTSEnergyCreator (core::energy_methods); FACTSPoseInfo (core::scoring::facts); FACTSPotential (core::scoring::facts); FACTSResidueInfo (core::scoring::facts); FACTSRotamerSetInfo (core::scoring::facts); FACTSRsdTypeInfo (core::scoring::facts); FACTSRsdTypeMap (core::scoring::facts); FadeFunc (core::scoring::func); FadeInterval (core::scoring::hbonds); FaDockingSlideIntoContact (protocols::docking); FAElecContextData (core::energy_methods); FalseFilter (protocols::filters); FalseFilterCreator (protocols::filters); FalseResidueSelector (core::select::residue_selector); FalseResidueSelectorCreator (core::select::residue_selector); FaMPAsymEzCBEnergy (core::energy_methods); FaMPAsymEzCBEnergyCreator (core::energy_methods); FaMPAsymEzCGEnergy (core::energy_methods); FaMPAsymEzCGEnergyCreator (core::energy_methods); FaMPEnvEnergy (core::energy_methods); FaMPEnvEnergyCreator (core::energy_methods); FaMPEnvSmoothEnergy (core::energy_methods); FaMPEnvSmoothEnergyCreator (core::energy_methods); FaMPSolvEnergy (core::energy_methods); FaMPSolvEnergyCreator (core::energy_methods); FAScatter (core::scoring::fiber_diffraction); FASelectSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd); FastDensEnergy (core::energy_methods); FastDensEnergyCreator (core::energy_methods); FastDesign (protocols::denovo_design::movers); FastDesignCreator (protocols::denovo_design::movers); FASTER_IG_Repacker (protocols::pack_daemon); FASTERAnnealer (core::pack::annealer); FASTEREdge (core::pack::interaction_graph); FASTERInteractionGraph (core::pack::interaction_graph); FASTERNode (core::pack::interaction_graph); FastForwardToNextResidueAlternative (protocols::stepwise::screener); FastForwardToNextRigidBody (protocols::stepwise::screener); FastGapMover (protocols::loophash); FastLinearFunc (protocols::moves); FastRelax (protocols::relax); FastRelaxCreator (protocols::relax); FastSAXSEnergy (core::energy_methods); FastSAXSEnergyCreator (core::energy_methods); FaSymDockingSlideTogether (protocols::symmetry); FavorNativeResidue (protocols::protein_interface_design); FavorNativeResiduePreCycle (protocols::protein_interface_design::movers); FavorNativeResiduePreCycleCreator (protocols::protein_interface_design::movers); FavorNonNativeResidue (protocols::protein_interface_design); FavorNonNativeResiduePreCycle (protocols::protein_interface_design::movers); FavorNonNativeResiduePreCycleCreator (protocols::protein_interface_design::movers); FavorSequenceProfile (protocols::simple_moves); FavorSequenceProfileCreator (protocols::simple_moves); FavorSymmetricSequence (protocols::simple_moves); FavorSymmetricSequenceCreator (protocols::simple_moves); FaWaterToBilayerEnergy (protocols::membrane::scoring); FaWaterToBilayerEnergyCreator (protocols::membrane::scoring); FeaturesReporter (protocols::features); FeaturesReporterCreator (protocols::features); FeaturesReporterFactory (protocols::features); FeaturesReporterRegistrator (protocols::features); FiberDiffraction (core::scoring::fiber_diffraction); FiberDiffractionEnergy (core::energy_methods); FiberDiffractionEnergyCreator (core::energy_methods); FiberDiffractionEnergyDens (core::energy_methods); FiberDiffractionEnergyDensCreator (core::energy_methods); FibrilModelingClaimer (protocols::topology_broker); Field (core::io::pdb); FileBuffer (protocols::checkpoint); FileConstraintGenerator (protocols::denovo_design::constraints); FileConstraintGeneratorCreator (protocols::denovo_design::constraints); FileExistFilter (protocols::simple_filters); FileExistFilterCreator (protocols::simple_filters); FileJobOutputter (protocols::jd2); FileRemoveFilter (protocols::simple_filters); FileRemoveFilterCreator (protocols::simple_filters); FileSystemJobDistributor (protocols::jd2); FillAUTOTaskOperation (core::pack::task::operation); FillAUTOTaskOperationCreator (core::pack::task::operation); Filter (protocols::filters); Filter (protocols::pose_selectors); FilterBucket (protocols::loophash); FilterByAmphetamine (protocols::constel); FilterByHistamine (protocols::constel); FilterByIndoleCOO (protocols::constel); FilterByProxTerm (protocols::constel); FilterBySASA (protocols::constel); FilterByTryptamine (protocols::constel); FilterCollection (protocols::filters); FilterCreator (protocols::filters); FilterCreator (protocols::pose_selectors); FilteredSolutions (protocols::kinematic_closure::solution_pickers); Filterer_Count (protocols::stepwise::modeler::rna); FilterFactory (protocols::filters); FilterMover (protocols::moves); FilterRegistrator (protocols::filters); FilterReportAsPoseExtraScoresMover (protocols::moves); FilterReportAsPoseExtraScoresMoverCreator (protocols::moves); FilterReporter (protocols::pose_reporters); FilterReporterCreator (protocols::pose_reporters); FilterReporterMover (protocols::moves); FilterScanFilter (protocols::protein_interface_design::filters); FilterScanFilterCreator (protocols::protein_interface_design::filters); FilterStructs (protocols::flxbb); FilterStructs_Packstat (protocols::flxbb); FilterStructs_TotalCharge (protocols::flxbb); FilterValueMetric (protocols::filters); FilterValueMetricCreator (protocols::filters); FinalMinimizer (protocols::ligand_docking); FinalMinimizerCreator (protocols::ligand_docking); FinalRMSDComparator (protocols::pose_length_moves); find_SilentStructOPs (protocols::wum); FindConsensusSequence (protocols::recon_design); FindConsensusSequenceCreator (protocols::recon_design); FindEndpointsOperation (protocols::splice); FindEndpointsOperationCreator (protocols::splice); FingerprintBase (protocols::pockets); FingerprintMultifunc (protocols::pockets); FirstClassEdge (core::pack::interaction_graph); FirstClassNode (core::pack::interaction_graph); FitBfactorsMover (protocols::cryst); FitBfactorsMoverCreator (protocols::cryst); FitnessFilter (protocols::recon_design); FitnessFilterCreator (protocols::recon_design); FitnessFunction (protocols::genetic_algorithm); FitSimpleHelix (protocols::helical_bundle); FitSimpleHelixCreator (protocols::helical_bundle); FitSimpleHelixMultiFunc (protocols::helical_bundle); FIX_HIS_TAUTOMER (core::pack::task); FixAllLoopsMover (protocols::pose_length_moves); FixAllLoopsMoverCreator (protocols::pose_length_moves); FixbbCoupledRotamerSimAnnealer (core::pack::annealer); FixbbLinkingRotamerSimAnnealer (core::pack::annealer); FixbbPwatSimAnnealer (core::pack::annealer); FixbbRotamerSets (core::pack::rotamer_set); FixbbSimAnnealer (core::pack::annealer); FixedBBEdge (core::pack::interaction_graph); FixedBBInteractionGraph (core::pack::interaction_graph); FixedBBNode (core::pack::interaction_graph); FixedOffsetPivots (protocols::kinematic_closure::pivot_pickers); FixedOffsetsPivots (protocols::kinematic_closure::pivot_pickers); FixedPivots (protocols::kinematic_closure::pivot_pickers); FixedTemperatureController (protocols::canonical_sampling); FixTemplateJumpSetup (protocols::abinitio); flat_set (boost::container); FlatHarmonicFunc (core::scoring::func); FlexBBDesignMeanField (protocols::mean_field); FlexbbEdge (protocols::flexpack::interaction_graph); FlexbbIGFactory (protocols::flexpack::interaction_graph); FlexbbInteractionGraph (protocols::flexpack::interaction_graph); FlexBBMeanField (protocols::mean_field); FlexbbNode (protocols::flexpack::interaction_graph); FlexbbRotamerSet (protocols::flexpack::rotamer_set); FlexbbRotamerSets (protocols::flexpack::rotamer_set); FlexbbSimAnnealer (protocols::flexpack::annealer); FlexbbSparseMatrixIndex (protocols::flexpack::interaction_graph); FlexPacker (protocols::flexpack); FlexPepDockingAbInitio (protocols::flexpep_docking); FlexPepDockingFlags (protocols::flexpep_docking); FlexPepDockingLowRes (protocols::flexpep_docking); FlexPepDockingPoseMetrics (protocols::flexpep_docking); FlexPepDockingProtocol (protocols::flexpep_docking); FlexPepDockingProtocolCreator (protocols::flexpep_docking); FlipChiralityMover (protocols::cyclic_peptide); FlipChiralityMoverCreator (protocols::cyclic_peptide); FlipMover (protocols::membrane); FlipMoverCreator (protocols::membrane); FloatingResonance (protocols::noesy_assign); FloppyTailMover (protocols::floppy_tail); FlxbbDesign (protocols::flxbb); FlxbbDesignCreator (protocols::flxbb); FlxbbDesignPack (protocols::flxbb); FNatFilter (protocols::protein_interface_design::filters); FNatFilterCreator (protocols::protein_interface_design::filters); FoldandDockClaimer (protocols::topology_broker); FoldArchitectMover (protocols::denovo_design::movers); FoldArchitectMoverCreator (protocols::denovo_design::movers); FoldConstraints (protocols::abinitio); FoldGraph (protocols::denovo_design::components); FoldResonance (protocols::noesy_assign); FoldTree (core::kinematics); FoldTreeFromFoldGraphMover (protocols::denovo_design::movers); FoldTreeFromFoldGraphMoverCreator (protocols::denovo_design::movers); FoldTreeFromLoops (protocols::loops); FoldTreeFromLoopsCreator (protocols::loops); FoldTreeFromMotif (protocols::simple_moves); FoldTreeFromMotifCreator (protocols::simple_moves); FoldTreeHybridize (protocols::hybridization); FoldTreeSketch (core::environment); ForceDisulfidesMover (protocols::calc_taskop_movers); ForceDisulfidesMoverCreator (protocols::calc_taskop_movers); FormFactor (core::scoring::saxs); FormFactorManager (core::scoring::saxs); FourAtomsConstraintData (protocols::frag_picker::scores); FourPointsFunc (core::scoring::func); FractionSelector (core::select::residue_selector); FractionSelectorCreator (core::select::residue_selector); FragCache (core::fragment); FragData (core::fragment); FragFactory (core::fragment); FragID (core::fragment); FragID_Iterator (core::fragment); FragInsertAndAlignMover (protocols::rbsegment_relax); FragLib (protocols::frags); FragmentAllAtomCrmsd (protocols::frag_picker::scores); FragmentBiasAssigner (protocols::hybridization); FragmentCandidate (protocols::frag_picker); FragmentChunkCrms (protocols::frag_picker::scores); FragmentClaimer (protocols::topology_broker); FragmentCM (protocols::abinitio::abscript); FragmentCMCreator (protocols::abinitio::abscript); FragmentComparatorBase (protocols::frag_picker); FragmentContainer (protocols::topology_broker); FragmentCost (protocols::simple_moves); FragmentCrmsd (protocols::frag_picker::scores); FragmentCrmsdResDepth (protocols::frag_picker::scores); FragmentDME (protocols::frag_picker::scores); FragmentExtension (protocols::loop_grower); FragmentExtensionCreator (protocols::loop_grower); FragmentIO (core::fragment); FragmentJumpClaimer (protocols::topology_broker); FragmentJumpCM (protocols::abinitio::abscript); FragmentJumpCMCreator (protocols::abinitio::abscript); FragmentLibrary (core::fragment::rna); FragmentLibrary (protocols::ligand_evolution); FragmentLibraryManager (core::fragment::picking_old); FragmentLookup (protocols::indexed_structure_store); FragmentLookupFilter (protocols::indexed_structure_store::filters); FragmentLookupFilterCreator (protocols::indexed_structure_store::filters); FragmentLookupResult (protocols::indexed_structure_store); FragmentMover (protocols::simple_moves); FragmentPair (protocols::features::helixAssembly); FragmentPerturber (protocols::kinematic_closure::perturbers); FragmentPicker (protocols::frag_picker); FragmentReader (protocols::parser); FragmentRmsd (core::fragment); FragmentRotamers (protocols::rotamer_gen); FragmentRotamersCreator (protocols::rotamer_gen); FragmentSampler (protocols::abinitio); FragmentScoreFilter (protocols::frag_picker); FragmentScoreFilterCreator (protocols::frag_picker); FragmentScoreManager (protocols::frag_picker::scores); FragmentScoreMap (protocols::frag_picker::scores); FragmentScoringMethod (protocols::frag_picker::scores); FragmentSelectingRule (protocols::frag_picker); FragmentSetLoader (core::fragment); FragmentSetLoaderCreator (core::fragment); FragmentSpecification (protocols::indexed_structure_store); FragmentStore (protocols::indexed_structure_store); FragmentStoreManager (protocols::indexed_structure_store); FragmentStoreProvider (protocols::indexed_structure_store); FragQualCalculator (protocols::pose_metric_calculators); FragQualFilter (protocols::fldsgn::filters); FragQualFilterCreator (protocols::fldsgn::filters); FragSet (core::fragment); FragSetCollection (core::fragment); FragSetLoader (protocols::parser); FragSetLoaderCreator (protocols::parser); FragsToAtomDist (protocols::noesy_assign); FragStore (core::fragment); Frame (core::fragment); DbTrajectoryRecorder::Frame (protocols::canonical_sampling); DbTrajectoryWriter::Frame (protocols::trajectory); FrameIterator (core::fragment); FrameIteratorWorker_ (core::fragment); FrameList (core::fragment); FrameListIterator_ (core::fragment); FrameWork (protocols::antibody); FreeDOF_Energy (core::energy_methods); FreeDOF_EnergyCreator (core::energy_methods); FreeDOF_Options (core::scoring::methods); FreePeptide (protocols::backbone_moves::local_backbone_mover); FreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers); FromScratchMover (protocols::stepwise::monte_carlo::mover); FromScratchMoverCreator (protocols::stepwise::monte_carlo::mover); FullatomCustomPairDistanceEnergy (core::scoring::custom_pair_distance); FullatomCustomPairDistanceEnergyCreator (core::scoring::custom_pair_distance); FullatomDisulfideEnergy (core::energy_methods); FullatomDisulfideEnergyComponents (core::scoring::disulfides); FullatomDisulfideEnergyContainer (core::scoring::disulfides); FullatomDisulfideEnergyCreator (core::energy_methods); FullatomDisulfideParams13 (core::scoring::disulfides); FullatomDisulfidePotential (core::scoring::disulfides); FullatomRelaxMover (protocols::surface_docking); FullAtomRNA_Fragments (core::fragment::rna); FullChiSampleSet (protocols::match::upstream); FullModelInfo (core::pose::full_model_info); FullModelInnerLarvalJob (protocols::jd3::full_model); FullModelInputSource (protocols::jd3::full_model_inputters); FullModelInputter (protocols::jd3::full_model_inputters); FullModelInputterCreator (protocols::jd3::full_model_inputters); FullModelInputterFactory (protocols::jd3::full_model_inputters); FullModelInputterRegistrator (protocols::jd3::full_model_inputters); FullModelJobQueen (protocols::jd3::full_model); FullModelParameters (core::pose::full_model_info); FullModelPoseBuilder (core::import_pose); FullModelPreliminaryLarvalJob (protocols::jd3::full_model); Func (core::scoring::func); func_1d (core::optimization); jagged_array::func_T2 (protocols::mean_field); FuncFactory (core::scoring::func); FunGroupTK (protocols::kinmatch)

G: G; GA_Minimizer (core::optimization); GADockStageParams (protocols::ligand_docking::ga_ligand_dock); GALigandDock (protocols::ligand_docking::ga_ligand_dock); GALigandDockCreator (protocols::ligand_docking::ga_ligand_dock); GAOptimizer (protocols::ligand_docking::ga_ligand_dock); GapCloser (protocols::backbone_moves::local_backbone_mover); GapSolutionPicker (protocols::backbone_moves::local_backbone_mover::gap_solution_pickers); GasteigerAtomTypeData (core::chemical::gasteiger); GasteigerAtomTypeSet (core::chemical::gasteiger); GatherPosesMover (protocols::cluster); GaussianChainDoubleFunc (core::scoring::func); GaussianChainFunc (core::scoring::func); GaussianChainFuncPotentialEvaluator (core::scoring::loop_graph::evaluator); GaussianChainGeneralFunc (core::scoring::func); GaussianChainQuadrupleFunc (core::scoring::func); GaussianChainSingleFunc (core::scoring::func); GaussianChainTripleFunc (core::scoring::func); GaussianFunc (core::scoring::func); GaussianOverlapEnergy (core::energy_methods); GaussianOverlapEnergyCreator (core::energy_methods); GaussianParameter (core::chemical::rna); GaussianRBSegmentMover (protocols::rbsegment_relax); GDB (protocols::sparta); GenBondedExclInfo (core::scoring); GenBornEnergy (core::energy_methods); GenBornEnergyCreator (core::energy_methods); GenBornPoseInfo (core::scoring); GenBornPotential (core::scoring); GenBornResidueInfo (core::scoring); GenBornRotamerSetInfo (core::scoring); GeneralAntibodyModeler (protocols::antibody::design); GeneralEvent (core::conformation::signals); GeneralEvent (core::pose::signals); GeneralizedKIC (protocols::generalized_kinematic_closure); GeneralizedKICCreator (protocols::generalized_kinematic_closure); GeneralizedKICfilter (protocols::generalized_kinematic_closure::filter); GeneralizedKICperturber (protocols::generalized_kinematic_closure::perturber); GeneralizedKICselector (protocols::generalized_kinematic_closure::selector); GenerateMainchainPotential (protocols::mainchain_potential); GenerateMainchainPotentialOptions (protocols::mainchain_potential); GenerateStoredRBConfs (protocols::enzdes); GenericBondedEnergy (core::energy_methods); GenericBondedEnergyCreator (core::energy_methods); GenericBondedPotential (core::scoring); GenericJobInputter (protocols::comparative_modeling); GenericJobInputterCreator (protocols::comparative_modeling); GenericMonteCarloMover (protocols::monte_carlo); GenericMonteCarloMoverCreator (protocols::monte_carlo); GenericRemodelConstraintGenerator (protocols::forge::remodel); GenericResidueConnectionData (core::scoring::etable::etrie); GenericSimulatedAnnealer (protocols::monte_carlo); GenericSimulatedAnnealerCreator (protocols::monte_carlo); GeneticAlgorithm (protocols::genetic_algorithm); GeneticAlgorithmBase (protocols::genetic_algorithm); GenMeanFieldMover (protocols::mean_field); GenMeanFieldMoverCreator (protocols::mean_field); GenPharmacophore (protocols::pockets); GenTorsionParams (core::scoring); GeometricFunc (protocols::moves); GeometricRenameIsomorphismCallback (core::io::pose_from_sfr); GeometricRenameVerticiesEquivalent (core::io::pose_from_sfr); GeometricSolEnergyEvaluator (core::scoring::geometric_solvation); GeometricSolvationFeatures (protocols::features); GeometricSolvationFeaturesCreator (protocols::features); GeometryFilter (protocols::score_filters); GeometryFilterCreator (protocols::score_filters); GeometrySecMatchRPE (protocols::match::downstream); GeomSampleInfo (protocols::toolbox::match_enzdes_util); GetRBDOFValues (protocols::matdes); GetRBDOFValuesCreator (protocols::matdes); GlobalResidueTypeSet (core::chemical); GlycanDockProtocol (protocols::glycan_docking); GlycanDockProtocolCreator (protocols::glycan_docking); GlycanInfoMover (protocols::analysis); GlycanInfoMoverCreator (protocols::analysis); GlycanLayerSelector (core::select::residue_selector); GlycanLayerSelectorCreator (core::select::residue_selector); GlycanNode (core::conformation::carbohydrates); GlycanPositionSelector (core::select::residue_selector); GlycanPositionSelectorCreator (core::select::residue_selector); GlycanResidueSelector (core::select::residue_selector); GlycanResidueSelectorCreator (core::select::residue_selector); GlycanSampler (protocols::carbohydrates); GlycanSamplerCreator (protocols::carbohydrates); GlycanSequonsSelector (core::select::residue_selector); GlycanSequonsSelectorCreator (core::select::residue_selector); GlycanTree (core::conformation::carbohydrates); GlycanTreeMinMover (protocols::carbohydrates); GlycanTreeMinMoverCreator (protocols::carbohydrates); GlycanTreeModeler (protocols::carbohydrates); GlycanTreeModelerCreator (protocols::carbohydrates); GlycanTreeSet (core::conformation::carbohydrates); GlycanTreeSetObserver (core::conformation::carbohydrates); GlycopeptideDockingFlags (protocols::glycopeptide_docking); GlycopeptideDockingHighResRefinement (protocols::glycopeptide_docking); GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking); GlycopeptideDockingProtocol (protocols::glycopeptide_docking); GlycopeptideDockingProtocolCreator (protocols::glycopeptide_docking); GlycosyltransferaseMover (protocols::enzymatic_movers); GlycosyltransferaseMoverCreator (protocols::enzymatic_movers); GoapEnergy (core::energy_methods); GoapEnergyCreator (core::energy_methods); GoapRsdType (core::energy_methods); GrabAllCollector (protocols::frag_picker); GraftCDRLoopsProtocol (protocols::antibody); GraftedStemOptimizer (protocols::antibody); Grafting_Base_Exception (protocols::antibody::grafting); GraftMover (protocols::antibody_legacy); GraftMoverBase (protocols::grafting); GraftOneCDRLoop (protocols::antibody); GraftOneMover (protocols::antibody_legacy); GraftSwitchMover (protocols::switches); GraftSwitchMoverCreator (protocols::switches); Graph (utility::graph); GraphicsState (protocols::viewer); GraphvizPropertyWriter (core::io::pose_from_sfr); GraphvizPropertyWriter (core::chemical); GreedyKCenter (protocols::toolbox); GreedyOptMutationMover (protocols::design_opt); GreedyOptMutationMoverCreator (protocols::design_opt); GreenPacker (protocols::minimization_packing); GridBase (protocols::qsar::scoring_grid); GridCreator (protocols::qsar::scoring_grid); GriddedAtomTreeMultifunc (protocols::ligand_docking::ga_ligand_dock); GridFactory (protocols::qsar::scoring_grid); GridHash3D (protocols::ligand_docking::ga_ligand_dock); GridInfo (core::energy_methods); GridManager (protocols::qsar::scoring_grid); GridRegistrator (protocols::qsar::scoring_grid); GridScorer (protocols::ligand_docking::ga_ligand_dock); GridSearchIterator (protocols::scoring::methods::pcs); GridSearchIterator_Ts1 (protocols::scoring::methods::pcsTs1); GridSearchIterator_Ts2 (protocols::scoring::methods::pcsTs2); GridSearchIterator_Ts3 (protocols::scoring::methods::pcsTs3); GridSearchIterator_Ts4 (protocols::scoring::methods::pcsTs4); GridSearchIteratorCA (protocols::scoring::methods::pcs2); GridSet (protocols::qsar::scoring_grid); GroupDiscriminator (protocols::minimization_packing); GroupElec (core::scoring::elec); GrowLeft (protocols::forge::build); GrowLigand (protocols::ligand_docking); GrowLigandCreator (protocols::ligand_docking); GrowPeptides (protocols::seeded_abinitio); GrowPeptidesCreator (protocols::seeded_abinitio); GrowPeptidesSegment (protocols::seeded_abinitio); GrowRight (protocols::forge::build); GuardedLoopsFromFile (protocols::loops); GunnCost (protocols::frag_picker::scores); GunnCost (protocols::simple_moves); GunnCostScore (protocols::frag_picker::scores); GunnTuple (protocols::frag_picker::scores); GunnTuple (protocols::simple_moves)

H: H3CterInsert (protocols::antibody); H3PerturbCCD (protocols::antibody); H3RefineCCD (protocols::antibody); HackAroEnergy (core::energy_methods); HackAroEnergyCreator (core::energy_methods); Hairpin (core::scoring); Hairpins (core::scoring); HamiltonianExchange (protocols::canonical_sampling); HamiltonianExchangeCreator (protocols::canonical_sampling); Hankel (core::scoring::fiber_diffraction); HarmonicFunc (core::scoring::func); HasDisulfideFilter (protocols::pose_sewing::filters); HasDisulfideFilterCreator (protocols::pose_sewing::filters); hash_upstream_hit (protocols::match::downstream); HashEdge (protocols::legacy_sewing); HashedSmartAssembly (protocols::sewing::data_storage); Hasher (protocols::sewing::hashing); Hasher (protocols::legacy_sewing); HasherSettings (protocols::sewing::hashing); ReactionBasedAnalogSampler::Product::HashFunction (protocols::drug_design); HashResult (protocols::legacy_sewing); HashValue (protocols::legacy_sewing); HashValue (protocols::sewing::hashing); hbAcc (protocols::ligand_docking::ga_ligand_dock); HbaGrid (protocols::qsar::scoring_grid); HbaGridCreator (protocols::qsar::scoring_grid); HBAtom (core::scoring::hbonds::hbtrie); HBCountPairFunction (core::scoring::hbonds::hbtrie); HBCPData (core::scoring::hbonds::hbtrie); HBDerivAssigner (core::scoring::hbonds); HbdGrid (protocols::qsar::scoring_grid); HbdGridCreator (protocols::qsar::scoring_grid); hbDon (protocols::ligand_docking::ga_ligand_dock); HBEvalTuple (core::scoring::hbonds); HBNet (protocols::hbnet); HBNetCreator (protocols::hbnet); HBNetEnergy (core::pack::guidance_scoreterms::hbnet_energy); HBNetEnergyCreator (core::pack::guidance_scoreterms::hbnet_energy); HBNetScore (protocols::hbnet); HBNetScoreFilterCreator (protocols::hbnet); HBNetStapleInterface (protocols::hbnet); HBNetStapleInterfaceCreator (protocols::hbnet); HBond (core::scoring::hbonds); HBondAcceptorFilter (protocols::ligand_docking); HBondAcceptorFilterCreator (protocols::ligand_docking); HBondBonusOptions (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty); HBondCommon (protocols::constel); HBondDatabase (core::scoring::hbonds); HBondDerivs (core::scoring::hbonds); HBondDonorFilter (protocols::ligand_docking); HBondDonorFilterCreator (protocols::ligand_docking); HBondEdge (core::scoring::hbonds::graph); HBondEnergy (core::scoring::hbonds); HBondEnergyCreator (core::scoring::hbonds); HBondFeatures (protocols::features); HBondFeaturesCreator (protocols::features); HBondGraph (core::scoring::hbonds::graph); HBondGraphInitializerIG (core::pack::hbonds); HBondInfo (core::scoring::hbonds::graph); HbondMetric (core::simple_metrics::per_residue_metrics); HbondMetricCreator (core::simple_metrics::per_residue_metrics); HBondNetStruct (protocols::hbnet); HBondNode (core::scoring::hbonds::graph); HBondOptions (core::scoring::hbonds); HBondParameterFeatures (protocols::features); HBondParameterFeaturesCreator (protocols::features); HBondResidueMinData (core::scoring::hbonds); HBondResPairMinData (core::scoring::hbonds); HBondResStruct (protocols::hbnet); HBondSelector (protocols::residue_selectors); HBondSelectorCreator (protocols::residue_selectors); HBondSet (core::scoring::hbonds); HbondsToAtomFilter (protocols::protein_interface_design::filters); HbondsToAtomFilterCreator (protocols::protein_interface_design::filters); HbondsToResidueFilter (protocols::protein_interface_design::filters); HbondsToResidueFilterCreator (protocols::protein_interface_design::filters); HBondsTrieVsTrieCachedDataContainer (core::scoring::hbonds::hbtrie); HBondTypeManager (core::scoring::hbonds); HBP_FinalFullatomRefinementMoveGenerator (protocols::helical_bundle_predict); HBP_HelixCoilMoveGenerator (protocols::helical_bundle_predict); HBP_MoveGenerator (protocols::helical_bundle_predict); HBP_SigmoidalTemperatureScheduleGenerator (protocols::helical_bundle_predict); HBP_TemperatureScheduleGenerator (protocols::helical_bundle_predict); HBPHelix (protocols::helical_bundle_predict); HBPHelixAssignments (protocols::helical_bundle_predict); HBPHelixParameters (protocols::helical_bundle_predict); HbsPatcher (protocols::simple_moves::hbs); hConvergenceCheck (protocols::abinitio); hConvergenceCheck (protocols::hybridization); HeaderInformation (core::io); Heat_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks); HeavyAtomFilter (core::chemical); HeavyAtomFilter (protocols::ligand_docking); HeavyAtomFilterCreator (protocols::ligand_docking); HeavyAtomNormalization (protocols::qsar::scoring_grid); HeavyAtomWithHydrogensFilter (core::chemical); HeavyAtomWithPolarHydrogensFilter (core::chemical); HedgeArchive (protocols::abinitio); HelicalBundlePredictApplication (protocols::helical_bundle_predict); HelicalBundlePredictApplicationOptions (protocols::helical_bundle_predict); HelicalFragment (protocols::features::helixAssembly); HelicalGaussianMover (protocols::rbsegment_relax); Helices (core::scoring); Helix (protocols::fldsgn::topology); HelixArchitect (protocols::denovo_design::architects); HelixArchitectCreator (protocols::denovo_design::architects); HelixBendFilter (protocols::fldsgn::filters); HelixBendFilterCreator (protocols::fldsgn::filters); HelixBundleFeatures (protocols::features::helixAssembly); HelixBundleFeaturesCreator (protocols::features::helixAssembly); HelixCapFeatures (protocols::features); HelixCapFeaturesCreator (protocols::features); HelixFromSequence (protocols::membrane); HelixFromSequenceCreator (protocols::membrane); HelixHelixAngleFilter (protocols::simple_filters); HelixHelixAngleFilterCreator (protocols::simple_filters); HELIXInformation (core::io); HelixKinkFilter (protocols::fldsgn::filters); HelixKinkFilterCreator (protocols::fldsgn::filters); HelixNCapperMover (protocols::helix_capper); HelixPairing (protocols::denovo_design::components); HelixPairing (protocols::fldsgn::topology); HelixPairingFilter (protocols::fldsgn::filters); HelixPairingFilterCreator (protocols::fldsgn::filters); HelixPairingSet (protocols::fldsgn::topology); HelixPerturber (protocols::denovo_design::components); HelixRotate (protocols::nonlocal); HelixScore (protocols::sic_dock); HelixSheetPairing (protocols::denovo_design::components); HeteroHeteroBondFilter (protocols::drug_design); HeteroHeteroBondFilterCreator (protocols::drug_design); HierarchicalHybridJD_JobResultsSummary (protocols::cyclic_peptide_predict); HierarchicalHybridJD_PNearToArbitraryStateSummary (protocols::cyclic_peptide_predict); HierarchicalHybridJD_ResultsSummaryBase (protocols::cyclic_peptide_predict); HierarchicalHybridJD_RMSDToBestSummary (protocols::cyclic_peptide_predict); HierarchicalHybridJD_SASASummary (protocols::cyclic_peptide_predict); HierarchicalLevel (protocols::canonical_sampling::mc_convergence_checks); HighResDocker (protocols::ligand_docking); HighResDockerCreator (protocols::ligand_docking); HighResEnsemble (protocols::ligand_docking); HighResEnsembleCreator (protocols::ligand_docking); BiasEnergy::Histogram (protocols::canonical_sampling); Histogram (protocols::recces); history_queue_struct (core::pack::interaction_graph); Hit (protocols::match); Hit (protocols::simple_moves); HitHasher (protocols::match); HitNeighborFinder (protocols::match); HolesEnergy (core::energy_methods); HolesEnergyCreator (core::energy_methods); HolesEnergyRes (core::scoring::packing); HolesFilter (protocols::simple_filters); HolesFilterCreator (protocols::simple_filters); HolesParams (core::scoring::packing); HolesParamsRes (core::scoring::packing); HolesResult (core::scoring::packing); HotspotDisjointedFoldTreeMover (protocols::protein_interface_design::movers); HotspotDisjointedFoldTreeMoverCreator (protocols::protein_interface_design::movers); HotspotHasherMover (protocols::protein_interface_design::movers); HotspotHasherMoverCreator (protocols::protein_interface_design::movers); HotspotStub (protocols::hotspot_hashing); HotspotStubSet (protocols::hotspot_hashing); HPatchBackgroundEdge (core::pack::interaction_graph); HPatchBackgroundNode (core::pack::interaction_graph); HPatchCalculator (protocols::pose_metric_calculators); HPatchEdge (core::pack::interaction_graph); HPatchEnergy (core::pack::interaction_graph); HPatchEnergyCreator (core::pack::interaction_graph); HPatchInteractionGraph (core::pack::interaction_graph); HPatchNode (core::pack::interaction_graph); HPool_RMSD (protocols::canonical_sampling::mc_convergence_checks); HRF_MSLabelingEnergy (core::energy_methods); HRF_MSLabelingEnergyCreator (core::energy_methods); HRFDynamicsEnergy (core::energy_methods); HRFDynamicsEnergyCreator (core::energy_methods); HSPairPotential (protocols::fldsgn::potentials::sspot); HSSTriplet (protocols::fldsgn::topology); HSSTripletFilter (protocols::fldsgn::filters); HSSTripletFilterCreator (protocols::fldsgn::filters); HSSTripletSet (protocols::fldsgn::topology); HTL_EventX (core::scoring::packstat); HybridizeFoldtreeDynamic (protocols::hybridization); HybridizeProtocol (protocols::hybridization); HybridizeProtocolCreator (protocols::hybridization); HybridVDW_Energy (core::energy_methods); HybridVDW_EnergyCreator (core::energy_methods); Hydrate (protocols::hydrate); HydrogenAtomFilter (core::chemical); HydrogenBondConstraintGenerator (protocols::constraint_generator); HydrogenBondConstraintGeneratorCreator (protocols::constraint_generator); HydrogenBondInfo (protocols::constraint_generator); HydrogenBondingAtom (protocols::constraint_generator); HydrophobicityProfileSimilarity (protocols::frag_picker::scores); HydrophobicitySimilarity (protocols::frag_picker::scores); HydroxylTorsionEnergy (core::energy_methods); HydroxylTorsionEnergyCreator (core::energy_methods); HydroxylTorsionPotential (core::scoring)

I: APBSConfig::I_PARAM (core::scoring); ICoorAtomID (core::chemical); ICoorOrbitalData (core::chemical::orbitals); IdealAbegoGenerator (protocols::denovo_design::components); IdealBondLengthSet (core::chemical); IdealContact (protocols::sewing::hashing); IdealizeAnomericHydrogens (protocols::carbohydrates); IdealizeAnomericHydrogensCreator (protocols::carbohydrates); IdealizeHelicesMover (protocols::rbsegment_relax); IdealizeHelicesMoverCreator (protocols::rbsegment_relax); IdealizeMover (protocols::idealize); IdealizeMoverCreator (protocols::idealize); IdealizeNonPhiPsi (protocols::kinematic_closure::perturbers); IdealParametersDatabase (core::energy_methods); IdentifyLigandMotifs; IdentityEval (core::fragment::picking_old::vall::eval); IdentityEvent (core::conformation::signals); IdentityFactory (protocols::ligand_evolution); IdentityFunc (core::scoring::func); IdManager (protocols::calc_taskop_filters); IfMover (protocols::moves); IfMoverCreator (protocols::moves); IfThenFilter (protocols::filters); IfThenFilterCreator (protocols::filters); IGEdgeReweightContainer (core::pack::task); IGEdgeReweighter (core::pack::task); IGInterfaceEdgeUpweighter (protocols::toolbox); IGLigandDesignEdgeUpweighter (protocols::toolbox); IgnoreSubsetConstraintSet (protocols::comparative_modeling); Implements; ImplicitFastClashCheck (protocols::scoring); ImplicitLipidInfo (core::conformation::membrane); ImplicitMembraneCoulomb (core::energy_methods); ImplicitMembraneElecEnergy (core::energy_methods); ImplicitMembraneElecEnergyCreator (core::energy_methods); ImportPoseOptions (core::import_pose); ImportUnboundRotamersOperation (protocols::task_operations); ImportUnboundRotamersOperationCreator (protocols::task_operations); IncludeCurrent (core::pack::task::operation); IncludeCurrentCreator (core::pack::task::operation); IncludeCurrentRLT (core::pack::task::operation); IncludeCurrentRLTCreator (core::pack::task::operation); IndelOptimizationMover (protocols::indel); IndependentBBTorsionSRFD (core::fragment); IndependentLoopMover (protocols::loops::loop_mover); Individual (protocols::ligand_evolution); InitializeByBins (protocols::simple_moves::bin_transitions); InitializeByBinsCreator (protocols::simple_moves::bin_transitions); InitializeExtraRotsFromCommandline (core::pack::task::operation); InitializeExtraRotsFromCommandlineCreator (core::pack::task::operation); InitializeFromCommandline (core::pack::task::operation); InitializeFromCommandlineCreator (core::pack::task::operation); InitializeFromOptionCollection (core::pack::task::operation); InitializeFromOptionCollectionCreator (core::pack::task::operation); InnerJob (protocols::jd2); InnerLarvalJob (protocols::jd3); InnerMultiThreadingJob (protocols::jd2); InputPoseDeallocationMessage (protocols::jd3::deallocation); InputSource (protocols::jd3); InputStreamStepWiseSampler (protocols::stepwise::sampler::input_streams); InputStreamWithResidueInfo (protocols::stepwise::modeler::protein); InsertChunkMover (protocols::hybridization); InsertPoseIntoPoseMover (protocols::grafting::simple_movers); InsertPoseIntoPoseMoverCreator (protocols::grafting::simple_movers); InsertResMover (protocols::pose_length_moves); InsertResMoverCreator (protocols::pose_length_moves); InSetExpression (protocols::pack_daemon); InstallFarnesylMover (protocols::farnesyl); InstallFarnesylMoverCreator (protocols::farnesyl); RemodelMover::instruction_flags (protocols::forge::remodel); IntegrationTestBreaker (protocols::stepwise::screener); InteractingRotamerExplosion (protocols::task_operations); InteractingRotamerExplosionCreator (protocols::task_operations); InteractionEnergyMetric (core::simple_metrics::metrics); InteractionEnergyMetricCreator (core::simple_metrics::metrics); InteractionGraphBase (core::pack::interaction_graph); InteractionGraphFactory (core::pack::interaction_graph); InteractionGraphSummaryMetric (protocols::quantum_annealing); InteractionGraphSummaryMetricCreator (protocols::quantum_annealing); InteratomicVarianceMatrix (protocols::toolbox); InterbondAngleScore (protocols::frag_picker::scores); InterchainEnvEnergy (protocols::scoring::methods); InterchainEnvEnergyCreator (protocols::scoring::methods); InterchainJumpSelector (core::select::jump_selector); InterchainJumpSelectorCreator (core::select::jump_selector); InterchainPairEnergy (protocols::scoring::methods); InterchainPairEnergyCreator (protocols::scoring::methods); InterchainPotential (protocols::scoring); Interface (protocols::scoring); Interface (protocols::ligand_docking::ligand_options); InterfaceAnalyzerMover (protocols::analysis); InterfaceAnalyzerMoverCreator (protocols::analysis); InterfaceBindingEnergyDensityFilter (protocols::simple_ddg); InterfaceBindingEnergyDensityFilterCreator (protocols::simple_ddg); InterfaceBuilder (protocols::ligand_docking); InterfaceBuilderLoader (protocols::ligand_docking); InterfaceBuilderLoaderCreator (protocols::ligand_docking); InterfaceData (protocols::analysis); InterfaceDdGMover (protocols::features); InterfaceDdGMoverCreator (protocols::features); InterfaceDefinitionCalculator (core::pose::metrics::simple_calculators); InterfaceDeltaEnergeticsCalculator (core::pose::metrics::simple_calculators); InterfaceFeatures (protocols::features); InterfaceFeaturesCreator (protocols::features); InterfaceHbondsFilter (protocols::simple_filters); InterfaceHbondsFilterCreator (protocols::simple_filters); InterfaceHolesFilter (protocols::protein_interface_design::filters); InterfaceHolesFilterCreator (protocols::protein_interface_design::filters); InterfaceHydrophobicResidueContactsFilter (protocols::simple_filters); InterfaceHydrophobicResidueContactsFilterCreator (protocols::simple_filters); InterfaceInfo (protocols::ligand_docking::ligand_options); InterfaceInfo (protocols::scoring); InterfaceNeighborDefinitionCalculator (core::pose::metrics::simple_calculators); InterfacePackingFilter (protocols::matdes); InterfacePackingFilterCreator (protocols::matdes); InterfaceRecapitulationMover (protocols::protein_interface_design::movers); InterfaceRecapitulationMoverCreator (protocols::protein_interface_design::movers); InterfaceSasaDefinitionCalculator (core::pose::metrics::simple_calculators); InterfaceSasaFilter (protocols::simple_filters); InterfaceSasaFilterCreator (protocols::simple_filters); InterfaceScoreCalculator (protocols::ligand_docking); InterfaceScoreCalculatorCreator (protocols::ligand_docking); InterfaceSidechainMinMover (protocols::docking); InterfaceTaskOperation (protocols::simple_task_operations); InterGroupInterfaceByVectorSelector (core::select::residue_selector); InterGroupInterfaceByVectorSelectorCreator (core::select::residue_selector); InterGroupNeighborsCalculator (protocols::pose_metric_calculators); InterlockAroma (protocols::flxbb); InterlockAromaCreator (protocols::flxbb); InterlockingAromaFilter (protocols::fldsgn::filters); InterlockingAromaFilterCreator (protocols::fldsgn::filters); InterModelMotifScorer (protocols::sewing::scoring); InterModelMotifScorerCreator (protocols::sewing::scoring); IntermolEnergy (core::energy_methods); IntermolEnergyCreator (core::energy_methods); InternalCoordAtoms (core::kinematics::inverse); InternalCoordGeometry (core::kinematics::inverse); InternalWorkingResidueParameter (protocols::stepwise::modeler::rna); InterRepeatContactFilter (protocols::simple_filters); InterRepeatContactFilterCreator (protocols::simple_filters); Interval (protocols::forge::build); Interval (protocols::jumping); IntraDesignTerminusMotifScorer (protocols::sewing::scoring); IntraDesignTerminusMotifScorerCreator (protocols::sewing::scoring); IntraRepeatContactFilter (protocols::simple_filters); IntraRepeatContactFilterCreator (protocols::simple_filters); InverseRotamersCstGeneratorCreator (protocols::forge::constraints); InverseRotamersRCG (protocols::forge::constraints); InvGeometricFunc (protocols::moves); Invoker (core::scoring::etable::count_pair); InvRotamerDots (core::pack::interaction_graph); InvrotCollector (protocols::toolbox::match_enzdes_util); InvrotTarget (protocols::toolbox::match_enzdes_util); InvrotTree (protocols::toolbox::match_enzdes_util); InvrotTreeCstGeneratorCreator (protocols::forge::constraints); InvrotTreeNode (protocols::toolbox::match_enzdes_util); InvrotTreeNodeBase (protocols::toolbox::match_enzdes_util); InvrotTreeRCG (protocols::forge::constraints); IonizableResidue (protocols::simple_moves); IRCollection (protocols::motifs); IRmsdFilter (protocols::protein_interface_design::filters); IRmsdFilterCreator (protocols::protein_interface_design::filters); IsHeavyAtomPredicate (core::scoring); IsMainAtomPredicate (core::scoring); IsProteinBackboneIncludingOPredicate (core::scoring); IsProteinBackbonePredicate (core::scoring); IsProteinCAPredicate (core::scoring); IsSpecificAtomsPredicate (core::scoring); LoggedFragmentMover::Item (protocols::simple_moves); IteratedConvergenceMover (protocols::moves); IteratedConvergenceMoverCreator (protocols::moves); IterativeAbrelax (protocols::abinitio); IterativeBase (protocols::abinitio); IterativeCentroid (protocols::abinitio); IterativeFullatom (protocols::abinitio); IterativeOptEDriver (protocols::optimize_weights); IterativeVectorExpression (protocols::pack_daemon); RawFileData::iterator (core::io::raw_data); SilentFileData::iterator (core::io::silent)

J: ModuleType1::jacobian_struct (core::kinematics::jacobian); JacobianStructure (core::kinematics::jacobian); JacobiLoopClosureMover (protocols::loops::loop_closure::jacobi); JacobiLoopClosureMoverCreator (protocols::loops::loop_closure::jacobi); jagged_array (protocols::mean_field); JCoupling (protocols::frag_picker::scores); JCouplingIO (protocols::frag_picker); JD2Failure (protocols::jd2); JGJobNode (protocols::jd3); JobGenealogist::JGJobNodeOP_hash (protocols::jd3); JGResultNode (protocols::jd3); JobGenealogist::JGResultNodeOP_hash (protocols::jd3); JJH_Minimizer (core::optimization); Job (protocols::jd2); Job (protocols::jd3); JobDataFeatures (protocols::features); JobDataFeaturesCreator (protocols::features); JobDigraph (protocols::jd3); JobDigraphUpdater (protocols::jd3); JobDirectedEdge (protocols::jd3); JobDirectedNode (protocols::jd3); JobDistributor (protocols::jd2); JobDistributor (protocols::jd3); JobDistributorFactory (protocols::jd2); JobDistributorFactory (protocols::jd3); JobExtractor (protocols::jd3::job_distributors); JobGenealogist (protocols::jd3); JobInputter (protocols::jd2); JobInputterCreator (protocols::jd2); JobInputterFactory (protocols::jd2); JobInputterRegistrator (protocols::jd2); JobOutputIndex (protocols::jd3); JobOutputter (protocols::jd2); JobOutputterCreator (protocols::jd2); JobOutputterFactory (protocols::jd2); JobOutputterObserver (protocols::jd2); JobOutputterRegistrator (protocols::jd2); JobQueen (protocols::jd3); JobResult (protocols::jd3); JobResultID_hash (protocols::multistage_rosetta_scripts); JobsContainer (protocols::jd2); JobSummary (protocols::jd3); JobTracker (protocols::jd3); JointScore (protocols::sic_dock); JointSequenceOperation (protocols::task_operations); JointSequenceOperationCreator (protocols::task_operations); JQKey (protocols::jd3); JScoreEvaluator (protocols::simple_filters); JScoreEvaluatorCreator (protocols::simple_filters); JSON_RPC (protocols::rpc); JSONFormattedLoopsFileReader (protocols::loops); JSONStructureStoreBackend (protocols::indexed_structure_store); Jump (core::kinematics); Jump_point (protocols::stepwise::modeler::rna); JumpAtom (core::kinematics::tree); RigidChunkClaimer::JumpCalculator (protocols::topology_broker); JumpClaim (protocols::environment::claims); JumpClaim (protocols::topology_broker::claims); JumpSetup::JumpDef (protocols::jumping); ResiduePairJumpSetup::JumpDef (protocols::jumping); JumpDownstreamSelector (core::select::residue_selector); JumpDownstreamSelectorCreator (core::select::residue_selector); JumpElement (protocols::environment::claims); JumpEvaluator (protocols::simple_filters); JumpForResidue (core::select::jump_selector); JumpForResidueCreator (core::select::jump_selector); JumpID (core::id); JumpIndexSelector (core::select::jump_selector); JumpIndexSelectorCreator (core::select::jump_selector); JumpingFoldConstraintsWrapper (protocols::abinitio); JumpingFrame (core::fragment); JumpMetric (protocols::multistage_rosetta_scripts::cluster::metrics); JumpMetricCreator (protocols::multistage_rosetta_scripts::cluster::metrics); JumpNrEvaluator (protocols::simple_filters); JumpNrEvaluatorCreator (protocols::simple_filters); JumpOutMover (protocols::moves); JumpRotamerSidechainMover (protocols::simple_moves::sidechain_moves); JumpRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves); JumpSample (protocols::jumping); JumpSampleData (protocols::abinitio::abscript); JumpSampleDataCreator (protocols::abinitio::abscript); JumpSelector (core::select::jump_selector); JumpSelector (protocols::jumping); JumpSelectorCreator (core::select::jump_selector); JumpSelectorFactory (core::select::jump_selector); JumpSelectorLoader (protocols::parser); JumpSelectorLoaderCreator (protocols::parser); JumpSelectorRegistrator (core::select::jump_selector); JumpSetup (protocols::jumping); JumpsFromAllPairings (protocols::jumping); JumpStepWiseSampler (protocols::stepwise::sampler::jump); JumpUpstreamSelector (core::select::residue_selector); JumpUpstreamSelectorCreator (core::select::residue_selector); JumpSelector::JumpWeightDef (protocols::jumping)

K: KarplusFunc (core::scoring::func); KCluster (protocols::toolbox); KClusterData (protocols::toolbox); KClusterElement (protocols::toolbox); KeepLigandContactsRequirement (protocols::sewing::requirements); KeepLigandContactsRequirementCreator (protocols::sewing::requirements); KeepRegionMover (protocols::grafting::simple_movers); KeepRegionMoverCreator (protocols::grafting::simple_movers); KeepSequenceSymmetry (core::pack::task::operation); KeepSequenceSymmetryCreator (core::pack::task::operation); Key (core::pack::annealer); KeyHasher (core::pack::annealer); KicMover (protocols::kinematic_closure); KicMoverCreator (protocols::kinematic_closure); KinaseMover (protocols::enzymatic_movers); KinaseMoverCreator (protocols::enzymatic_movers); KinematicAbinitio (protocols::abinitio); KinematicControl (protocols::abinitio); KinematicMover (protocols::loops::loop_closure::kinematic_closure); KinematicPerturber (protocols::loops::loop_closure::kinematic_closure); KinematicTaskControl (protocols::abinitio); KinematicWrapper (protocols::loops::loop_closure::kinematic_closure); KinFunGroupTK (protocols::kinmatch); KMedoid (protocols::toolbox); KofNConstraint (core::scoring::constraints); KofNConstraintCreator (core::scoring::constraints); KromerMann (core::scoring::electron_density); KromerMann (core::scoring::fiber_diffraction); KRSQuery (protocols::kinmatch)

L: L1ScoringScheme (core::sequence); LabelPoseFromResidueSelectorMover (protocols::fold_from_loops::movers); LabelPoseFromResidueSelectorMoverCreator (protocols::fold_from_loops::movers); LabelResonance (protocols::noesy_assign); LAMBEGO_IO (protocols::frag_picker); LAMBEGO_Similarity (protocols::frag_picker::scores); Lanthionine_Helper (protocols::cyclic_peptide::crosslinker); LargeFragWeight (protocols::topology_broker::weights); LargeNstructJobInputter (protocols::jd2); LargeNstructJobInputterCreator (protocols::jd2); LarvalJob (protocols::jd3); LayerDesignOperation (protocols::flxbb); LayerDesignOperationCreator (protocols::flxbb); LayerSelector (core::select::residue_selector); LayerSelectorCreator (core::select::residue_selector); LazyEdge (core::pack::interaction_graph); LazyInteractionGraph (core::pack::interaction_graph); LazyNode (core::pack::interaction_graph); LazySilentFileJobInputter (protocols::jd2); LazySilentFileJobInputterCreator (protocols::jd2); LazySilentFilePoseInputStream (core::import_pose::pose_stream); LazySortedVector1 (protocols::frag_picker); lbfgs_iteration_data (core::optimization); lDDT_Calculator::lDDT_Cache (core::scoring); lDDT_Calculator (core::scoring); lDDT_Calculator::lDDT_Data (core::scoring); LeapIndex (protocols::loophash); LeeRichards (core::scoring::packstat); LegacyAddStartnodeFragments (protocols::legacy_sewing); LegacyAddStartnodeFragmentsCreator (protocols::legacy_sewing); LegacyAppendAssemblyMover (protocols::legacy_sewing); LegacyAppendAssemblyMoverCreator (protocols::legacy_sewing); LegacyAssemblyConstraintsMover (protocols::legacy_sewing); LegacyAssemblyConstraintsMoverCreator (protocols::legacy_sewing); LegacyAssemblyMover (protocols::legacy_sewing); LegacyAssemblyScoreFunction (protocols::legacy_sewing::scoring); LegacyAssemblyScorer (protocols::legacy_sewing::scoring); LegacyBlosumScorer (protocols::legacy_sewing::scoring); LegacyCalciumMotifScorer (protocols::legacy_sewing::scoring); LegacyClashScorer (protocols::legacy_sewing::scoring); LegacyEnumerateAssemblyMover (protocols::legacy_sewing); LegacyEnumerateAssemblyMoverCreator (protocols::legacy_sewing); LegacyGivenPathAssemblyMover (protocols::legacy_sewing); LegacyGivenPathAssemblyMoverCreator (protocols::legacy_sewing); LegacyGlobalLengthRequirement (protocols::legacy_sewing::sampling::requirements); LegacyGlobalLengthRequirementCreator (protocols::legacy_sewing::sampling::requirements); LegacyGlobalRequirement (protocols::legacy_sewing::sampling::requirements); LegacyGlobalRequirementCreator (protocols::legacy_sewing::sampling::requirements); LegacyGreedyAssemblyMover (protocols::legacy_sewing); LegacyGreedyAssemblyMoverCreator (protocols::legacy_sewing); LegacyInterModelMotifScorer (protocols::legacy_sewing::scoring); LegacyIntraSegmentRequirement (protocols::legacy_sewing::sampling::requirements); LegacyIntraSegmentRequirementCreator (protocols::legacy_sewing::sampling::requirements); LegacyKicSampler (protocols::loop_modeling::samplers); LegacyKicSamplerCreator (protocols::loop_modeling::samplers); LegacyLeapIndex (protocols::loophash); LegacyMonteCarloAssemblyMover (protocols::legacy_sewing); LegacyMonteCarloAssemblyMoverCreator (protocols::legacy_sewing); LegacyMotifScorer (protocols::legacy_sewing::scoring); LegacyPartnerMotifScorer (protocols::legacy_sewing::scoring); LegacyReadNativeRotamersFile (protocols::legacy_sewing); LegacyReadNativeRotamersFileCreator (protocols::legacy_sewing); LegacyReadRepeatNativeRotamersFile (protocols::legacy_sewing); LegacyReadRepeatNativeRotamersFileCreator (protocols::legacy_sewing); LegacyRepeatAssemblyMover (protocols::legacy_sewing); LegacyRepeatAssemblyMoverCreator (protocols::legacy_sewing); LegacyRequirementFactory (protocols::legacy_sewing::sampling::requirements); LegacyRequirementRegistrator (protocols::legacy_sewing::sampling::requirements); LegacyRequirementSet (protocols::legacy_sewing::sampling::requirements); LegacyResidueRetentionRequirement (protocols::legacy_sewing::sampling::requirements); LegacyResidueRetentionRequirementCreator (protocols::legacy_sewing::sampling::requirements); LegacyRootClaim (protocols::topology_broker::claims); LegacySegmentDsspRequirement (protocols::legacy_sewing::sampling::requirements); LegacySegmentDsspRequirementCreator (protocols::legacy_sewing::sampling::requirements); LegacySegmentLengthRequirement (protocols::legacy_sewing::sampling::requirements); LegacySegmentLengthRequirementCreator (protocols::legacy_sewing::sampling::requirements); LeGrandSasa (core::scoring::sasa); LengthChecker (core::environment); LengthEvent (core::conformation::signals); LengthEventCollector (core::pose::datacache); LengthGen (core::fragment::picking_old::vall::gen); LengthInResiduesRequirement (protocols::sewing::requirements); LengthInResiduesRequirementCreator (protocols::sewing::requirements); less_then_match_rmsd (protocols::simple_moves); LHRepulsiveRamp (protocols::antibody); LHRepulsiveRampLegacy (protocols::antibody); LHSnugFitLegacy (protocols::antibody); Librarian (core::fragment::picking_old::concepts); Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary (core::fragment::picking_old::concepts); Library (core::fragment::picking_old::concepts); Library_VallSections (core::fragment::picking_old::concepts); Ligand_info (protocols::ligand_docking); LigandAligner (protocols::ligand_docking::ga_ligand_dock); LigandArea (protocols::ligand_docking); LigandAreaLoader (protocols::ligand_docking); LigandAreaLoaderCreator (protocols::ligand_docking); LigandAssemblyRequirement (protocols::sewing::requirements); LigandAssemblyScorer (protocols::sewing::scoring); LigandBaseProtocol (protocols::ligand_docking); LigandBindingAssemblyMover (protocols::sewing::movers); LigandBindingAssemblyMoverCreator (protocols::sewing::movers); LigandBindingResPlacer (protocols::sewing::hashing); LigandClashRequirement (protocols::sewing::requirements); LigandClashRequirementCreator (protocols::sewing::requirements); LigandConformer (protocols::ligand_docking::ga_ligand_dock); LigandConformer (protocols::toolbox::match_enzdes_util); LigandConformerBuilder (protocols::match::downstream); LigandContact (protocols::sewing::data_storage); LigandCoordInfo (protocols::sewing::hashing); LigandDescription (protocols::sewing::data_storage); LigandDesign (protocols::ligand_docking); LigandDesignCreator (protocols::ligand_docking); LigandDiscoverySearch; LigandDockMain (protocols::ligand_docking); LigandDockProtocol (protocols::ligand_docking); LigandLocationFilter (protocols::drug_design); LigandLocationFilterCreator (protocols::drug_design); LigandMetalContactSelector (protocols::residue_selectors); LigandMetalContactSelectorCreator (protocols::residue_selectors); LigandMotifSearch (protocols::motifs); LigandPropertyScore (protocols::qsar::scoring_grid); LigandPropertyScoreCreator (protocols::qsar::scoring_grid); LigandResidue (protocols::sewing::data_storage); LigandScorer (protocols::sewing::scoring); LigandScorerCreator (protocols::sewing::scoring); LigandSegment (protocols::sewing::data_storage); LigBurialFilter (protocols::enzdes); LigBurialFilterCreator (protocols::enzdes); LigDSasaFilter (protocols::enzdes); LigDSasaFilterCreator (protocols::enzdes); LigInterfaceEnergyFilter (protocols::enzdes); LigInterfaceEnergyFilterCreator (protocols::enzdes); LimitAromaChi2_RotamerSetOperation (protocols::task_operations); LimitAromaChi2Operation (protocols::task_operations); LimitAromaChi2OperationCreator (protocols::task_operations); LimitHitsPerRotamerFilter (protocols::match::output); Line (core::sequence); LinearBranchEnergy (core::energy_methods); LinearBranchEnergyCreator (core::energy_methods); LinearChainbreakEnergy (core::energy_methods); LinearChainbreakEnergyCreator (core::energy_methods); LinearFunc (protocols::moves); LinearMemEdge (core::pack::interaction_graph); LinearMemNode (core::pack::interaction_graph); LinearMemoryInteractionGraph (core::pack::interaction_graph); LinearPenaltyFunction (core::scoring::func); LineMinimizationAlgorithm (core::optimization); LineObject (protocols::forge::remodel); LinkageConformerData (core::chemical::carbohydrates); LinkageConformerMover (protocols::carbohydrates); LinkageConformerMoverCreator (protocols::carbohydrates); LinkerScore (protocols::sic_dock); LinkInformation (core::io); LinkResidues (protocols::task_operations); LinkResiduesCreator (protocols::task_operations); LipidMemGrid (protocols::qsar::scoring_grid); LipidMemGridCreator (protocols::qsar::scoring_grid); LK_Ball_BB_BB_E_Invoker (core::scoring::lkball); LK_Ball_BB_SC_E_Invoker (core::scoring::lkball); LK_Ball_RPE_Invoker (core::scoring::lkball); LK_Ball_SC_SC_E_Invoker (core::scoring::lkball); LK_BallEnergy (core::scoring::lkball); LK_BallEnergyCreator (core::scoring::lkball); LK_BallInvoker (core::scoring::lkball); LK_Dome_RPE_Invoker (core::scoring::lkball); LK_DomeEnergy (core::scoring::lkball); LK_DomeEnergyCreator (core::scoring::lkball); LK_DomeHelper (core::pack::guidance_scoreterms::lk_dome); LK_DomeInvoker (core::scoring::lkball); LK_DomePackEnergy (core::pack::guidance_scoreterms::lk_dome); LK_DomePackEnergyCreator (core::pack::guidance_scoreterms::lk_dome); LK_hack (core::energy_methods); LK_hackCreator (core::energy_methods); LK_PolarNonPolarEnergy (core::energy_methods); LK_PolarNonPolarEnergyCreator (core::energy_methods); LK_SigmoidalFunc (core::energy_methods); LKB_ResidueInfo (core::scoring::lkball); LKB_ResiduesInfo (core::scoring::lkball); LKB_ResPairMinData (core::scoring::lkball); LKBallDatabase (core::scoring::lkball); LKBAtom (core::scoring::lkball::lkbtrie); LKBTrieEvaluator (core::scoring::lkball::lkbtrie); LKD_ResidueInfo (core::scoring::lkball); LKD_ResPairMinData (core::scoring::lkball); LKHBondInfo (core::scoring::hbonds::graph); PCSLigandTransformMover::LMMinPCSDataRef (protocols::nmr::pcs); LnExpression (protocols::pack_daemon); LoadDensityMapMover (protocols::cryst); LoadDensityMapMoverCreator (protocols::cryst); LoadedProbabilitiesMetric (core::simple_metrics::per_residue_metrics); LoadedProbabilitiesMetricCreator (core::simple_metrics::per_residue_metrics); LoadPDBMover (protocols::simple_moves); LoadPDBMoverCreator (protocols::simple_moves); LoadUnboundRotMover (protocols::simple_moves); LoadUnboundRotMoverCreator (protocols::simple_moves); LoadVarSolDistSasaCalculatorMover (protocols::vardist_solaccess); LoadVarSolDistSasaCalculatorMoverCreator (protocols::vardist_solaccess); LocalBackboneMover (protocols::backbone_moves::local_backbone_mover); LocalBackboneMoverCreator (protocols::backbone_moves::local_backbone_mover); LocalCoordinateConstraint (core::scoring::constraints); LocalCoordinateConstraintCreator (core::scoring::constraints); LocalInserter (protocols::loophash); LocalInserter_SimpleMin (protocols::loophash); LocalPosition (core::environment); LocalRelax (protocols::relax); LocalRelaxCreator (protocols::relax); LogFilePerturber (protocols::kinematic_closure::perturbers); LoggedFragmentMover (protocols::simple_moves); LogicalSelector (protocols::pose_selectors); LogicResidueSelector (core::select::residue_selector); LogicResidueSelectorCreator (core::select::residue_selector); LongAxisRotationFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers); LongestContinuousApolarSegmentFilter (protocols::simple_filters); LongestContinuousApolarSegmentFilterCreator (protocols::simple_filters); LongestContinuousPolarSegmentFilter (protocols::simple_filters); LongestContinuousPolarSegmentFilterCreator (protocols::simple_filters); LongRangeTwoBodyEnergy (core::scoring::methods); Loop (core::scoring::loop_graph); Loop (protocols::fldsgn::topology); Loop (protocols::loops); Loop_lt (protocols::loops); LoopAnalyzerFilter (protocols::loops::filters); LoopAnalyzerFilterCreator (protocols::loops::filters); LoopAnalyzerMover (protocols::analysis); LoopAnalyzerMoverCreator (protocols::analysis); LoopAnchorFeatures (protocols::features); LoopAnchorFeaturesCreator (protocols::features); LoopBuilder (protocols::loop_modeling); LoopBuilderCreator (protocols::loop_modeling); LoopBuildMover (protocols::loop_build); LoopCloseEnergy (core::energy_methods); LoopCloseEnergyCreator (core::energy_methods); LoopClosePotentialEvaluator (core::scoring::loop_graph::evaluator); LoopClosure (protocols::loops::loop_closure::ccd); LoopCM (protocols::loops::loop_mover); LoopCMCreator (protocols::loops::loop_mover); LoopComparator (protocols::loop_grower); LoopCycle (core::scoring::loop_graph); LoopFilter (protocols::loop_modeling::utilities); LoopFinder (protocols::protein_interface_design::movers); LoopFinderCreator (protocols::protein_interface_design::movers); LoopFragmentClaimer (protocols::topology_broker); LoopFromFileData (protocols::loops); LoopGraph (core::scoring::loop_graph); LoopGrower (protocols::loop_grower); LoopHashDiversifier (protocols::loophash); LoopHashDiversifierCreator (protocols::loophash); LoopHashLibrary (protocols::loophash); LoopHashLibraryLoader (protocols::loophash); LoopHashLibraryLoaderCreator (protocols::loophash); LoopHashMap (protocols::loophash); LoopHashMoverWrapper (protocols::loophash); LoopHashMoverWrapperCreator (protocols::loophash); LoopHashPerturber (protocols::loop_modeler::perturbers); LoopHashRelaxProtocol (protocols::loophash); LoopHashSampler (protocols::loophash); LoopInfo (protocols::denovo_design::task_operations); LoopJumpFoldCst (protocols::abinitio); LoopLengthChange (protocols::protein_interface_design::movers); LoopLengthChangeCreator (protocols::protein_interface_design::movers); LoopModeler (protocols::loop_modeler); LoopModelerCreator (protocols::loop_modeler); LoopmodelWrapper (protocols::loop_build); LoopmodelWrapperCreator (protocols::loop_build); LoopMover (protocols::loops::loop_mover); LoopMover (protocols::loop_modeling); LoopMover_Perturb_CCD (protocols::loops::loop_mover::perturb); LoopMover_Perturb_CCDCreator (protocols::loops::loop_mover::perturb); LoopMover_Perturb_KIC (protocols::loops::loop_mover::perturb); LoopMover_Perturb_KICCreator (protocols::loops::loop_mover::perturb); LoopMover_Perturb_QuickCCD (protocols::loops::loop_mover::perturb); LoopMover_Perturb_QuickCCD_Moves (protocols::loops::loop_mover::perturb); LoopMover_Perturb_QuickCCD_MovesCreator (protocols::loops::loop_mover::perturb); LoopMover_Perturb_QuickCCDCreator (protocols::loops::loop_mover::perturb); LoopMover_Refine_Backrub (protocols::loops::loop_mover::refine); LoopMover_Refine_BackrubCreator (protocols::loops::loop_mover::refine); LoopMover_Refine_CCD (protocols::loops::loop_mover::refine); LoopMover_Refine_CCDCreator (protocols::loops::loop_mover::refine); LoopMover_Refine_KIC (protocols::loops::loop_mover::refine); LoopMover_Refine_KICCreator (protocols::loops::loop_mover::refine); LoopMover_SlidingWindow (protocols::loop_build); LoopMover_SlidingWindowCreator (protocols::loop_build); LoopMoverFactory (protocols::loops); LoopMoverFromCommandLine (protocols::protein_interface_design::movers); LoopMoverFromCommandLineCreator (protocols::protein_interface_design::movers); LoopMoverGroup (protocols::loop_modeling::utilities); LoopOver (protocols::protein_interface_design::movers); LoopOverCreator (protocols::protein_interface_design::movers); LoopPartialSolution (protocols::loop_grower); LoopPartialSolutionStore (protocols::loop_grower); LoopPivots (protocols::kinematic_closure::pivot_pickers); LoopProtocol (protocols::loop_modeling); LoopProtocolCreator (protocols::loop_modeling); LoopRebuild (protocols); LoopRefine (protocols); LoopRefineInnerCycle (protocols::loops::loop_mover::refine); LoopRefineInnerCycleContainer (protocols::loops::loop_mover::refine); LoopRefineInnerCycleContainerCreator (protocols::loops::loop_mover::refine); LoopRefineInnerCycleFactory (protocols::loops::loop_mover::refine); LoopRelaxMover (protocols::relax::loop); LoopRelaxMoverCreator (protocols::relax::loop); LoopRelaxThreadingMover (protocols::comparative_modeling); LoopRemodel (protocols::protein_interface_design::movers); LoopRemodelCreator (protocols::protein_interface_design::movers); LoopRlxMover (protocols::antibody_legacy); LoopRmsdEvaluator (protocols::simple_filters); Loops (protocols::loops); LoopsDatabaseDefiner (protocols::loops::loops_definers); LoopsDatabaseDefinerCreator (protocols::loops::loops_definers); LoopsDefiner (protocols::loops::loops_definers); LoopsDefinerCreator (protocols::loops::loops_definers); LoopsDefinerFactory (protocols::loops::loops_definers); LoopsDefinerLoader (protocols::loops::loops_definers); LoopsDefinerLoaderCreator (protocols::loops::loops_definers); LoopsDefinerRegistrator (protocols::loops::loops_definers); LoopsExplicitDefiner (protocols::loops::loops_definers); LoopsExplicitDefinerCreator (protocols::loops::loops_definers); LoopsFileData (protocols::loops); LoopsFileDefiner (protocols::loops::loops_definers); LoopsFileDefinerCreator (protocols::loops::loops_definers); LoopsFileIO (protocols::loops); LoopsFileLoader (protocols::loops); LoopsFileLoaderCreator (protocols::loops); LoopsStringDefiner (protocols::loops::loops_definers); LoopsStringDefinerCreator (protocols::loops::loops_definers); LowMemEdge (utility::graph); LowMemGraph (utility::graph); LowMemNode (utility::graph); LR_AtomData (core::scoring::packstat); LR_MP_AtomData (core::scoring::packstat); LREnergyContainer (core::scoring); LRmsdFilter (protocols::protein_interface_design::filters); LRmsdFilterCreator (protocols::protein_interface_design::filters); LSMSearchPattern (protocols::hotspot_hashing)

M: MainchainScoreTable (core::chemical::mainchain_potential); MainchainTorsionReporter (core::pack::dunbrack); MainChainTorsionSet (protocols::stepwise::modeler::protein); MakeABEGO_SS_Score (protocols::frag_picker::scores); MakeAmbigCSScore (protocols::frag_picker::scores); MakeAsymmetricStructureDataMover (protocols::denovo_design::movers); MakeAsymmetricStructureDataMoverCreator (protocols::denovo_design::movers); MakeAtomPairConstraintsScore (protocols::frag_picker::scores); MakeBFactor (protocols::frag_picker::scores); MakeBundle (protocols::helical_bundle); MakeBundleCreator (protocols::helical_bundle); MakeBundleHelix (protocols::helical_bundle); MakeBundleHelixCreator (protocols::helical_bundle); MakeCanonicalHelix (protocols::membrane::benchmark); MakeCanonicalHelixCreator (protocols::membrane::benchmark); MakeConstScore (protocols::frag_picker::scores); MakeCSScore (protocols::frag_picker::scores); MakeDihedralConstraintsScore (protocols::frag_picker::scores); MakeDisulfideDistance (protocols::frag_picker::scores); MakeDisulfideIdentity (protocols::frag_picker::scores); MakeFragmentAllAtomCrmsd (protocols::frag_picker::scores); MakeFragmentChunkCrms (protocols::frag_picker::scores); MakeFragmentCrmsd (protocols::frag_picker::scores); MakeFragmentCrmsdResDepth (protocols::frag_picker::scores); MakeFragmentDME (protocols::frag_picker::scores); MakeFragmentScoringMethod (protocols::frag_picker::scores); MakeGunnCostScore (protocols::frag_picker::scores); MakeHydrophobicityProfileSimilarity (protocols::frag_picker::scores); MakeHydrophobicitySimilarity (protocols::frag_picker::scores); MakeInterbondAngleScore (protocols::frag_picker::scores); MakeJCoupling (protocols::frag_picker::scores); MakeJunctionsMover (protocols::pose_creation); MakeJunctionsMoverCreator (protocols::pose_creation); MakeLAMBEGO_Similarity (protocols::frag_picker::scores); MakeLatticeMover (protocols::cryst); MakeLatticeMoverCreator (protocols::cryst); MakeLayerMover (protocols::cryst); MakeLayerMoverCreator (protocols::cryst); MakeMidPhiOut (protocols::frag_picker::scores); MakeMidPsiOut (protocols::frag_picker::scores); MakePartialSecondarySimilarity (protocols::frag_picker::scores); MakePCS_FragDistance (protocols::frag_picker::scores); MakePhi (protocols::frag_picker::scores); MakePhiPsiRmsd (protocols::frag_picker::scores); MakePhiPsiSquareWell (protocols::frag_picker::scores); MakePolyXMover (protocols::pose_creation); MakePolyXMoverCreator (protocols::pose_creation); MakeProfileScore (protocols::frag_picker::scores); MakeProfileScoreBlosum62 (protocols::frag_picker::scores); MakeProfileScoreDistWeight (protocols::frag_picker::scores); MakeProfileScoreL1 (protocols::frag_picker::scores); MakeProfileScoreStructL1 (protocols::frag_picker::scores); MakeProfileScoreSubMatrix (protocols::frag_picker::scores); MakeProlinePhiScore (protocols::frag_picker::scores); MakePsi (protocols::frag_picker::scores); MakeRamaScore (protocols::frag_picker::scores); MakeRDCScore (protocols::frag_picker::scores); MakeRotLibJob (protocols::make_rot_lib); MakeRotLibJobInputter (protocols::make_rot_lib); MakeRotLibJobInputterCreator (protocols::make_rot_lib); MakeRotLibMover (protocols::make_rot_lib); MakeRotLibOptionsData (protocols::make_rot_lib); MakeScoreEValuator (protocols::frag_picker::scores); MakeSecondaryIdentity (protocols::frag_picker::scores); MakeSecondarySimilarity (protocols::frag_picker::scores); MakeSequenceIdentity (protocols::frag_picker::scores); MakeSolventAccessibility (protocols::frag_picker::scores); MakeStarTopologyMover (protocols::rbsegment_relax); MakeStarTopologyMoverCreator (protocols::rbsegment_relax); MakeTalosSSSimilarity (protocols::frag_picker::scores); MakeTorsionBinSimilarity (protocols::frag_picker::scores); MapCacheUnit (core::fragment); MapHotspot (protocols::protein_interface_design::movers); MapHotspotCreator (protocols::protein_interface_design::movers); AtomPairConstraintGenerator::MappedAtom (protocols::constraint_generator); MasterFilter (protocols::constel); match_dspos1 (protocols::match); match_lite_equals (protocols::match); match_lite_hasher (protocols::match); MatchCollisionFilter (protocols::match::output); MatchConsolidator (protocols::match::output); MatchConstraintFileInfo (protocols::toolbox::match_enzdes_util); MatchConstraintFileInfoList (protocols::toolbox::match_enzdes_util); MatchCounter (protocols::match); Matcher (protocols::match); MatcherMover (protocols::match); MatcherMoverCreator (protocols::match); MatcherOutputStats (protocols::match); MatcherTask (protocols::match); MatchEvaluator (protocols::match::output); MatchFilter (protocols::match::output); MatchGrafter (protocols::metal_interface); MatchGrouper (protocols::match::output); MatchOutputter (protocols::match::output); MatchOutputTracker (protocols::match); MatchPositionModifier (protocols::match); MatchProcessor (protocols::match::output); MatchResidues (protocols::fldsgn); MatchResiduesMover (protocols::fldsgn); MatchResiduesMoverCreator (protocols::fldsgn); MatchScoreWriter (protocols::match::output); MatDesGreedyOptMutationMover (protocols::matdes); MatDesGreedyOptMutationMoverCreator (protocols::matdes); MatDesPointMutationCalculator (protocols::matdes); MatrixScoringScheme (core::sequence); MaxSeqSepConstraintSet (protocols::constraints_additional); MC_Any (protocols::recces::sampler); MC_Comb (protocols::recces::sampler); MC_Loop (protocols::recces::sampler); MC_OneTorsion (protocols::recces::sampler); MC_RNA_KIC_Sampler (protocols::recces::sampler::rna); MC_RNA_MultiSuite (protocols::recces::sampler::rna); MC_RNA_OneJump (protocols::recces::sampler::rna); MC_RNA_Sugar (protocols::recces::sampler::rna); MC_RNA_Suite (protocols::recces::sampler::rna); MC_Sampler (protocols::recces::sampler); MCAligner (core::sequence); MCSAligner (protocols::ligand_docking::ga_ligand_dock); MCSAlignerOptions (protocols::ligand_docking::ga_ligand_dock); MCShowMover (protocols::moves); MD_Angle (protocols::cartesian); MD_Bond (protocols::cartesian); MD_HarmonicDihedral (protocols::cartesian); MDBase (protocols::md); MDscheduleData (protocols::md); Mean (protocols::pack_daemon); MeanField (protocols::mean_field); MeanFieldFactory (protocols::mean_field); MedalExchangeMover (protocols::medal); MedalMover (protocols::medal); MembAccesResidueLipophilicityFilter (protocols::simple_filters); MembAccesResidueLipophilicityFilterCreator (protocols::simple_filters); MembEtable (core::scoring::etable); Membrane_FAEmbed (core::scoring); Membrane_FAPotential (core::scoring); MembraneAbinitio (protocols::abinitio); MembraneCbetaEnergy (core::energy_methods); MembraneCbetaEnergyCreator (core::energy_methods); MembraneCenPairEnergy (core::energy_methods); MembraneCenPairEnergyCreator (core::energy_methods); MembraneCenterPerturbationMover (protocols::rigid); MembraneData (core::scoring::membrane); MembraneEmbed (core::scoring); MembraneEnergyLandscapeSampler (protocols::membrane_benchmark); MembraneEnergyLandscapeSamplerCreator (protocols::membrane_benchmark); MembraneEnvEnergy (core::energy_methods); MembraneEnvEnergyCreator (core::energy_methods); MembraneEnvPenalties (core::energy_methods); MembraneEnvPenaltiesCreator (core::energy_methods); MembraneEnvSmoothEnergy (core::energy_methods); MembraneEnvSmoothEnergyCreator (core::energy_methods); MembraneGeometry (core::conformation::membrane); MembraneInfo (core::conformation::membrane); MembraneJump (protocols::jumping); MembraneLipo (core::energy_methods); MembraneLipoCreator (core::energy_methods); MembraneNormalPerturbationMover (protocols::rigid); MembranePositionFromTopologyMover (protocols::membrane); MembranePositionFromTopologyMoverCreator (protocols::membrane); MembranePotential (core::scoring); MembraneSpanConstraint (core::scoring::constraints); MembraneSpanConstraintGenerator (protocols::constraint_generator); MembraneSpanConstraintGeneratorCreator (protocols::constraint_generator); MembraneSpanTermZConstraint (core::scoring::constraints); MembraneTopology (core::scoring); MembraneTopology (protocols::simple_moves); MembraneTopologyClaimer (protocols::topology_broker); MembraneTopologyCreator (protocols::simple_moves); ClosureProblem::Memento (protocols::kinematic_closure); MEnvAtomParams (protocols::membrane::scoring); MEnvElectroAtomParams (protocols::membrane::scoring); MergeAndSplitBehaviorManager (core::chemical::io); MergePDBatOverlapMover (protocols::pose_creation); MergePDBatOverlapMoverCreator (protocols::pose_creation); MergePDBMover (protocols::pose_creation); MergePDBMoverCreator (protocols::pose_creation); Metal_HelperBase (protocols::cyclic_peptide::crosslinker); MetalContactsConstraintGenerator (protocols::constraint_generator); MetalContactsConstraintGeneratorCreator (protocols::constraint_generator); MetalloClaimer (protocols::topology_broker); MetalSiteResidue (protocols::metal_interface); Metapatch (core::chemical); MetapatchEnumeration (protocols::residue_optimization); MetaPoseEvaluator (protocols::evaluation); MetaPoseInputStream (core::import_pose::pose_stream); MethodParams (protocols::mpi_refinement); MethylNameLibrary (protocols::noesy_assign); MethylNames (protocols::noesy_assign); MetricCalculatorFitnessFunction (protocols::multistate_design); MetricData (protocols::features); MetricKey (core::simple_metrics); MetricRecorder (protocols::canonical_sampling); MetricRecorderCreator (protocols::canonical_sampling); MetricValueGetter (protocols::pose_metric_calculators); MetropolisHastingsMover (protocols::canonical_sampling); MetropolisHastingsMoverCreator (protocols::canonical_sampling); MgEnergy (core::energy_methods); MgEnergyCreator (core::energy_methods); MgHydrater (protocols::magnesium); MgKnowledgeBasedPotential (core::scoring::magnesium); MgMinimizer (protocols::magnesium); MgMonteCarlo (protocols::magnesium); MgOrbitalFrameFinder (protocols::magnesium); MgScanner (protocols::magnesium); MgWaterHydrogenPacker (protocols::magnesium); MHCEpitopeConstraint (core::scoring::mhc_epitope_energy); MHCEpitopeEnergy (core::energy_methods); MHCEpitopeEnergyCreator (core::energy_methods); MHCEpitopeEnergySetup (core::scoring::mhc_epitope_energy); MHCEpitopePredictor (core::scoring::mhc_epitope_energy); MHCEpitopePredictorExternal (core::scoring::mhc_epitope_energy); MHCEpitopePredictorMatrix (core::scoring::mhc_epitope_energy); MHCEpitopePredictorPreLoaded (core::scoring::mhc_epitope_energy); MHCEpitopePredictorSVM (core::scoring::mhc_epitope_energy); MidPhiOut (protocols::frag_picker::scores); MidPsiOut (protocols::frag_picker::scores); MIFSTProbabilitiesMetric (protocols::inverse_folding); MIFSTProbabilitiesMetricCreator (protocols::inverse_folding); MinDebug (core::optimization::symmetry); MinimalFragSet (core::fragment); MinimalFragSetIterator_ (core::fragment); MinimalistFlexbbEdge (protocols::flexpack::interaction_graph); MinimalistFlexbbInteractionGraph (protocols::flexpack::interaction_graph); MinimalistFlexbbNode (protocols::flexpack::interaction_graph); MinimalRotamer (protocols::minimization_packing); MinimizationEdge (core::scoring); MinimizationGraph (core::scoring); MinimizationNode (core::scoring); MinimizationRefiner (protocols::loop_modeling::refiners); MinimizationRefinerCreator (protocols::loop_modeling::refiners); MinimizeBackbone (protocols::ligand_docking); MinimizeBackboneCreator (protocols::ligand_docking); MinimizeLigand (protocols::ligand_docking); MinimizePoseIntoDensityOptions (protocols::electron_density); Minimizer (core::optimization); MinimizerMap (core::optimization); MinimizerMapBase (core::kinematics); MinimizerOptions (core::optimization); MinimizeStoredRBConfs (protocols::enzdes); MinimumInterAlphaDistanceMetric (protocols::pose_sewing::simple_metrics); MinimumInterAlphaDistanceMetricCreator (protocols::pose_sewing::simple_metrics); MiniPose (core::pose); MiniRelax (protocols::relax); MinMover (protocols::minimization_packing); MinMoverCreator (protocols::minimization_packing); MinMultiHarmonicFunc (core::scoring::func); MinPackMover (protocols::minimization_packing); MinPackMoverCreator (protocols::minimization_packing); MinScoreScoreFunction (core::scoring); MirrorSymmetricConformation (core::conformation::symmetry); missing_fraction_sorter_biggest_first (protocols::frag_picker::quota); MissingDensityToJumpMover (protocols::simple_moves); MissingEnergy (core::energy_methods); MissingEnergyCreator (core::energy_methods); MixedMonteCarlo (protocols::moves); MixtureFunc (core::scoring::func); MMAtomType (core::chemical); MMAtomTypeSet (core::chemical); MMBondAngleEnergy (core::scoring::methods); MMBondAngleEnergyCreator (core::scoring::methods); MMBondAngleLibrary (core::scoring::mm); MMBondAngleResidueTypeParam (core::scoring::mm); MMBondAngleResidueTypeParamSet (core::scoring::mm); MMBondAngleScore (core::scoring::mm); MMBondLengthEnergy (core::scoring::methods); MMBondLengthEnergyCreator (core::scoring::methods); MMBondLengthLibrary (core::scoring::mm); MMBondLengthScore (core::scoring::mm); mmCIFJobOutputter (protocols::jd2); mmCIFJobOutputterCreator (protocols::jd2); mmCIFParser (core::chemical::mmCIF); MMEnergyTableAtom (core::scoring::mm::mmtrie); MoveMapFactory::MMJumpAction (core::select::movemap); MMLJEnergyInter (core::scoring::methods); MMLJEnergyInterCreator (core::scoring::methods); MMLJEnergyIntra (core::scoring::methods); MMLJEnergyIntraCreator (core::scoring::methods); MMLJEnergyTable (core::scoring::mm); MMLJLibrary (core::scoring::mm); MMLJScore (core::scoring::mm); MoveMapFactory::MMResAction (core::select::movemap); MoveMapFactory::MMResIndexAction (core::select::movemap); mmtfJobOutputter (protocols::jd2); mmtfJobOutputterCreator (protocols::jd2); mmTFPoseOutputSpecification (protocols::jd3::pose_outputters); mmTFPoseOutputter (protocols::jd3::pose_outputters); mmTFPoseOutputterCreator (protocols::jd3::pose_outputters); MMTorsionEnergy (core::scoring::methods); MMTorsionEnergyCreator (core::scoring::methods); MMTorsionLibrary (core::scoring::mm); MMTorsionScore (core::scoring::mm); Model (protocols::legacy_sewing); ModelConstIterator (protocols::legacy_sewing); ModelFeatures (protocols::features); ModelFeaturesCreator (protocols::features); ModelFileReader (protocols::sewing::hashing); ModelIterator (protocols::legacy_sewing); ModelNode (protocols::legacy_sewing); ModifiedResidueInformation (core::io); ModifyAnnealer (protocols::task_operations); ModifyAnnealerCreator (protocols::task_operations); ModifyStoredRBConfs (protocols::enzdes); ModifyVariantTypeMover (protocols::simple_moves); ModifyVariantTypeMoverCreator (protocols::simple_moves); ModuleType1 (core::kinematics::jacobian); MolarMassFilter (protocols::ligand_docking); MolarMassFilterCreator (protocols::ligand_docking); MolecularDynamics (protocols::cartesian); MolecularMassFilter (protocols::ligand_docking); MolecularMassFilterCreator (protocols::ligand_docking); MolecularSurfaceCalculator (core::scoring::sc); MolecularWeightNormalization (protocols::qsar::scoring_grid); MoleculeSubstitution (protocols::drug_design); MolFileIOAtom (core::chemical::sdf); MolFileIOBond (core::chemical::sdf); MolFileIOMolecule (core::chemical::sdf); MolFileIOReader (core::chemical::sdf); MolWriter (core::chemical::sdf); MonteCarlo (protocols::moves); MonteCarloExceptionConverge (protocols::moves); MonteCarloInterface (protocols::monte_carlo); MonteCarloLoader (protocols::parser); MonteCarloLoaderCreator (protocols::parser); MonteCarloRecover (protocols::monte_carlo); MonteCarloRecoverCreator (protocols::monte_carlo); MonteCarloReset (protocols::monte_carlo); MonteCarloResetCreator (protocols::monte_carlo); MonteCarloTest (protocols::monte_carlo); MonteCarloTestCreator (protocols::monte_carlo); MonteCarloUtil (protocols::moves); Motif (protocols::motifs); motif2scaffold_data (protocols::motif_grafting::movers); motif2scaffold_indexes (protocols::motif_grafting::movers); MotifArchitect (protocols::denovo_design::architects); MotifArchitectCreator (protocols::denovo_design::architects); MotifDnaPacker (protocols::motifs); MotifDnaPackerCreator (protocols::motifs); MotifDockEnergy (core::energy_methods); MotifDockEnergyCreator (core::energy_methods); MotifGraftCreator (protocols::motif_grafting::movers); MotifGraftMover (protocols::motif_grafting::movers); MotifHash (core::scoring::motif); MotifHashManager (core::scoring::motif); MotifHashRigidScore (protocols::sic_dock::scores); MotifHit (core::scoring::motif); MotifHit (protocols::motifs); MotifHits (core::scoring::motif); MotifHitsRotamersOperation (protocols::matdes); MotifHitStats (core::scoring::motif); MotifLibrary (protocols::motifs); MotifMatch (protocols::motif_grafting::movers); MotifScoreFilter (protocols::simple_filters); MotifScoreFilterCreator (protocols::simple_filters); MotifScorer (protocols::sewing::scoring); MotifScorerCreator (protocols::sewing::scoring); MotifSearch (protocols::motifs); MoveBeforeFilter (protocols::filters); MoveBeforeFilterCreator (protocols::filters); MoveMap (core::kinematics); MoveMapBuilder (protocols::ligand_docking); MoveMapBuilderLoader (protocols::ligand_docking); MoveMapBuilderLoaderCreator (protocols::ligand_docking); MoveMapFactory (core::select::movemap); MoveMapFactoryLoader (protocols::parser); MoveMapFactoryLoaderCreator (protocols::parser); MoveMapFactoryToNamedMoveMapMover (protocols::fold_from_loops::movers); MoveMapFactoryToNamedMoveMapMoverCreator (protocols::fold_from_loops::movers); MoveMapMover (protocols::moves); MovePoseToMembraneCenterMover (protocols::rigid); Mover (protocols::moves); Mover_LoopHashRefine (protocols::loophash); mover_or_filter (protocols::multistage_rosetta_scripts); MoverAndChunkLibraryJob (protocols::jd3::chunk_library); MoverApplyingMover (protocols::moves); MoverContainer (protocols::moves); MoverCreator (protocols::moves); MoverFactory (protocols::moves); MoverForPoseList (protocols::moves); MoverJob (protocols::jd3::jobs); MoverList (protocols::wum); MoverRegistrator (protocols::moves); MoverStatistics (protocols::moves); MPCbetaEnergy (core::energy_methods); MPCbetaEnergyCreator (core::energy_methods); MPDockingMover (protocols::docking::membrane); MPDockingMoverCreator (protocols::docking::membrane); MPDockingSetupMover (protocols::docking::membrane); MPDockingSetupMoverCreator (protocols::docking::membrane); MPEnvEnergy (core::energy_methods); MPEnvEnergyCreator (core::energy_methods); MPFastRelaxMover (protocols::relax::membrane); MPFastRelaxMoverCreator (protocols::relax::membrane); MPFindInterfaceMover (protocols::docking::membrane); MPFindInterfaceMoverCreator (protocols::docking::membrane); MPHelicalityEnergy (core::energy_methods); MPHelicalityEnergyCreator (core::energy_methods); MPI_LoopHashRefine (protocols::loophash); MPI_LoopHashRefine_Emperor (protocols::loophash); MPI_LoopHashRefine_Master (protocols::loophash); MPI_Refine_Emperor (protocols::mpi_refinement); MPI_Refine_Master (protocols::mpi_refinement); MPI_Refinement (protocols::mpi_refinement); MPI_WorkUnitManager (protocols::wum); MPI_WorkUnitManager_Slave (protocols::wum); MPIArchiveJobDistributor (protocols::jd2::archive); MpiFileBuffer (protocols::jd2); MPIFileBufJobDistributor (protocols::jd2); MPIMultiCommJobDistributor (protocols::jd2); MPIMultistateFitnessFunction (protocols::pack_daemon); MPIWorkPartitionJobDistributor (protocols::jd2); MPIWorkPoolJobDistributor (protocols::jd2); MPLipidAccessibility (protocols::membrane); MPLipidAccessibilityCreator (protocols::membrane); MPMutateRelaxMover (protocols::membrane); MPMutateRelaxMoverCreator (protocols::membrane); MPNonHelixPenalty (core::scoring::membrane); MPNonHelixPenaltyCreator (core::scoring::membrane); MPPairEnergy (core::energy_methods); MPPairEnergyCreator (core::energy_methods); MPQuickRelaxMover (protocols::membrane); MPQuickRelaxMoverCreator (protocols::membrane); MPRangeRelaxMover (protocols::relax::membrane); MPResidueLipophilicityEnergy (core::energy_methods); MPResidueLipophilicityEnergyCreator (core::energy_methods); MPSpanAngleEnergy (core::energy_methods); MPSpanAngleEnergyCreator (core::energy_methods); MPSpanAngleFilter (protocols::simple_filters); MPSpanAngleFilterCreator (protocols::simple_filters); MPSpanInsertionEnergy (core::energy_methods); MPSpanInsertionEnergyCreator (core::energy_methods); MPSymDockMover (protocols::symmetric_docking::membrane); MPSymDockMoverCreator (protocols::symmetric_docking::membrane); MPTerminiPenalty (core::scoring::membrane); MPTerminiPenaltyCreator (core::scoring::membrane); MPTMProjPenalty (core::scoring::membrane); MPTMProjPenaltyCreator (core::scoring::membrane); MRMover (protocols::hybridization); MRSJob (protocols::multistage_rosetta_scripts); MRSJobQueen (protocols::multistage_rosetta_scripts); MRSJobQueenChecker (protocols::multistage_rosetta_scripts); MRSJobSummary (protocols::multistage_rosetta_scripts); MSDMover (protocols::recon_design); MSDMoverCreator (protocols::recon_design); MulliganPNearEvaluator (protocols::toolbox); MultiConstraint (core::scoring::constraints); MultiConstraintCreator (core::scoring::constraints); MultiCoolAnnealer (core::pack::annealer); Multifunc (core::optimization); MultiObjective (protocols::mpi_refinement); MultiPhosphateSampler (protocols::stepwise::modeler::rna::phosphate); MultipleDomainMover (protocols::rna::denovo::coarse); MultipleOutputSpecification (protocols::jd3::output); MultipleOutputter (protocols::jd3::output); MultipleOutputWrapper (protocols::rosetta_scripts); MultipleOutputWrapperCreator (protocols::rosetta_scripts); MultiplePoseMover (protocols::rosetta_scripts); MultiplePoseMoverCreator (protocols::rosetta_scripts); MultipleSigmoids (protocols::calc_taskop_filters); MultipleSigmoidsFilterCreator (protocols::calc_taskop_filters); MultiplexedAnnealableGraph (core::pack::interaction_graph); MultipoleElecEnergy (core::energy_methods); MultipoleElecEnergyCreator (core::energy_methods); MultipoleElecPoseInfo (core::scoring); MultipoleElecPotential (core::scoring); MultipoleElecResidueInfo (core::scoring); MultipoleElecResPairMinData (core::energy_methods); MultipoleElecRotamerSetInfo (core::scoring); MultipoleParameter (core::scoring); MultiProbePerSphereAccumulator (core::scoring::packstat); MultiProbePoseAccumulator (core::scoring::packstat); MultistateAggregateFunction (protocols::pack_daemon); MultiStateAggregateFunction (protocols::multistate_design); MultiStateEntity (protocols::multistate_design); MultiStateFitnessFunction (protocols::multistate_design); MultistateFitnessFunction (protocols::pack_daemon); MultiStatePacker (protocols::multistate_design); MultiTemperatureTrialCounter (protocols::canonical_sampling); MultiThreadingJob (protocols::jd2); MultiThreadingMover (protocols::comparative_modeling); MutableChiRecord (core::chemical); MutableICoorRecord (core::chemical); MutableResidueConnection (core::chemical); MutableResidueType (core::chemical); Mutant (protocols::pmut_scan); MutantPosition (protocols::antibody::design); Mutate1Randomizer (protocols::genetic_algorithm); MutateFrameworkForCluster (protocols::antibody::design); MutateFrameworkForClusterCreator (protocols::antibody::design); MutateResidue (protocols::simple_moves); MutateResidueCreator (protocols::simple_moves); MutationData (protocols::pmut_scan); MutationSetDesignOperation (protocols::task_operations); MutationsFilter (protocols::simple_filters); MutationsFilterCreator (protocols::simple_filters); Mutator (protocols::ligand_evolution); SecretionOptimizationMover::mutt (protocols::protein_interface_design::movers); SecretionPredictionFilter::mutt (protocols::simple_filters); MyAtom (protocols::fldsgn); MyHash (core::scoring::motif); MyPred (core::scoring::motif); MyTemplatePointerHash1 (core::pack::guidance_scoreterms::sap); MyWaterHolder (core::pack::guidance_scoreterms::lk_dome)

N: NamedAngleConstraint (core::scoring::constraints); NamedAngleConstraintCreator (core::scoring::constraints); NamedAtomID (core::id); NamedAtomID_Map (core::id); NamedAtomID_Map_NamedAtomID (core::id); NamedAtomPairConstraint (core::scoring::constraints); NamedAtomPairConstraintCreator (protocols::constraints_additional); NamedAtomPairConstraintCreator (core::scoring::constraints); NamedDihedralConstraint (core::scoring::constraints); NamedSegmentSelector (protocols::denovo_design::residue_selectors); NamedSegmentSelectorCreator (protocols::denovo_design::residue_selectors); NamedSolution (protocols::denovo_design::components); NamedSolutions (protocols::denovo_design::components); NamedStubID (core::id); NATAA (core::pack::task); NatbiasHelicesSheetPotential (protocols::fldsgn::potentials::sspot); NatbiasHelixPairPotential (protocols::fldsgn::potentials::sspot); NatbiasSecondaryStructureEnergy (protocols::fldsgn::potentials::sspot); NatbiasSecondaryStructureEnergyCreator (protocols::fldsgn::potentials::sspot); NatbiasStrandPairPotential (protocols::fldsgn::potentials::sspot); NativeAntibodySeq (protocols::antibody::design); NativeEvaluatorCreator (protocols::simple_filters); NativeSelector (protocols::residue_selectors); NativeSelectorCreator (protocols::residue_selectors); NATRO (core::pack::task); NbrAtomCreator (core::chemical); NbrRadiusCreator (core::chemical); NCAADefaultPackerPalette (core::pack::palette); NCAADefaultPackerPaletteCreator (core::pack::palette); NCAARotamerLibrarySpecification (core::chemical::rotamers); NCAARotamerLibrarySpecificationCreator (core::chemical::rotamers); NCAARotLibBBTorsions (core::chemical); NCAARotlibBBTorsionsCreator (core::chemical); NCAARotLibNumRotamerBins (core::chemical); NCAARotlibNumRotamerBinsCreator (core::chemical); NCAARotLibPath (core::chemical); NCAARotlibPathCreator (core::chemical); NCaCaC_Dihedral_Func (core::scoring::disulfides); NcbbDockDesignProtocol (protocols::ncbb); NcbbDockDesignProtocolCreator (protocols::ncbb); NChiFilter (protocols::drug_design); NChiFilterCreator (protocols::drug_design); NcontactsCalculator (protocols::fldsgn); NcontactsFilter (protocols::fldsgn::filters); NcontactsFilterCreator (protocols::fldsgn::filters); NCSResMapping (protocols::symmetry); NearNativeLoopCloser (protocols::pose_length_moves); NearNativeLoopCloserCreator (protocols::pose_length_moves); NeighborDependentTabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); NeighborDependentTorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); Neighborhood (protocols::neighbor); NeighborhoodByDistanceCalculator (protocols::pose_metric_calculators); NeighborhoodResidueSelector (core::select::residue_selector); NeighborhoodResidueSelectorCreator (core::select::residue_selector); NeighborList (core::scoring); NeighborListData (core::scoring::methods); NeighborsByDistanceCalculator (protocols::pose_metric_calculators); NeighborTypeFilter (protocols::simple_filters); NeighborTypeFilterCreator (protocols::simple_filters); NeighTeller (protocols::constel); NelderMeadSimplex (core::optimization); NestedEnergyTermDDGMutationOptEData (protocols::optimize_weights); NestedEnergyTermPNatAAOptEPositionData (protocols::optimize_weights); NetChargeConstraint (core::scoring::netcharge_energy); NetChargeEnergy (core::energy_methods); NetChargeEnergyCreator (core::energy_methods); NetChargeEnergySetup (core::scoring::netcharge_energy); NetChargeFilter (protocols::simple_filters); NetChargeFilterCreator (protocols::simple_filters); NetworkQueue (protocols::network); NetworkState (protocols::hbnet); NetworkStateScoreComparator (protocols::hbnet); nmer_svm_res_data (protocols::simple_filters); NMerPSSMEnergy (core::scoring::methods); NMerPSSMEnergyCreator (core::scoring::methods); NMerPSSMEnergyFilter (protocols::simple_filters); NMerPSSMEnergyFilterCreator (protocols::simple_filters); NMerRefEnergy (core::scoring::methods); NMerRefEnergyCreator (core::scoring::methods); NMerSVMEnergy (core::scoring::methods); NMerSVMEnergyCreator (core::scoring::methods); NMerSVMEnergyFilter (protocols::simple_filters); NMerSVMEnergyFilterCreator (protocols::simple_filters); NMRDataFactory (core::scoring::nmr); NMRDummySpinlabelAtom (core::scoring::nmr); NMRDummySpinlabelConformer (core::scoring::nmr); NMRDummySpinlabelEnsemble (core::scoring::nmr); NMRDummySpinlabelVoxelGrid (core::scoring::nmr); NMRGridSearch (core::scoring::nmr); NMRSpinlabel (core::scoring::nmr); NMRTensor (core::scoring::nmr); NO_ADDUCTS (core::pack::task); PDBPoseMap::no_segID_comp (core::pose); FoldTreeSketch::Node (core::environment); Node (core::kinematics); Node (protocols::toolbox); Node (utility::graph); NodeBase (core::pack::interaction_graph); NodeManager (protocols::jd3::dag_node_managers); NodeManagerStorageMatrix (protocols::jd3::dag_node_managers); NoDesignPackerPalette (core::pack::palette); NoDesignPackerPaletteCreator (core::pack::palette); NoesyModule (protocols::noesy_assign); NoFailDataMap (protocols::multistage_rosetta_scripts); NomenclatureManager (core::io); NonContinuousFrame (core::fragment); NonlocalContactsCalculator (protocols::pose_metric_calculators); NonlocalFrags (protocols::frag_picker::nonlocal); NonlocalPair (protocols::frag_picker::nonlocal); NonPlaidFingerprint (protocols::pockets); NonResidueTypeConstraint (core::scoring::constraints); NonSequentialNeighborsFilter (protocols::simple_filters); NonSequentialNeighborsFilterCreator (protocols::simple_filters); NonTerminalStartingSegmentRequirement (protocols::sewing::requirements); NonTerminalStartingSegmentRequirementCreator (protocols::sewing::requirements); NoOutputJobOutputter (protocols::jd2); NoOutputJobOutputterCreator (protocols::jd2); NoPoseXYX_Func (protocols::sic_dock); NoRepackDisulfides (core::pack::task::operation); NoRepackDisulfidesCreator (core::pack::task::operation); NoResFilter (core::pack::task::operation); NoResFilterCreator (core::pack::task::operation); NormalizedEvaluatedArchive (protocols::jd2::archive); NormalMode (protocols::normalmode); NormalModeMinimizer (protocols::normalmode); NormalModeMinimizerCreator (protocols::normalmode); NormalModeMultifunc (protocols::normalmode); NormalModeRelaxMover (protocols::normalmode); NormalModeRelaxMoverCreator (protocols::normalmode); NOTAA (core::pack::task); NotJumpSelector (core::select::jump_selector); NotJumpSelectorCreator (core::select::jump_selector); NotResidueSelector (core::select::residue_selector); NotResidueSelectorCreator (core::select::residue_selector); NPDHBond (core::pack::interaction_graph); NPDHBondBackgroundEdge (core::pack::interaction_graph); NPDHBondBackgroundNode (core::pack::interaction_graph); NPDHBondEdge (core::pack::interaction_graph); NPDHBondEnergy (core::energy_methods); NPDHBondEnergyCreator (core::energy_methods); NPDHBondInteractionGraph (core::pack::interaction_graph); NPDHBondNode (core::pack::interaction_graph); NPDHBondSet (core::scoring::hbonds); NPDHBSimpleEdge (core::pack::interaction_graph); NPDHBSimpleInteractionGraph (core::pack::interaction_graph); NPDHBSimpleNode (core::pack::interaction_graph); NPDPropCalculator (protocols::pack_daemon); NPDPropCalculatorCreator (protocols::pack_daemon); NTerminalAcetyltransferaseMover (protocols::enzymatic_movers); NTerminalAcetyltransferaseMoverCreator (protocols::enzymatic_movers); NtoCConstraintGenerator (protocols::forge::constraints); NtoCConstraintGeneratorCreator (protocols::forge::constraints); Nub (protocols::fold_from_loops::utils); NubInitioLoopClosureMover (protocols::fold_from_loops::movers); NubInitioLoopClosureMoverCreator (protocols::fold_from_loops::movers); NubInitioMover (protocols::fold_from_loops); NubInitioMoverCreator (protocols::fold_from_loops); NubSegment (protocols::fold_from_loops::utils); NucleotideMutation (protocols::evolution); NucleotideMutationCreator (protocols::evolution); null_bfs_prune_visitor (utility::graph); NullMover (protocols::moves); NullPerturber (protocols::denovo_design::components); NullPoseFolder (protocols::denovo_design::components); NumberHBondsCalculator (protocols::simple_pose_metric_calculators); NumDerivCheckData (core::optimization); NumericalDerivCheckResult (core::optimization); NumNeighborsMPM (protocols::match); NumNeighborsSelector (core::select::residue_selector); NumNeighborsSelectorCreator (core::select::residue_selector); NVlookup (core::scoring::nv); NVscore (core::scoring::nv); NVscoreCreator (core::scoring::nv); NWAligner (core::sequence)

O: O2PrimePacker (protocols::stepwise::modeler::rna::o2prime); O2PrimeScreener (protocols::stepwise::screener); O_1A (protocols::toolbox::py_inheritance_test); O_1B (protocols::toolbox::py_inheritance_test); O_2A (protocols::toolbox::py_inheritance_test); O_2A2B (protocols::toolbox::py_inheritance_test); O_2B (protocols::toolbox::py_inheritance_test); ObserverCache (core::pose::datacache); Obsolet_NamedAtomPairConstraint (core::scoring::constraints); OccludedHbondSolEnergy (core::energy_methods); OccludedHbondSolEnergy_onebody (core::energy_methods); OccludedHbondSolEnergy_onebodyCreator (core::energy_methods); OccludedHbondSolEnergyCreator (core::energy_methods); OccupiedSpaceHash (protocols::match); OctahedralMetal_Helper (protocols::cyclic_peptide::crosslinker); Octree2D (core::scoring::packstat); OffsetPeriodicBoundFunc (core::scoring::constraints); OffspringFactory (protocols::ligand_evolution); OligomericAverageDegreeFilter (protocols::matdes); OligomericAverageDegreeFilterCreator (protocols::matdes); OmegaBundleParameter (protocols::helical_bundle::parameters); OmegaPerturber (protocols::kinematic_closure::perturbers); OmegaPreferenceSamplingData (core::scoring::carbohydrates); OmegaPreferencesFunction (core::scoring::carbohydrates); OmegaTether (core::scoring); OmegaTetherEnergy (core::energy_methods); OmegaTetherEnergyCreator (core::energy_methods); OmnibusDisulfideAnalysisLabelerMover (protocols::pose_sewing::movers); OmnibusDisulfideAnalysisLabelerMoverCreator (protocols::pose_sewing::movers); One_Four_BBMB_Helper (protocols::cyclic_peptide::crosslinker); OneBodyEnergy (core::scoring::methods); OneDDistPotential (core::scoring); OneGaussianScattering (core::scoring::electron_density); OneGaussianScattering (core::scoring::fiber_diffraction); OneToAllEnergyContainer (core::scoring); OneToAllNeighborConstIterator (core::scoring); OneToAllNeighborIterator (core::scoring); OnTheFlyEdge (core::pack::interaction_graph); OnTheFlyInteractionGraph (core::pack::interaction_graph); OnTheFlyNode (core::pack::interaction_graph); OopCreatorMover (protocols::ncbb::oop); OopCreatorMoverCreator (protocols::ncbb::oop); OopDockDesignProtocol (protocols::ncbb::oop); OopDockDesignProtocolCreator (protocols::ncbb::oop); OopDPuckMinusMover (protocols::simple_moves::oop); OopDPuckPlusMover (protocols::simple_moves::oop); OopMover (protocols::simple_moves::oop); OopPatcher (protocols::simple_moves::oop); OopPuckMinusMover (protocols::simple_moves::oop); OopPuckPlusMover (protocols::simple_moves::oop); OopRandomPuckMover (protocols::simple_moves::oop); OopRandomSmallMover (protocols::simple_moves::oop); OP_const_iterator (protocols::toolbox); OperateOnCertainResidues (core::pack::task::operation); OperateOnCertainResiduesCreator (core::pack::task::operation); OperateOnResidueSubset (core::pack::task::operation); OperateOnResidueSubsetCreator (core::pack::task::operation); Operator (protocols::calc_taskop_filters); OperatorFilterCreator (protocols::calc_taskop_filters); OptCysHG (core::pack::task::operation); OptCysHGCreator (core::pack::task::operation); OptEData (protocols::optimize_weights); OptEMultifunc (protocols::optimize_weights); OptEPositionData (protocols::optimize_weights); OptEPositionDataFactory (protocols::optimize_weights); OptEVariableExpression (protocols::optimize_weights); OptH (core::pack::task::operation); OptHCreator (core::pack::task::operation); OptimizeMembranePositionMover (protocols::membrane); OptimizeMembranePositionMoverCreator (protocols::membrane); OptimizeProteinEmbeddingMover (protocols::membrane); OptimizeProteinEmbeddingMoverCreator (protocols::membrane); OptimizeThreadingMover (protocols::rbsegment_relax); OptimizeThreadingMoverCreator (protocols::rbsegment_relax); Orbital (core::chemical); OrbitalsFeatures (protocols::features); OrbitalsFeaturesCreator (protocols::features); OrbitalsLookup (core::scoring::orbitals); OrbitalsScore (core::scoring::orbitals); OrbitalsScoreCreator (core::scoring::orbitals); OrbitalsStatistics (core::scoring::orbitals); OrbitalType (core::chemical::orbitals); OrbitalTypeMapper (core::chemical::orbitals); OrbitalTypeSet (core::chemical::orbitals); OrbitalXYZCoords (core::conformation::orbitals); OrderCavBallOnR (core::scoring::packstat); OrderCavBallOnRmAnb (core::scoring::packstat); OrderCavBallOnRmE (core::scoring::packstat); OrderCavBallOnX (core::scoring::packstat); OrderCBC (core::scoring::packstat); OrderedFragSet (core::fragment); OrderedFragSetIterator_ (core::fragment); OrderedSequentialSymmetrySlider (protocols::symmetry); OrderSortPredicate (protocols::abinitio); OrderSphereOnID (core::scoring::packstat); OrderSphereOnX (core::scoring::packstat); OrientCommon (protocols::constel); OriginalBackboneBuildPoint (protocols::match::upstream); OrJumpSelector (core::select::jump_selector); OrJumpSelectorCreator (core::select::jump_selector); OrResidueSelector (core::select::residue_selector); OrResidueSelectorCreator (core::select::residue_selector); OrSelector (protocols::pose_selectors); OrSelectorCreator (protocols::pose_selectors); OTFFlexbbEdge (protocols::flexpack::interaction_graph); OTFFlexbbInteractionGraph (protocols::flexpack::interaction_graph); OTFFlexbbNode (protocols::flexpack::interaction_graph); OtherContextScoreFunction (protocols::flexpack); OtherPoseEnergy (core::energy_methods); OtherPoseEnergyCreator (core::energy_methods); output_data_struct (protocols::stepwise::modeler::rna); OutputSpecification (protocols::jd3::output); OutputStructureStore (protocols::ligand_docking::ga_ligand_dock); OutputWriter (protocols::match::output); MergePDBMover::Overlap (protocols::pose_creation); OversaturatedHbondAcceptorFilter (protocols::cyclic_peptide); OversaturatedHbondAcceptorFilterCreator (protocols::cyclic_peptide)

P: P_AA (core::scoring); P_AA_ABEGO3 (core::scoring); P_AA_Energy (core::energy_methods); P_AA_EnergyCreator (core::energy_methods); P_AA_pp_Energy (core::energy_methods); P_AA_pp_EnergyCreator (core::energy_methods); P_AA_ss (core::scoring); P_AA_ss_Energy (core::energy_methods); P_AA_ss_EnergyCreator (core::energy_methods); PackDaemon (protocols::pack_daemon); PackedDunbrackRotamer (core::pack::dunbrack); PackerNeighborGraphFilter (protocols::simple_filters); PackerPalette (core::pack::palette); PackerPaletteCreator (core::pack::palette); PackerPaletteFactory (core::pack::palette); PackerPaletteLoader (protocols::parser); PackerPaletteLoaderCreator (protocols::parser); PackerPaletteRegistrator (core::pack::palette); PackerTask (core::pack::task); PackerTask_ (core::pack::task); PackingScore (core::scoring::packstat); PackingScoreResData (core::scoring::packstat); PackingState (protocols::multistate_design); PackRotamersMover (protocols::minimization_packing); PackRotamersMoverCreator (protocols::minimization_packing); PackRotamersMoverLazy (protocols::minimization_packing); PackRotamersMoverLazyCreator (protocols::minimization_packing); PackRotamersMoverPartGreedy (protocols::enzdes); PackRotamersMoverPartGreedyCreator (protocols::enzdes); PackScreener (protocols::stepwise::screener); PackstatCalculator (protocols::pose_metric_calculators); PackStatEnergy (core::energy_methods); PackStatEnergyCreator (core::energy_methods); PackStatFilter (protocols::simple_filters); PackStatFilterCreator (protocols::simple_filters); PackStatMover (protocols::analysis); PairedSheetResidueSelector (protocols::denovo_design::residue_selectors); PairedSheetResidueSelectorCreator (protocols::denovo_design::residue_selectors); PairEnergy (core::energy_methods); PairEnergyCreator (core::energy_methods); PairEPotential (core::scoring); PairFeatures (protocols::features); PairFeaturesCreator (protocols::features); PairFuncMap (core::scoring::custom_pair_distance); Pairing (core::scoring::dssp); PairingLibrary (protocols::jumping); PairingStatEntry (protocols::abinitio); PairingStatistics (protocols::abinitio); PairingTemplate (protocols::jumping); PairQueryExecutor (protocols::indexed_structure_store::search); PairQuerySummaryStatistics (protocols::indexed_structure_store::search); PairScoringScheme (core::sequence); PalesEvaluator (protocols::simple_filters); PalesEvaluatorCreator (protocols::simple_filters); ParaIon (core::io::nmr); ParallelBetaPairingPreferenceFilter (protocols::fldsgn::filters); ParallelBetaPairingPreferenceFilterCreator (protocols::fldsgn::filters); ParallelTempering (protocols::canonical_sampling); ParallelTemperingCreator (protocols::canonical_sampling); ParamagneticDatabaseHandler (core::io::nmr); Parameter (core::conformation::parametric); ParameterizationCalculatorProperties (core::conformation::parametric); Parameters (core::conformation::parametric); CentroidRelax::parameters (protocols::relax); ParametersSet (core::conformation::parametric); ParametrizationCalculator (core::conformation::parametric); ParaNMRScoreMover (protocols::nmr); ParaNMRScoreMoverCreator (protocols::nmr); ParatopeEpitopeSiteConstraintMover (protocols::antibody::constraints); ParatopeEpitopeSiteConstraintMoverCreator (protocols::antibody::constraints); ParatopeMetric (protocols::antibody); ParatopeSiteConstraintMover (protocols::antibody::constraints); ParatopeSiteConstraintMoverCreator (protocols::antibody::constraints); ParsedProtocol (protocols::rosetta_scripts); ParsedProtocolCreator (protocols::rosetta_scripts); ParsedProtocol::ParsedProtocolStep (protocols::rosetta_scripts); ParsedTagCache (protocols::multistage_rosetta_scripts); ParserJobInputter (protocols::protein_interface_design); ParserJobInputterCreator (protocols::protein_interface_design); PartialAtomID (core::id); PartialSecondarySimilarity (protocols::frag_picker::scores); PartialThreadingMover (protocols::comparative_modeling); Particle (core::optimization); ParticleSwarmMinimizer (core::optimization); PartitionAggregateFunction (protocols::multistate_design); PartitionContactScreener (protocols::stepwise::screener); PartitionedSearchPattern (protocols::hotspot_hashing); PartnerMotifScorer (protocols::sewing::scoring); PartnerMotifScorerCreator (protocols::sewing::scoring); Patch (core::chemical); PatchCase (core::chemical); PatchChemistry (protocols::chemistries); PatchChemistryCreator (protocols::chemistries); PatchdockReader (protocols::protein_interface_design); PatchdockTransform (protocols::protein_interface_design::movers); PatchdockTransformCreator (protocols::protein_interface_design::movers); PatchOperation (core::chemical); PatchOperation (protocols::canonical_sampling); PatchOperationCreator (core::chemical); PatchOperationFactory (core::chemical); PatchOperationRegistrator (core::chemical); PBLifetimeCache (core::energy_methods); PCA (protocols::evaluation); PcaEvaluator (protocols::abinitio); PCluster (protocols::pockets); PClusterSet (protocols::pockets); PCS_data (protocols::scoring::methods::pcs); PCS_data_input (protocols::scoring::methods::pcs); PCS_data_input_manager (protocols::scoring::methods::pcs); PCS_data_input_manager_Ts1 (protocols::scoring::methods::pcsTs1); PCS_data_input_manager_Ts2 (protocols::scoring::methods::pcsTs2); PCS_data_input_manager_Ts3 (protocols::scoring::methods::pcsTs3); PCS_data_input_manager_Ts4 (protocols::scoring::methods::pcsTs4); PCS_data_input_Ts1 (protocols::scoring::methods::pcsTs1); PCS_data_input_Ts2 (protocols::scoring::methods::pcsTs2); PCS_data_input_Ts3 (protocols::scoring::methods::pcsTs3); PCS_data_input_Ts4 (protocols::scoring::methods::pcsTs4); PCS_data_per_lanthanides (protocols::scoring::methods::pcs); PCS_data_per_lanthanides_Ts1 (protocols::scoring::methods::pcsTs1); PCS_data_per_lanthanides_Ts2 (protocols::scoring::methods::pcsTs2); PCS_data_per_lanthanides_Ts3 (protocols::scoring::methods::pcsTs3); PCS_data_per_lanthanides_Ts4 (protocols::scoring::methods::pcsTs4); PCS_data_Ts1 (protocols::scoring::methods::pcsTs1); PCS_data_Ts2 (protocols::scoring::methods::pcsTs2); PCS_data_Ts3 (protocols::scoring::methods::pcsTs3); PCS_data_Ts4 (protocols::scoring::methods::pcsTs4); PCS_Energy (protocols::scoring::methods::pcs); PCS_Energy_parameters_manager (protocols::scoring::methods::pcs); PCS_Energy_parameters_manager_Ts1 (protocols::scoring::methods::pcsTs1); PCS_Energy_parameters_manager_Ts2 (protocols::scoring::methods::pcsTs2); PCS_Energy_parameters_manager_Ts3 (protocols::scoring::methods::pcsTs3); PCS_Energy_parameters_manager_Ts4 (protocols::scoring::methods::pcsTs4); PCS_Energy_Ts1 (protocols::scoring::methods::pcsTs1); PCS_Energy_Ts2 (protocols::scoring::methods::pcsTs2); PCS_Energy_Ts3 (protocols::scoring::methods::pcsTs3); PCS_Energy_Ts4 (protocols::scoring::methods::pcsTs4); PCS_file_data (protocols::scoring::methods::pcs); PCS_file_data_Ts1 (protocols::scoring::methods::pcsTs1); PCS_file_data_Ts2 (protocols::scoring::methods::pcsTs2); PCS_file_data_Ts3 (protocols::scoring::methods::pcsTs3); PCS_file_data_Ts4 (protocols::scoring::methods::pcsTs4); PCS_FragDistance (protocols::frag_picker::scores); PCS_line_data (protocols::scoring::methods::pcs); PCS_line_data_Ts1 (protocols::scoring::methods::pcsTs1); PCS_line_data_Ts2 (protocols::scoring::methods::pcsTs2); PCS_line_data_Ts3 (protocols::scoring::methods::pcsTs3); PCS_line_data_Ts4 (protocols::scoring::methods::pcsTs4); PCS_tensor (protocols::scoring::methods::pcs); PCS_tensor_Ts1 (protocols::scoring::methods::pcsTs1); PCS_tensor_Ts2 (protocols::scoring::methods::pcsTs2); PCS_tensor_Ts3 (protocols::scoring::methods::pcsTs3); PCS_tensor_Ts4 (protocols::scoring::methods::pcsTs4); PCSData (core::scoring::nmr::pcs); PcsDataCenter (protocols::scoring::methods::pcs2); PcsDataCenterManager (protocols::scoring::methods::pcs2); PcsDataCenterManagerSingleton (protocols::scoring::methods::pcs2); PcsDataLanthanide (protocols::scoring::methods::pcs2); PCSEnergy (protocols::nmr::pcs); PcsEnergy (protocols::scoring::methods::pcs2); PcsEnergyController (protocols::topology_broker); PcsEnergyCreator (protocols::scoring::methods::pcs2); PCSEnergyCreator (protocols::nmr::pcs); PcsEnergyParameter (protocols::scoring::methods::pcs2); PcsEnergyParameterManager (protocols::scoring::methods::pcs2); PcsGridSearchParameter (protocols::scoring::methods::pcs2); PcsGridSearchParameterManager (protocols::scoring::methods::pcs2); PcsInputCenter (protocols::scoring::methods::pcs2); PcsInputCenterManager (protocols::scoring::methods::pcs2); PcsInputFile (protocols::scoring::methods::pcs2); PcsInputLine (protocols::scoring::methods::pcs2); PCSLigandTransformMover (protocols::nmr::pcs); PCSLigandTransformMoverCreator (protocols::nmr::pcs); PCSMultiGrid (protocols::qsar::scoring_grid); PCSMultiGridCreator (protocols::qsar::scoring_grid); PCSMultiSet (core::scoring::nmr::pcs); PCSSingle (core::scoring::nmr::pcs); PCSSingleGrid (protocols::qsar::scoring_grid); PCSSingleGridCreator (protocols::qsar::scoring_grid); PCSSingleSet (core::scoring::nmr::pcs); PCSTensor (core::scoring::nmr::pcs); PcsTensor (protocols::scoring::methods::pcs2); PCSTensorOptimizer (protocols::nmr::pcs); PDatom (core::scoring); PDB (protocols::sparta); PDB_Entry (protocols::sparta); PDBChunkLibraryInputter (protocols::jd3::chunk_library_inputters); PDBChunkLibraryInputterCreator (protocols::jd3::chunk_library_inputters); PdbDataFeatures (protocols::features); PdbDataFeaturesCreator (protocols::features); PDBDumpMover (protocols::moves); PDBFullModelInputter (protocols::jd3::full_model_inputters); PDBFullModelInputterCreator (protocols::jd3::full_model_inputters); PdbIdChunkFilter (protocols::frag_picker); PDBInfo (core::pose); PDBJobInputter (protocols::jd2); PDBJobInputterCreator (protocols::jd2); PDBJobOutputter (protocols::jd2); PDBJobOutputterCreator (protocols::jd2); PDBLandmark (protocols::antibody); PDBNumbering (protocols::antibody::design); PDBOutput (protocols::dna); PDBPoseInputStream (core::import_pose::pose_stream); PDBPoseInputter (protocols::jd3::pose_inputters); PDBPoseInputterCreator (protocols::jd3::pose_inputters); PDBPoseMap (core::pose); PDBPoseOutputSpecification (protocols::jd3::pose_outputters); PDBPoseOutputter (protocols::jd3::pose_outputters); PDBPoseOutputterCreator (protocols::jd3::pose_outputters); PDBReloadMover (protocols::simple_moves); PDBReloadMoverCreator (protocols::simple_moves); PDBRotamerLibrarySpecification (core::chemical::rotamers); PDBRotamerLibrarySpecificationCreator (core::chemical::rotamers); PDBSilentStruct (core::import_pose); PDBSilentStructCreator (core::import_pose); PDBTrajectoryRecorder (protocols::canonical_sampling); PDBTrajectoryRecorderCreator (protocols::canonical_sampling); PDBWriter (protocols::match::output); PDDFEnergy (protocols::scoring::methods::saxs); PDDFEnergyCreator (protocols::scoring::methods::saxs); PDDFScoreFilter (protocols::simple_filters); PDEdge (core::pack::interaction_graph); PDinter (core::scoring::power_diagram); PDinter (core::scoring); PDInteractionGraph (core::pack::interaction_graph); PDNode (core::pack::interaction_graph); PDsphere (core::scoring::power_diagram); PDvertex (core::scoring); PDvertex (core::scoring::power_diagram); PeakAssignment (protocols::noesy_assign); PeakAssignmentParameters (protocols::noesy_assign); PeakAssignmentResidueMap (protocols::noesy_assign); PeakCalibrator (protocols::noesy_assign); PeakCalibratorMap (protocols::noesy_assign); PeakFileFormat (protocols::noesy_assign); PeakFileFormat_Base (protocols::noesy_assign); PeakFileFormat_Sparky (protocols::noesy_assign); PeakFileFormat_xeasy (protocols::noesy_assign); PeakFileFormat_xpk (protocols::noesy_assign); PeptideBondEnergy (core::energy_methods); PeptideBondEnergyCreator (core::energy_methods); PeptideCyclizeMover (protocols::cyclic_peptide); PeptideCyclizeMoverCreator (protocols::cyclic_peptide); PeptideDeriverBasicStreamOutputter (protocols::peptide_deriver); PeptideDeriverFilter (protocols::peptide_deriver); PeptideDeriverFilterCreator (protocols::peptide_deriver); PeptideDeriverMarkdownStreamOutputter (protocols::peptide_deriver); PeptideDeriverOutputter (protocols::peptide_deriver); PeptideDeriverOutputterContainer (protocols::peptide_deriver); PeptideDeriverPoseOutputter (protocols::peptide_deriver); PeptideInternalHbondsFilter (protocols::cyclic_peptide); PeptideInternalHbondsFilterCreator (protocols::cyclic_peptide); PeptideInternalHbondsMetric (protocols::cyclic_peptide); PeptideInternalHbondsMetricCreator (protocols::cyclic_peptide); PeptideOrientationMover (protocols::membrane_benchmark); PeptideOrientationMoverCreator (protocols::membrane_benchmark); PeptideStapleDesignMover (protocols::protein_interface_design::movers); PeptideStapleDesignMoverCreator (protocols::protein_interface_design::movers); PeptideStapleMover (protocols::simple_moves); PeptideStubMover (protocols::cyclic_peptide); PeptideStubMoverCreator (protocols::cyclic_peptide); PeptideTorsionReporter (core::pack::dunbrack); PeptoidGeneralDOFReporter (core::pack::dunbrack); PeptoidOmegaReporter (core::pack::dunbrack); PeriodicBoundFunc (core::scoring::constraints); PeriodicBoxMover (protocols::simple_moves); PeriodicBoxMoverCreator (protocols::simple_moves); PeriodicFunc (core::scoring::func); PerlinNoise (protocols::electron_density); PerNativeRRReporterHuman (protocols::rotamer_recovery); PerResidueBfactorMetric (core::simple_metrics::per_residue_metrics); PerResidueBfactorMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueClashMetric (core::simple_metrics::per_residue_metrics); PerResidueClashMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueDensityFitMetric (core::simple_metrics::per_residue_metrics); PerResidueDensityFitMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueEnergyMetric (core::simple_metrics::per_residue_metrics); PerResidueEnergyMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueEsmProbabilitiesMetric (protocols::esm_perplexity); PerResidueEsmProbabilitiesMetricCreator (protocols::esm_perplexity); PerResidueGlycanLayerMetric (core::simple_metrics::per_residue_metrics); PerResidueGlycanLayerMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueInterfaceData (protocols::analysis); PerResidueProbabilitiesMetric (core::simple_metrics); PerResidueRealMetric (core::simple_metrics); PerResidueRMSDMetric (core::simple_metrics::per_residue_metrics); PerResidueRMSDMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueSapScoreMetric (core::pack::guidance_scoreterms::sap); PerResidueSapScoreMetricCreator (core::pack::guidance_scoreterms::sap); PerResidueSasaMetric (core::simple_metrics::per_residue_metrics); PerResidueSasaMetricCreator (core::simple_metrics::per_residue_metrics); PerResidueStringMetric (core::simple_metrics); PerSphereAccumulator (core::scoring::packstat); PertMinMover (protocols::minimization_packing); PertMinMoverCreator (protocols::minimization_packing); PerturbBundle (protocols::helical_bundle); PerturbBundleCreator (protocols::helical_bundle); PerturbBundleHelix (protocols::helical_bundle); PerturbBundleHelixCreator (protocols::helical_bundle); PerturbByBins (protocols::simple_moves::bin_transitions); PerturbByBinsCreator (protocols::simple_moves::bin_transitions); PerturbChiSidechainMover (protocols::simple_moves::sidechain_moves); PerturbChiSidechainMoverCreator (protocols::simple_moves::sidechain_moves); Perturber (protocols::kinematic_closure::perturbers); PerturberSet (protocols::kinematic_closure::perturbers); PerturbRotamerSidechainMover (protocols::simple_moves::sidechain_moves); PerturbRotamerSidechainMoverCreator (protocols::simple_moves::sidechain_moves); Pharmacophore (protocols::ligand_docking::ga_ligand_dock); pHEnergy (core::energy_methods); pHEnergyCreator (core::energy_methods); PhenixInterface (core::scoring::cryst); Phi (protocols::frag_picker::scores); PhiPsiRmsd (protocols::frag_picker::scores); PhiPsiSquareWell (protocols::frag_picker::scores); PhiPsiTalosIO (protocols::frag_picker); PhiSelector (core::select::residue_selector); PhiSelectorCreator (core::select::residue_selector); PhosphateMove (protocols::stepwise::modeler::rna::phosphate); PhosphateMover (protocols::stepwise::modeler::rna::phosphate); PhosphateScreener (protocols::stepwise::screener); pHVariantTaskOperation (protocols::task_operations); pHVariantTaskOperationCreator (protocols::task_operations); Picker (protocols::denovo_design::components); PickRandomSegmentMover (protocols::pose_sewing::movers); PickRandomSegmentMoverCreator (protocols::pose_sewing::movers); PIKAA (core::pack::task); PIKNA (core::pack::task); PiPiCalculator (protocols::pose_metric_calculators); PivotPicker (protocols::kinematic_closure::pivot_pickers); PlaceableRotamer (protocols::ligand_docking::ga_ligand_dock); PlacementAuctionMover (protocols::protein_interface_design::movers); PlacementAuctionMoverCreator (protocols::protein_interface_design::movers); PlacementMinimizationMover (protocols::protein_interface_design::movers); PlacementMinimizationMoverCreator (protocols::protein_interface_design::movers); PlaceOnLoop (protocols::protein_interface_design::movers); PlaceOnLoopCreator (protocols::protein_interface_design::movers); PlaceProbeMover (protocols::hotspot_hashing::movers); PlaceSimultaneouslyMover (protocols::protein_interface_design::movers); PlaceSimultaneouslyMoverCreator (protocols::protein_interface_design::movers); PlaceStubMover (protocols::protein_interface_design::movers); PlaceStubMoverCreator (protocols::protein_interface_design::movers); PlaceSurfaceProbe (protocols::hotspot_hashing::movers); PlaceSurfaceProbeCreator (protocols::hotspot_hashing::movers); PlaidFingerprint (protocols::pockets); PlainPdbJobDistributor (protocols::jobdist); PlainRawJobDistributor (protocols::jobdist); PlainSilentFileJobDistributor (protocols::jobdist); PNatAAOptEPositionData (protocols::optimize_weights); PNatAAOptERotamerData (protocols::optimize_weights); PNatLigPoseOptEData (protocols::optimize_weights); PNatRotOptEPositionData (protocols::optimize_weights); PNatRotOptERotamerData (protocols::optimize_weights); PNatStructureOptEData (protocols::optimize_weights); PNearCalculator (protocols::cyclic_peptide_predict); PocketConstraint (protocols::pockets); PocketConstraintCreator (protocols::pockets); PocketExemplarMultifunc (protocols::pockets); PocketGrid (protocols::pockets); Point (core::scoring::packstat); point3d (core::scoring::atomic_depth); PointDwell (core::pack::annealer); PointGraphEdgeData (core::conformation); PointGraphVertexData (core::conformation); PointMutationCalculator (protocols::design_opt); PointMutScanDriver (protocols::pmut_scan); PointPair (core::scoring::packstat); PointScoreComparator (protocols::electron_density); PointScoreComparator (protocols::ligand_docking::ga_ligand_dock); PointWaterEnergy (core::energy_methods); PointWaterEnergyCreator (core::energy_methods); PointWaterPotential (core::scoring); PoissonBoltzmannEnergy (core::energy_methods); PoissonBoltzmannEnergyCreator (core::energy_methods); PoissonBoltzmannPotential (core::scoring); POLAR (core::pack::task); PolarGroupBurialPyMolStringMetric (protocols::analysis::burial_metrics); PolarGroupBurialPyMolStringMetricCreator (protocols::analysis::burial_metrics); PolarHydrogenFilter (core::chemical); PolarHydrogenPacker (protocols::stepwise::modeler::polar_hydrogens); Policy (protocols::nonlocal); PolicyFactory (protocols::nonlocal); Poly (protocols::sasa_scores); PolymerBondedEnergyContainer (core::scoring); PolymerBondedNeighborConstIterator (core::scoring); PolymerBondedNeighborIterator (core::scoring); Polynomial_1d (core::scoring::hbonds); Pool_ConvergenceCheck (protocols::canonical_sampling::mc_convergence_checks); Pool_Evaluator (protocols::canonical_sampling::mc_convergence_checks); Pool_RMSD (protocols::canonical_sampling::mc_convergence_checks); PoolData (protocols::canonical_sampling::mc_convergence_checks); PoolEvaluatorCreator (protocols::simple_filters); Population (protocols::ligand_evolution); Pose (core::pose); PoseArchitect (protocols::denovo_design::architects); PoseArchitectCreator (protocols::denovo_design::architects); PoseBalls (core::scoring::packing); PoseBallsLite (core::scoring::packing); PoseBuilder (protocols::denovo_design::components); PoseComment (protocols::simple_filters); PoseCommentFilterCreator (protocols::simple_filters); PoseCommentsFeatures (protocols::features); PoseCommentsFeaturesCreator (protocols::features); PoseCondition (protocols::moves); PoseConformationFeatures (protocols::features); PoseConformationFeaturesCreator (protocols::features); poseCoord (core::scoring::electron_density); PoseEvaluator (protocols::evaluation); PoseFolder (protocols::denovo_design::components); PoseForPoseID (protocols::multistage_rosetta_scripts); PoseFoundResiduesCombination (protocols::enzdes); PoseFromPoseResourceMover (protocols::simple_moves); PoseFromPoseResourceMoverCreator (protocols::simple_moves); PoseFromSequenceMover (protocols::pose_creation); PoseFromSequenceMoverCreator (protocols::pose_creation); PoseFromSFRBuilder (core::io::pose_from_sfr); PoseInfoFilter (protocols::simple_filters); PoseInfoFilterCreator (protocols::simple_filters); PoseInputSource (protocols::jd3::pose_inputters); PoseInputStream (core::import_pose::pose_stream); PoseInputStreamJobInputter (protocols::jd2); PoseInputStreamJobInputterCreator (protocols::jd2); PoseInputter (protocols::jd3::pose_inputters); PoseInputterCreator (protocols::jd3::pose_inputters); PoseInputterFactory (protocols::jd3::pose_inputters); PoseInputterRegistrator (protocols::jd3::pose_inputters); PoseInserter (protocols::match::output); PoseJobResult (protocols::jd3::job_results); PoseMatchOutputWriter (protocols::match::output); PoseMetricCalculator (core::pose::metrics); PoseMetricContainer (core::pose::metrics); PoseMetricEvaluator (protocols::simple_filters); PoseNumberedLoopFileReader (protocols::loops); PoseOutputSpecification (protocols::jd3::pose_outputters); PoseOutputter (protocols::jd3::pose_outputters); PoseOutputterCreator (protocols::jd3::pose_outputters); PoseOutputterFactory (protocols::jd3::pose_outputters); PoseOutputterRegistrator (protocols::jd3::pose_outputters); PosePackData (core::scoring::packstat); PosePropertyReporter (protocols::rosetta_scripts); PosePropertyReporterCreator (protocols::rosetta_scripts); PosePropertyReporterFactory (protocols::rosetta_scripts); PosePropertyReporterRegistrator (protocols::rosetta_scripts); PoseResidueTypeSet (core::chemical); PoseResource (core::import_pose); PoseResourceLoader (core::import_pose); PoseResourceLoaderCreator (core::import_pose); PoseSegment (protocols::pose_sewing::data_storage); PoseSelectionScreener (protocols::stepwise::screener); PoseSelector (protocols::rosetta_scripts); PoseSelectorCreator (protocols::rosetta_scripts); PoseSelectorFactory (protocols::rosetta_scripts); PoseSelectorRegistrator (protocols::rosetta_scripts); PoseSequence (core::energy_methods); PoseSphericalSamplesOptions (protocols::electron_density); PoseToStructFileRepConverter (core::io::pose_to_sfr); PoseUtilityPlaceholder (protocols::indexed_structure_store); PoseWithTerminalSegmentsOfKnownDSSP (protocols::pose_sewing::data_storage); PositionConservedResiduesStore (core::pose::datacache); PositionDdGInfo (core::io::PositionDdGInfo); PositionSpecificRandomizer (protocols::genetic_algorithm); PositionType (protocols::dna); PossibleAtomTypesForAtom (core::chemical::gasteiger); PossibleLoop (protocols::pose_length_moves); PostDockAssemblyScorer (protocols::domain_assembly); PosType (protocols::multistate_design); PosTypeCreator (protocols::multistate_design); PowerDiagram (core::scoring::power_diagram); PowExpression (protocols::pack_daemon); PPoly (protocols::sasa_scores); PQR (core::scoring); pre_talaris_2013_behavior_settings (core::init); PrecomputedFlexbbInteractionGraph (protocols::flexpack::interaction_graph); PrecomputedLibraryMover (protocols::stepwise::modeler::precomputed); PrecomputedPairEnergiesEdge (core::pack::interaction_graph); PrecomputedPairEnergiesInteractionGraph (core::pack::interaction_graph); PrecomputedPairEnergiesNode (core::pack::interaction_graph); PREData (core::scoring::nmr::pre); PredesignPerturbMover (protocols::enzdes); PredesignPerturbMoverCreator (protocols::enzdes); Predicate (core::scoring); PredictedBurialEvaluator (protocols::simple_filters); PredictedBurialFnEvaluatorCreator (protocols::simple_filters); PREDistanceRecord (protocols::nmr::pre); PREEnergy (protocols::nmr::pre); PREEnergyCreator (protocols::nmr::pre); PreliminaryLarvalJob (protocols::jd3::standard); PreliminaryLarvalJobTracker (protocols::jd3::standard); PreloadedPDB (protocols::cluster::calibur); PREMover (protocols::nmr::pre); PREMoverCreator (protocols::nmr::pre); PREMultiSet (core::scoring::nmr::pre); PrepackMover (protocols::protein_interface_design::movers); PrepackMoverCreator (protocols::protein_interface_design::movers); PrepareForCentroid (protocols::loop_modeling::utilities); PrepareForCentroidCreator (protocols::loop_modeling::utilities); PrepareForFullatom (protocols::loop_modeling::utilities); PrepareForFullatomCreator (protocols::loop_modeling::utilities); PrependMainchainAtom (core::chemical); PrependMainchainAtomCreator (core::chemical); PreProlineFilter (protocols::denovo_design::filters); PreProlineFilterCreator (protocols::denovo_design::filters); PreSelectedResidRange (core::select); PresenceCommon (protocols::constel); PreserveCBeta (core::pack::task::operation); PreserveCBetaCreator (core::pack::task::operation); PreserveCBetaRLT (core::pack::task::operation); PreserveCBetaRLTCreator (core::pack::task::operation); PRESingle (core::scoring::nmr::pre); PRESingleSet (core::scoring::nmr::pre); PreventChainFromRepackingOperation (protocols::task_operations); PreventChainFromRepackingOperationCreator (protocols::task_operations); PreventRepacking (core::pack::task::operation); PreventRepackingCreator (core::pack::task::operation); PreventRepackingRLT (core::pack::task::operation); PreventRepackingRLTCreator (core::pack::task::operation); PreventResiduesFromRepackingOperation (protocols::task_operations); PreventResiduesFromRepackingOperationCreator (protocols::task_operations); PrimarySequenceNeighborhoodSelector (core::select::residue_selector); PrimarySequenceNeighborhoodSelectorCreator (core::select::residue_selector); principal_angle_degrees (core::pose::rna); ProbabilityConservationMetric (core::simple_metrics::per_residue_metrics); ProbabilityConservationMetricCreator (core::simple_metrics::per_residue_metrics); ProbSortClass (core::pack::dunbrack); ProcessorFactory (protocols::match::output); ProClosureEnergy (core::energy_methods); ProClosureEnergyCreator (core::energy_methods); ReactionBasedAnalogSampler::Product (protocols::drug_design); ProfilerMover (protocols::moves); ProfileScore (protocols::frag_picker::scores); ProfileScoreBlosum62 (protocols::frag_picker::scores); ProfileScoreDistWeight (protocols::frag_picker::scores); ProfileScoreL1 (protocols::frag_picker::scores); ProfileScoreStructL1 (protocols::frag_picker::scores); ProfileScoreSubMatrix (protocols::frag_picker::scores); ProfSimScoringScheme (core::sequence); ProgressBarObserver (protocols::canonical_sampling); ProgressBarObserverCreator (protocols::canonical_sampling); ProhibitResidueProperties (core::pack::task::operation); ProhibitResiduePropertiesCreator (core::pack::task::operation); ProhibitSpecifiedBaseResidueTypes (core::pack::task::operation); ProhibitSpecifiedBaseResidueTypesCreator (core::pack::task::operation); ProlineFixMover (protocols::simple_moves); ProlinePhiScore (protocols::frag_picker::scores); PropagateClashCheckFilter (protocols::dna_dock); PropagateClashCheckFilterCreator (protocols::dna_dock); PROPERTY (core::pack::task); ProQ_Energy (core::energy_methods); ProQ_EnergyCreator (core::energy_methods); ProQPotential (core::scoring); ProtectedConformation (protocols::environment); ProteinAtrRepChecker (protocols::stepwise::modeler::protein::checker); ProteinAtrRepScreener (protocols::stepwise::legacy::screener); ProteinBackboneAtomAtomPairFeatures (protocols::features); ProteinBackboneAtomAtomPairFeaturesCreator (protocols::features); ProteinBackboneBuildPoint (protocols::match::upstream); ProteinBackboneTorsionAngleFeatures (protocols::features); ProteinBackboneTorsionAngleFeaturesCreator (protocols::features); ProteinBetaAntiParallelStepWiseSampler (protocols::stepwise::sampler::protein); ProteinBondGeometryFeatures (protocols::features); ProteinBondGeometryFeaturesCreator (protocols::features); ProteinCCD_ClosureScreener (protocols::stepwise::screener); ProteinCore (protocols::task_operations); ProteinCoreFilterCreator (protocols::task_operations); ProteinFragmentStepWiseSampler (protocols::stepwise::sampler::protein); ProteinGrid (protocols::protein_grid); ProteinInterfaceDesignOperation (protocols::task_operations); ProteinInterfaceDesignOperationCreator (protocols::task_operations); ProteinInterfaceMultiStateDesignMover (protocols::protein_interface_design::movers); ProteinInterfaceMultiStateDesignMoverCreator (protocols::protein_interface_design::movers); ProteinLigandInterfaceUpweighter (protocols::enzdes); ProteinLigandInterfaceUpweighterOperationCreator (protocols::enzdes); ProteinMainChainStepWiseSampler (protocols::stepwise::sampler::protein); ProteinMPNNMover (protocols::protein_mpnn); ProteinMPNNMoverCreator (protocols::protein_mpnn); ProteinMPNNProbabilitiesMetric (protocols::protein_mpnn); ProteinMPNNProbabilitiesMetricCreator (protocols::protein_mpnn); ProteinProteinInterfaceUpweighter (protocols::pack_interface); ProteinProteinInterfaceUpweighterTaskOperationCreator (protocols::pack_interface); ProteinResidueConformationFeatures (protocols::features); ProteinResidueConformationFeaturesCreator (protocols::features); ProteinResidueSelector (protocols::fold_from_loops::selectors); ProteinResidueSelectorCreator (protocols::fold_from_loops::selectors); ProteinRMSDFeatures (protocols::features); ProteinRMSDFeaturesCreator (protocols::features); ProteinRMSDNoSuperpositionFeatures (protocols::features); ProteinRMSDNoSuperpositionFeaturesCreator (protocols::features); ProteinSCSampler (protocols::match::upstream); ProteinSilentReport (protocols::features); ProteinSilentStruct_SinglePrecCreator (core::io::silent); ProteinSilentStruct_Template (core::io::silent); ProteinSilentStructCreator (core::io::silent); ProteinUpstreamBuilder (protocols::match::upstream); ProtLigEnsemble (protocols::ligand_docking); ProtLigEnsembleCreator (protocols::ligand_docking); ProtLigPair_info (protocols::ligand_docking); Protocol (protocols::abinitio); ProtocolFeatures (protocols::features); ProtocolSettingsMetric (core::simple_metrics::composite_metrics); ProtocolSettingsMetricCreator (core::simple_metrics::composite_metrics); ProtonResonance (protocols::noesy_assign); PruneBuriedUnsats_RotamerSetsOperation (protocols::task_operations); PruneBuriedUnsatsOperation (protocols::task_operations); PruneBuriedUnsatsOperationCreator (protocols::task_operations); PseudoBond (core::conformation); PseudoBondCollection (core::conformation); PseudocontactShiftEnergyController (protocols::topology_broker); PseudocontactShiftEnergyController_Ts1 (protocols::topology_broker); PseudocontactShiftEnergyController_Ts2 (protocols::topology_broker); PseudocontactShiftEnergyController_Ts3 (protocols::topology_broker); PseudocontactShiftEnergyController_Ts4 (protocols::topology_broker); PseudocontactShiftEnergyCreator (protocols::scoring::methods::pcs); PseudocontactShiftEnergyCreator_Ts1 (protocols::scoring::methods::pcsTs1); PseudocontactShiftEnergyCreator_Ts2 (protocols::scoring::methods::pcsTs2); PseudocontactShiftEnergyCreator_Ts3 (protocols::scoring::methods::pcsTs3); PseudocontactShiftEnergyCreator_Ts4 (protocols::scoring::methods::pcsTs4); PseudoPerplexityMetric (protocols::esm_perplexity); PseudoPerplexityMetricCreator (protocols::esm_perplexity); Psi (protocols::frag_picker::scores); PsiPredInterface (core::io::external); PsiPredResult (core::io::external); PSSM2BfactorMover (protocols::simple_moves); PSSM2BfactorMoverCreator (protocols::simple_moves); PSSMOptEPositionData (protocols::optimize_weights); PTMPredictionMetric (protocols::ptm_prediction); PTMPredictionMetricCreator (protocols::ptm_prediction); PTMPredictionTensorflowProtocol (protocols::ptm_prediction); PTMPredictionTensorflowProtocolBase (protocols::ptm_prediction); PValuedFragmentScoreManager (protocols::frag_picker::scores); PyEnergyMethodRegistrator (core::scoring::methods); PyMOLMover (protocols::moves); PyMOLMoverCreator (protocols::moves); PyMOLObserver (protocols::moves); PyRotamerEliminator (core::pack::rotamer_set); PyRotamerEliminatorTaskOperation (core::pack::rotamer_set)

R: APBSConfig::R_PARAM (core::scoring); RadiusOfGyrationFeatures (protocols::features); RadiusOfGyrationFeaturesCreator (protocols::features); Rama2bPerturber (protocols::kinematic_closure::perturbers); Ramachandran (core::scoring); Ramachandran2B (core::scoring); RamachandranEnergy (core::energy_methods); RamachandranEnergy2B (core::energy_methods); RamachandranEnergy2BCreator (core::energy_methods); RamachandranEnergyCreator (core::energy_methods); RamaCheck1B (protocols::loops::loop_closure::ccd); RamaCheck2B (protocols::loops::loop_closure::ccd); RamaCheckBase (protocols::loops::loop_closure::ccd); RamaMutationSelector (protocols::cyclic_peptide); RamaMutationSelectorCreator (protocols::cyclic_peptide); RamaPerturber (protocols::kinematic_closure::perturbers); RamaPrePro (core::scoring); RamaPreProEnergy (core::energy_methods); RamaPreProEnergyCreator (core::energy_methods); RamaPreproFilename (core::chemical); RamaPreproFilenameCreator (core::chemical); RamaPreproResname (core::chemical); RamaPreproResnameCreator (core::chemical); RamaScore (protocols::frag_picker::scores); RampingFunc (protocols::moves); RampingMover (protocols::moves); RampingMoverCreator (protocols::moves); RandomConformerMover (protocols::ligand_docking); RandomConformers (protocols::ligand_docking); RandomConformersCreator (protocols::ligand_docking); RandomFragmentLigand (protocols::drug_design); RandomFragmentLigandCreator (protocols::drug_design); RandomGapSolutionPicker (protocols::backbone_moves::local_backbone_mover::gap_solution_pickers); RandomGlycanFoliageSelector (core::select::residue_selector); RandomGlycanFoliageSelectorCreator (core::select::residue_selector); RandomizeBBByRamaPrePro (protocols::backbone_moves); RandomizeBBByRamaPreProCreator (protocols::backbone_moves); RandomMover (protocols::moves); RandomMoverCreator (protocols::moves); RandomMutation (protocols::protein_interface_design::movers); RandomMutationCreator (protocols::protein_interface_design::movers); RandomOmegaFlipMover (protocols::simple_moves); RandomOmegaFlipMoverCreator (protocols::simple_moves); RandomPositionRotationMover (protocols::membrane); RandomPositionTranslationMover (protocols::membrane); RandomResidueSelector (core::select::residue_selector); RandomResidueSelectorCreator (core::select::residue_selector); RandomSheetBuilder (protocols::jumping); RandomSolutions (protocols::kinematic_closure::solution_pickers); RandomSymmetrySlider (protocols::symmetry); RandomTorsionMover (protocols::simple_moves); RandomTorsionMoverCreator (protocols::simple_moves); RandomTorsionPoseFolder (protocols::denovo_design::components); RandomVectorSelector (protocols::denovo_design::components); RangeFilter (protocols::simple_filters); RangeFilterCreator (protocols::simple_filters); RangeRelaxMover (protocols::relax); RationalLoopComparator (protocols::loops); RationalMonteCarlo (protocols::simple_moves::rational_mc); Rattle (protocols::md); RawFileData (core::io::raw_data); RawStruct (core::io::raw_data); ray_distance_derivs (protocols::pockets); RB_lt (protocols::rbsegment_relax); RBfitResult (protocols::electron_density); RBfitResultComparitor (protocols::electron_density); RBInMover (protocols::splice); RBInMoverCreator (protocols::splice); RBOutMover (protocols::splice); RBOutMoverCreator (protocols::splice); RBResidueRange (protocols::rbsegment_relax); RBSegment (protocols::rbsegment_relax); RBSegmentMover (protocols::rbsegment_relax); RBSegmentRelax (protocols::rbsegment_relax); RBSegmentRelaxImpl (protocols); RDAT (core::io::rna); RDC (core::scoring); RDC_Evaluator (protocols::simple_filters); RDC_Rohl (core::scoring); RDCData (core::scoring::nmr::rdc); RDCEnergy (protocols::nmr::rdc); RDCEnergyCreator (protocols::nmr::rdc); RdcEvaluatorCreator (protocols::simple_filters); RDCMultiSet (core::scoring::nmr::rdc); RDCScore (protocols::frag_picker::scores); RdcSelectEvaluatorCreator (protocols::simple_filters); RDCSingle (core::scoring::nmr::rdc); RDCSingleSet (core::scoring::nmr::rdc); RdcTargetEvaluatorCreator (protocols::simple_filters); RDCTensor (core::scoring::nmr::rdc); RDFBase (protocols::ligand_docking::rdf); RDFBinaryHbondCreator (protocols::ligand_docking::rdf); RDFBinaryHbondFunction (protocols::ligand_docking::rdf); RDFBinaryOrbitalFunction (protocols::ligand_docking::rdf); RDFBinaryOrbitalFunctionCreator (protocols::ligand_docking::rdf); RDFChargeCreator (protocols::ligand_docking::rdf); RDFChargeFunction (protocols::ligand_docking::rdf); RDFElecCreator (protocols::ligand_docking::rdf); RDFElecFunction (protocols::ligand_docking::rdf); RDFEtableCreator (protocols::ligand_docking::rdf); RDFEtableFunction (protocols::ligand_docking::rdf); RDFFunctionCreator (protocols::ligand_docking::rdf); RDFFunctionFactory (protocols::ligand_docking::rdf); RDFFunctionRegistrator (protocols::ligand_docking::rdf); RDFHbondCreator (protocols::ligand_docking::rdf); RDFHbondFunction (protocols::ligand_docking::rdf); RDFOrbitalFunction (protocols::ligand_docking::rdf); RDFOrbitalFunctionCreator (protocols::ligand_docking::rdf); RDKitMetric (protocols::drug_design); RDKitMetricCreator (protocols::drug_design); RDKitMetricFilter (protocols::drug_design); RDKitMetricFilterCreator (protocols::drug_design); RDKitMetricsMover (protocols::drug_design); RDKitMetricsMoverCreator (protocols::drug_design); RDKitRotamers (protocols::rotamer_gen); RDKitRotamersCreator (protocols::rotamer_gen); RDMolToRestype (core::chemical::rdkit); Reaction (protocols::ligand_evolution); ReactionBasedAnalogSampler (protocols::drug_design); ReactionBasedAnalogSamplerCreator (protocols::drug_design); ReactionChemistry (protocols::drug_design); ReactionFragment (protocols::drug_design); ReactionFragmentCreator (protocols::drug_design); ReactionGrow (protocols::drug_design); ReactionGrowCreator (protocols::drug_design); ReactionMultiTransform (protocols::drug_design); ReactionMultiTransformCreator (protocols::drug_design); ReadPoseExtraScoreFilter (protocols::simple_filters); ReadPoseExtraScoreFilterCreator (protocols::simple_filters); ReadResfile (core::pack::task::operation); ReadResfileAndObeyLengthEvents (core::pack::task::operation); ReadResfileAndObeyLengthEventsCreator (core::pack::task::operation); ReadResfileCreator (core::pack::task::operation); ReadResfileFromDB (protocols::task_operations); ReadResfileFromDBCreator (protocols::task_operations); ReadResidueCoordinatesFromPDB (protocols::chromophore); ReactionBasedAnalogSampler::Reagent (protocols::drug_design); Reagent (protocols::ligand_evolution); RealFilter (core::chemical); RealMetric (core::simple_metrics); RealValuedParameter (core::conformation::parametric); RealVectorValuedParameter (core::conformation::parametric); RECCES_Mover (protocols::recces); RECCES_Options (protocols::recces::options); RECCES_Parameters (protocols::recces::params); RecomputeDensityMapMover (protocols::cryst); RecomputeDensityMapMoverCreator (protocols::cryst); RecordCollection (core::io::pdb); RecoverSideChainsMover (protocols::comparative_modeling); RedefineChi (core::chemical); RedefineChiCreator (core::chemical); RefConvert (core::chemical); RefConvert< core::Size > (core::chemical); RefConvert< std::string > (core::chemical); RefConvert< VD > (core::chemical); ReferenceEnergy (core::energy_methods); ReferenceEnergyCreator (core::energy_methods); ReferenceEnergyNoncanonical (core::energy_methods); ReferenceEnergyNoncanonicalCreator (core::energy_methods); ReferencePose (core::pose::reference_pose); ReferencePoseSet (core::pose::reference_pose); RefineBetaBarrel (protocols::antibody); RefinementResult (protocols::electron_density); RefinementResultComparitor (protocols::electron_density); Region (protocols::nonlocal); RegionalConnections (protocols::simple_filters); RelativeConnectRight (protocols::forge::build); RelativePoseFilter (protocols::calc_taskop_filters); RelativePoseFilterCreator (protocols::calc_taskop_filters); RelativeSegmentFilter (protocols::protein_interface_design::filters); RelativeSegmentFilterCreator (protocols::protein_interface_design::filters); RelativeSequencePosition (protocols::forge::build); RelaxProtocolBase (protocols::relax); RelaxScriptCommand (protocols::denovo_design::movers); RelaxScriptCommand (protocols::relax); RelaxScriptFileContents (protocols::relax); RelaxScriptManager (protocols::relax); ReleaseConstraintFromResidueMover (protocols::fold_from_loops::movers); ReleaseConstraintFromResidueMoverCreator (protocols::fold_from_loops::movers); RemarkInfo (core::io); Remarks (core::io); RemodelAccumulator (protocols::forge::remodel); RemodelConstraintGenerator (protocols::forge::remodel); RemodelData (protocols::forge::remodel); RemodelDesignMover (protocols::forge::remodel); RemodelEnzdesCstModule (protocols::forge::remodel); RemodelGlobalFrame (protocols::forge::remodel); RemodelLigandHandler (protocols::forge::remodel); RemodelLoopMover (protocols::forge::remodel); RemodelLoopMoverPoseFolder (protocols::denovo_design::components); RemodelMover (protocols::forge::remodel); RemodelMoverCreator (protocols::forge::remodel); RemodelRotamerLinks (protocols::forge::remodel); RemodelRotamerLinksCreator (protocols::forge::remodel); RemodelWorkingSet (protocols::forge::remodel); RemoveConstraints (protocols::constraint_generator); RemoveConstraintsCreator (protocols::constraint_generator); RemoveLigandFilter (protocols::enzdes); RemoveLigandFilterCreator (protocols::enzdes); RemoveMetalConnectionsMover (protocols::metal_interface); RemoveMetalConnectionsMoverCreator (protocols::metal_interface); RemoveNorCTermMPM (protocols::match); RemoveRemodelCsts (protocols::forge::constraints); RemoveRemodelCstsCreator (protocols::forge::constraints); RemoveRotamerSpecifications (core::chemical); RemoveRotamerSpecificationsCreator (core::chemical); RenameAtom (core::chemical); RenameAtomCreator (core::chemical); RenderGridsToKinemage (protocols::qsar); RenderGridsToKinemageCreator (protocols::qsar); RepackingRefiner (protocols::loop_modeling::refiners); RepackingRefinerCreator (protocols::loop_modeling::refiners); RepackLigandSiteWithoutLigandMover (protocols::enzdes); RepackMinimize (protocols::protein_interface_design::movers); RepackMinimizeCreator (protocols::protein_interface_design::movers); RepackSidechainsMover (protocols::minimization_packing); RepackSidechainsMoverCreator (protocols::minimization_packing); RepackTrial (protocols::loops::loop_mover::refine); RepackTrialCreator (protocols::loops::loop_mover::refine); RepackWithoutLigandFilter (protocols::enzdes); RepackWithoutLigandFilterCreator (protocols::enzdes); RepeatMover (protocols::moves); RepeatParameterFilter (protocols::simple_filters); RepeatParameterFilterCreator (protocols::simple_filters); RepeatPropagationMover (protocols::simple_moves); RepeatPropagationMoverCreator (protocols::simple_moves); RepeatProteinRelax (protocols::relax); RepeatProteinRelaxCreator (protocols::relax); RepGrid (protocols::qsar::scoring_grid); RepGridCreator (protocols::qsar::scoring_grid); ReplaceMainchainAtom (core::chemical); ReplaceMainchainAtomCreator (core::chemical); ReplaceProtonWithBromine (core::chemical); ReplaceProtonWithBromineCreator (core::chemical); ReplaceProtonWithChlorine (core::chemical); ReplaceProtonWithChlorineCreator (core::chemical); ReplaceProtonWithEthyl (core::chemical); ReplaceProtonWithEthylCreator (core::chemical); ReplaceProtonWithFluorine (core::chemical); ReplaceProtonWithFluorineCreator (core::chemical); ReplaceProtonWithHydroxyl (core::chemical); ReplaceProtonWithHydroxylCreator (core::chemical); ReplaceProtonWithIodine (core::chemical); ReplaceProtonWithIodineCreator (core::chemical); ReplaceProtonWithMethoxy (core::chemical); ReplaceProtonWithMethoxyCreator (core::chemical); ReplaceProtonWithMethyl (core::chemical); ReplaceProtonWithMethylCreator (core::chemical); ReplaceProtonWithTrifluoromethyl (core::chemical); ReplaceProtonWithTrifluoromethylCreator (core::chemical); ReplaceRegionMover (protocols::grafting::simple_movers); ReplaceRegionMoverCreator (protocols::grafting::simple_movers); ReplicaExchangeMC (protocols::moves); ReplicateFilter (protocols::filters); ReplicateFilterCreator (protocols::filters); ReplicateTask (core::pack::task::operation); Report (protocols::features); ReportEffectivePKA (protocols::simple_moves); ReportEffectivePKACreator (protocols::simple_moves); ReportFilter (protocols::simple_filters); ReportFilterCreator (protocols::simple_filters); ReportFSC (protocols::electron_density); ReportFSCCreator (protocols::electron_density); ReportGradientsMover (protocols::cryst); ReportGradientsMoverCreator (protocols::cryst); ReportPSSMDifferences (protocols::protein_interface_design); ReportSequenceDifferences (protocols::protein_interface_design); ReportToDB (protocols::features); ReportToDBCreator (protocols::features); ReportXYZ (protocols::simple_moves); ReportXYZCreator (protocols::simple_moves); Reprotonate (core::chemical::modifications); ReprotonateChemistry (protocols::chemistries); ReprotonateCreator (protocols::chemistries); RepulsiveOnlyMover (protocols::simple_moves); RerootEdgeSorter (core::chemical); RerootRestypeVisitor (core::chemical); ResampleMover (protocols::stepwise::monte_carlo::mover); ResampleMoverCreator (protocols::stepwise::monte_carlo::mover); resatom_and_func_struct (core::scoring::custom_pair_distance); ResConnID (core::chemical); ResetBaselineMover (protocols::monte_carlo); ResetBaselineMoverCreator (protocols::monte_carlo); ResetBondLength (core::chemical); ResetBondLengthCreator (core::chemical); ResetFoldTree (protocols::simple_moves); ResetFoldTreeCreator (protocols::simple_moves); ResetFullModelInfoMover (protocols::simple_moves); ResetFullModelInfoMoverCreator (protocols::simple_moves); ResfileCommand (core::pack::task); ResfileCommandOperation (protocols::task_operations); ResfileCommandOperationCreator (protocols::task_operations); ResfileContents (core::pack::task); ResfileReaderException (core::pack::task); ResFilter (core::pack::task::operation); ResFilterComposition (core::pack::task::operation); ResFilterCreator (core::pack::task::operation); ResFilterFactory (core::pack::task::operation); ResFilterRegistrator (core::pack::task::operation); ResHasher (protocols::mean_field); ResHashMap (protocols::mean_field); ResId (protocols::moves); ResidualDipolarCoupling (core::scoring); ResidualDipolarCoupling_Rohl (core::scoring); ResidualDipolarCouplingEnergy (core::energy_methods); ResidualDipolarCouplingEnergy_Rohl (core::energy_methods); ResidualDipolarCouplingEnergy_RohlCreator (core::energy_methods); ResidualDipolarCouplingEnergyCreator (core::energy_methods); ResidualDipolarCouplingEnergyRigidSegments (protocols::scoring::methods); ResidualDipolarCouplingEnergyRigidSegmentsCreator (protocols::scoring::methods); ResidualDipolarCouplingRigidSegments (protocols::scoring); Residue (core::conformation); Residue (protocols::backbone_moves::local_backbone_mover); Residue_info (protocols::stepwise::modeler::rna); ResidueAlternativeSet (protocols::stepwise::sampler::copy_dofs); ResidueAlternativeStepWiseSampler (protocols::stepwise::sampler::copy_dofs); ResidueAlternativeStepWiseSamplerComb (protocols::stepwise::sampler::copy_dofs); ResidueArrayAnnealableEnergy (core::scoring::annealing); ResidueArrayAnnealingEvaluator (core::pack::interaction_graph); ResidueAtomOverlaps (core::scoring::methods); ResidueAtomTreeCollection (core::pack::scmin); ResidueAtomTreeCollectionMomento (core::pack::scmin); ResidueBackboneEntry (protocols::indexed_structure_store); ResidueBBDofs (protocols::splice); ResidueBurialFeatures (protocols::features); ResidueBurialFeaturesCreator (protocols::features); ResidueBurialFilter (protocols::simple_filters); ResidueBurialFilterCreator (protocols::simple_filters); ResidueCartBondedParameters (core::energy_methods); ResidueChiralityFilter (protocols::simple_filters); ResidueChiralityFilterCreator (protocols::simple_filters); ResidueChunkSelection (protocols::abinitio::abscript); ResidueConformationFeatures (protocols::features); ResidueConformationFeaturesCreator (protocols::features); ResidueConformerFilter (protocols::enzdes); ResidueConformerFilterCreator (protocols::enzdes); ResidueConnection (core::chemical); ResidueConstraints (core::scoring::constraints); ResidueContactScreener (protocols::stepwise::screener); ResidueCoordinateChangeList (core::kinematics); ResidueCountFilter (protocols::simple_filters); ResidueCountFilterCreator (protocols::simple_filters); ResidueCouplingConstraint (core::scoring::constraints); ResidueDatabaseIO (core::chemical); ResidueDecompositionByChainCalculator (protocols::pose_metric_calculators); ResidueDecompositionCalculator (protocols::pose_metric_calculators); ResidueDepthCalculator (protocols::simple_filters); ResidueDepthData (protocols::simple_filters); ResidueDepthFilter (protocols::simple_filters); ResidueDepthFilterCreator (protocols::simple_filters); ResidueDepthFrag (protocols::simple_filters); ResidueDihedrals (protocols::denovo_design::components); ResidueDistanceFilter (protocols::simple_filters); ResidueDistanceFilterCreator (protocols::simple_filters); ResidueDOFReporter (core::pack::dunbrack); ResidueElement (protocols::environment::claims); ResidueEntry (protocols::indexed_structure_store); ResidueExclParams (core::scoring); ResidueFactory (core::conformation); ResidueFeature (protocols::comparative_modeling::features); ResidueFeatureFactory (protocols::comparative_modeling::features); ResidueFeatures (protocols::features); ResidueFeaturesCreator (protocols::features); ResidueGridScoresFeatures (protocols::features); ResidueGridScoresFeaturesCreator (protocols::features); ResidueGroupIGEdgeUpweighter (protocols::toolbox); ResidueHasProperty (core::pack::task::operation); ResidueHasPropertyCreator (core::pack::task::operation); ResidueIEFilter (protocols::simple_filters); ResidueIEFilterCreator (protocols::simple_filters); ResidueIndexDescription (core::pose); ResidueIndexDescriptionChainEnd (core::pose); ResidueIndexDescriptionLastResidue (core::pose); ResidueIndexDescriptionPDB (core::pose); ResidueIndexDescriptionPoseNum (core::pose); ResidueIndexDescriptionRefPose (core::pose); ResidueIndexIs (core::pack::task::operation); ResidueIndexIsCreator (core::pack::task::operation); ResidueIndexIsnt (core::pack::task::operation); ResidueIndexIsntCreator (core::pack::task::operation); ResidueIndexSelector (core::select::residue_selector); ResidueIndexSelectorCreator (core::select::residue_selector); ResidueInformation (core::io); ResidueInMembraneSelector (core::select::residue_selector); ResidueInMembraneSelectorCreator (core::select::residue_selector); ResidueInSequenceMotifSelector (core::select::residue_selector); ResidueInSequenceMotifSelectorCreator (core::select::residue_selector); PDBPoseMap::ResidueKey (core::pose); ResidueKinemageWriter (protocols::match::output); ResidueKinWriter (core::conformation); ResidueLabelsToPymolSelectionMover (protocols::fold_from_loops::movers); ResidueLabelsToPymolSelectionMoverCreator (protocols::fold_from_loops::movers); ResidueLacksProperty (core::pack::task::operation); ResidueLacksPropertyCreator (core::pack::task::operation); ResidueLevelTask (core::pack::task); ResidueLevelTask_ (core::pack::task); ResidueLipophilicityFilter (protocols::simple_filters); ResidueLipophilicityFilterCreator (protocols::simple_filters); ResidueListStepWiseSampler (protocols::stepwise::sampler::copy_dofs); ResidueMask (protocols::constel); ResidueMatcher (core::conformation); ResidueName3Is (core::pack::task::operation); ResidueName3IsCreator (core::pack::task::operation); ResidueName3Isnt (core::pack::task::operation); ResidueName3IsntCreator (core::pack::task::operation); ResidueNameSelector (core::select::residue_selector); ResidueNameSelectorCreator (core::select::residue_selector); ResidueNblistData (core::scoring); ResidueNeighborConstIterator (core::scoring); ResidueNeighborIterator (core::scoring); ResidueNetwork (protocols::toolbox); ResidueOrientEntry (protocols::indexed_structure_store); ResiduePair (protocols::fldsgn); ResiduePairJump (protocols::jumping); ResiduePairJumpSetup (protocols::jumping); ResiduePairJumpSingle (protocols::jumping); ResiduePairNeighborList (core::scoring); ResiduePairXYZ (core::scoring::func); ResiduePDBIndexIs (core::pack::task::operation); ResiduePDBIndexIsCreator (core::pack::task::operation); ResiduePDBIndexIsnt (core::pack::task::operation); ResiduePDBIndexIsntCreator (core::pack::task::operation); ResiduePDBInfoHasLabel (core::pack::task::operation); ResiduePDBInfoHasLabelCreator (core::pack::task::operation); ResiduePDBInfoHasLabelSelector (core::select::residue_selector); ResiduePDBInfoHasLabelSelectorCreator (core::select::residue_selector); ResiduePDBInfoLacksLabel (core::pack::task::operation); ResiduePDBInfoLacksLabelCreator (core::pack::task::operation); ResidueProbDesignOperation (protocols::task_operations); ResidueProbDesignOperationCreator (protocols::task_operations); ResidueProperties (core::chemical); ResiduePropertySelector (core::select::residue_selector); ResiduePropertySelectorCreator (core::select::residue_selector); ResidueRange (core::select::residue_selector); ResidueRanges (core::select::residue_selector); PDBInfo::ResidueRecord (core::pose); ResidueReplacementRebuildMover (protocols::ncbb); ResidueReplacementRebuildMoverCreator (protocols::ncbb); ResidueScoresFeatures (protocols::features); ResidueScoresFeaturesCreator (protocols::features); ResidueSecondaryStructureFeatures (protocols::features); ResidueSecondaryStructureFeaturesCreator (protocols::features); ResidueSelectionDistanceFilter (protocols::simple_filters); ResidueSelectionDistanceFilterCreator (protocols::simple_filters); ResidueSelector (core::select::residue_selector); ResidueSelectorCreator (core::select::residue_selector); ResidueSelectorFactory (core::select::residue_selector); ResidueSelectorLoader (protocols::parser); ResidueSelectorLoaderCreator (protocols::parser); ResidueSelectorRegistrator (core::select::residue_selector); ResidueSetChainEnergyFilter (protocols::simple_filters); ResidueSetChainEnergyFilterCreator (protocols::simple_filters); ResidueSidechainEntry (protocols::indexed_structure_store); ResiduesInInterfaceFilter (protocols::simple_filters); ResiduesInInterfaceFilterCreator (protocols::simple_filters); ResidueSpanSelector (core::select::residue_selector); ResidueSpanSelectorCreator (core::select::residue_selector); ResidueSummaryMetric (core::simple_metrics::metrics); ResidueSummaryMetricCreator (core::simple_metrics::metrics); ResidueTorsionRestraints (protocols::ligand_docking); ResidueTotalScoresFeatures (protocols::features); ResidueTotalScoresFeaturesCreator (protocols::features); ResidueType (core::chemical); ResidueTypeBase (core::chemical); ResidueTypeConstraint (core::scoring::constraints); ResidueTypeConstraintGenerator (protocols::constraint_generator); ResidueTypeConstraintGeneratorCreator (protocols::constraint_generator); ResidueTypeConstraintMover (protocols::constraint_movers); ResidueTypeConstraintMoverCreator (protocols::constraint_movers); ResidueTypeFilter (core::pack::task::operation); ResidueTypeFilterCreator (core::pack::task::operation); ResidueTypeFinder (core::chemical); ResidueTypeKinWriter (core::chemical); ResidueTypeLinkingConstraint (core::scoring::constraints); ResidueTypeSelector (core::chemical); ResidueTypeSelectorSingle (core::chemical); ResidueTypeSet (core::chemical); ResidueTypeSetCache (core::chemical); ResidueTypesFeatures (protocols::features); ResidueTypesFeaturesCreator (protocols::features); ResidueVector (core::select::residue_selector); ResidueVicinityCstGeneratorCreator (protocols::forge::remodel); ResidueVicinityInfo (protocols::forge::remodel); ResidueVicinityRCG (protocols::forge::remodel); ResidueXYZ (core::scoring::func); ResInteractions (protocols::toolbox::match_enzdes_util); ResLvlTaskOperation (core::pack::task::operation); ResLvlTaskOperationCreator (core::pack::task::operation); ResLvlTaskOperationFactory (core::pack::task::operation); ResLvlTaskOperationLoader (protocols::parser); ResLvlTaskOperationLoaderCreator (protocols::parser); ResLvlTaskOperationRegistrator (core::pack::task::operation); ResMut (protocols::constel); DisulfideFile::ResNum (core::io::raw_data); ResnumFromStringsWithRangesSelector (protocols::antibody::design); ResolutionSwitcher (protocols::abinitio); Resonance (protocols::noesy_assign); ResonanceList (protocols::noesy_assign); ResourceDeallocationMessage (protocols::jd3::deallocation); ResourceLoader (basic::resource_manager); ResourceLoaderCreator (basic::resource_manager); RespairInteractions (core::scoring::custom_pair_distance); ResPairMinimizationData (core::scoring); ResPairMotif (core::scoring::motif); ResPairMotifMetaBinner (core::scoring::motif); ResPairMotifQuery (core::scoring::motif); ResPairMotifs (core::scoring::motif); ResPred (protocols::mean_field); ResRangePredicate (core::scoring); ResResEnergyInvoker (core::scoring::etable); ResSingleMinimizationData (core::scoring); ResTorsions (protocols::loop_grower); RestrictAAsFromProbabilities (protocols::task_operations); RestrictAAsFromProbabilitiesCreator (protocols::task_operations); RestrictAbsentCanonicalAAS (core::pack::task::operation); RestrictAbsentCanonicalAASCreator (core::pack::task::operation); RestrictAbsentCanonicalAASExceptNativeRLT (core::pack::task::operation); RestrictAbsentCanonicalAASExceptNativeRLTCreator (core::pack::task::operation); RestrictAbsentCanonicalAASRLT (core::pack::task::operation); RestrictAbsentCanonicalAASRLTCreator (core::pack::task::operation); RestrictByCalculatorsOperation (protocols::task_operations); RestrictByCalculatorsOperationCreator (protocols::task_operations); RestrictChainToRepackingOperation (protocols::task_operations); RestrictChainToRepackingOperationCreator (protocols::task_operations); RestrictConservedLowDdgOperation (protocols::task_operations); RestrictConservedLowDdgOperationCreator (protocols::task_operations); RestrictDesignToProteinDNAInterface (protocols::dna); RestrictDesignToProteinDNAInterfaceCreator (protocols::dna); RestrictIdentitiesAtAlignedPositionsOperation (protocols::task_operations); RestrictIdentitiesAtAlignedPositionsOperationCreator (protocols::task_operations); RestrictIdentitiesOperation (protocols::task_operations); RestrictIdentitiesOperationCreator (protocols::task_operations); RestrictInteractionGraphThreadsOperation (core::pack::task::operation); RestrictInteractionGraphThreadsOperationCreator (core::pack::task::operation); RestrictInterGroupVectorOperation (protocols::task_operations); RestrictInterGroupVectorOperationCreator (protocols::task_operations); RestrictNativeResiduesOperation (protocols::task_operations); RestrictNativeResiduesOperationCreator (protocols::task_operations); RestrictNonSurfaceToRepackingOperation (protocols::task_operations); RestrictNonSurfaceToRepackingOperationCreator (protocols::task_operations); RestrictOperationsBase (protocols::task_operations); RestrictResiduesToRepackingOperation (protocols::task_operations); RestrictResiduesToRepackingOperationCreator (protocols::task_operations); RestrictResidueToRepacking (core::pack::task::operation); RestrictResidueToRepackingCreator (core::pack::task::operation); RestrictToAlignedSegmentsOperation (protocols::task_operations); RestrictToAlignedSegmentsOperationCreator (protocols::task_operations); RestrictToCDRH3Loop (protocols::task_operations); RestrictToCDRH3LoopCreator (protocols::task_operations); RestrictToCDRsAndNeighbors (protocols::antibody::task_operations); RestrictToCDRsAndNeighborsCreator (protocols::antibody::task_operations); RestrictToInterface (protocols::simple_task_operations); RestrictToInterfaceCreator (protocols::simple_task_operations); RestrictToInterfaceOperation (protocols::task_operations); RestrictToInterfaceOperationCreator (protocols::task_operations); RestrictToInterfaceVectorOperation (protocols::task_operations); RestrictToInterfaceVectorOperationCreator (protocols::task_operations); RestrictToLoops (protocols::simple_task_operations); RestrictToLoopsAndNeighbors (protocols::simple_task_operations); RestrictToLoopsAndNeighborsCreator (protocols::simple_task_operations); RestrictToLoopsCreator (protocols::simple_task_operations); RestrictToMoveMapChiOperation (protocols::task_operations); RestrictToNeighborhoodOperation (protocols::task_operations); RestrictToNeighborhoodOperationCreator (protocols::task_operations); RestrictToRepacking (core::pack::task::operation); RestrictToRepackingCreator (core::pack::task::operation); RestrictToRepackingRLT (core::pack::task::operation); RestrictToRepackingRLTCreator (core::pack::task::operation); RestrictToResidueProperties (core::pack::task::operation); RestrictToResiduePropertiesCreator (core::pack::task::operation); RestrictToSpecifiedBaseResidueTypes (core::pack::task::operation); RestrictToSpecifiedBaseResidueTypesCreator (core::pack::task::operation); RestrictToTerminiOperation (protocols::task_operations); RestrictToTerminiOperationCreator (protocols::task_operations); RestrictYSDesign (core::pack::task::operation); RestrictYSDesignCreator (core::pack::task::operation); RestypeDestructionEvent (core::chemical); ResTypeFragmentMover (protocols::simple_moves); ResTypeSequence_lt (protocols::dna); RestypeToRDMol (core::chemical::rdkit); RestypeToRDMolOptions (core::chemical::rdkit); ResultDB (protocols::electron_density); ResultElements (protocols::jd3::dag_node_managers); ResultOutputter (protocols::jd3::output); RetrieveStoredTaskOperation (protocols::task_operations); RetrieveStoredTaskOperationCreator (protocols::task_operations); ReturnResidueSubsetSelector (core::select::residue_selector); ReturnSidechainMover (protocols::simple_moves); Reversion (protocols::dna); Revert (protocols::protein_interface_design); RevRefinementResultComparitor (protocols::electron_density); ReweightableRepEnergy (protocols::ligand_docking::ga_ligand_dock); ReweightData (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty); RG_Energy_Fast (core::energy_methods); RG_Energy_FastCreator (core::energy_methods); RG_Energy_RNA (core::energy_methods); RG_Energy_RNACreator (core::energy_methods); RG_Local_MinData (core::energy_methods); RG_LocalEnergy (core::energy_methods); RG_LocalEnergyCreator (core::energy_methods); RG_MinData (core::energy_methods); RGFilter (protocols::simple_filters); RID_FileSource (core::pose); RID_Source (core::pose); RigidBodyDeterministicSpinMover (protocols::rigid); RigidBodyDofPerturbMover (protocols::rigid); RigidBodyDofRandomizeMover (protocols::rigid); RigidBodyDofRandomTransMover (protocols::rigid); RigidBodyDofSeqPerturbMover (protocols::rigid); RigidBodyDofSeqRandomizeMover (protocols::rigid); RigidBodyDofSeqTransMover (protocols::rigid); RigidBodyDofTransMover (protocols::rigid); RigidBodyInfo (protocols::docking); RigidBodyMotionMover (protocols::rigid); RigidBodyMoveBaseRSO (protocols::toolbox::rotamer_set_operations); RigidBodyMover (protocols::rigid); RigidBodyMoveRSO (protocols::toolbox::rotamer_set_operations); RigidBodyPerturbMover (protocols::rigid); RigidBodyPerturbNoCenterMover (protocols::rigid); RigidBodyPerturbNoCenterMoverCreator (protocols::rigid); RigidBodyPerturbRandomJumpMover (protocols::rigid); RigidBodyRandomizeMover (protocols::rigid); RigidBodyRandomTMHMover (protocols::topology_broker); RigidBodySilentStruct (core::io::silent); RigidBodySilentStructCreator (core::io::silent); RigidBodySpinMover (protocols::rigid); RigidBodyStepWiseSampler (protocols::stepwise::sampler::rigid_body); RigidBodyStepWiseSamplerValueRange (protocols::stepwise::sampler::rigid_body); RigidBodyStepWiseSamplerWithResidueAlternatives (protocols::stepwise::sampler::rigid_body); RigidBodyStepWiseSamplerWithResidueList (protocols::stepwise::sampler::rigid_body); RigidBodyTiltMover (protocols::rigid); RigidBodyTiltMoverCreator (protocols::rigid); RigidBodyTransMover (protocols::rigid); RigidBodyTransMoverCreator (protocols::rigid); RigidChunkClaimer (protocols::topology_broker); RigidChunkCM (protocols::abinitio::abscript); RigidChunkCMCreator (protocols::abinitio::abscript); RigidDistanceVisitor (core::chemical); RigidLigandBuilder (protocols::match::downstream); RigidScore (protocols::sic_dock); RigidSearchMover (protocols::ligand_docking); RingClosureEnergy (core::energy_methods); RingClosureEnergyCreator (core::energy_methods); RingConformationMover (protocols::simple_moves); RingConformationMoverCreator (protocols::simple_moves); RingConformer (core::chemical::rings); RingConformerManager (core::chemical::rings); RingConformerSet (core::chemical::rings); RingData (protocols::sparta); RingPlaneFlipMover (protocols::carbohydrates); RingPlaneFlipMoverCreator (protocols::carbohydrates); RMS_Energy (core::energy_methods); RMS_EnergyCreator (core::energy_methods); RMSandEnergyCMP (core::scoring::motif); RMSComparator (protocols::loop_grower); RmsdEvaluator (protocols::simple_filters); RmsdEvaluatorCreator (protocols::simple_filters); RmsdFilter (protocols::protein_interface_design::filters); RmsdFilterCreator (protocols::protein_interface_design::filters); RmsdFromResidueSelectorFilter (protocols::fold_from_loops::filters); RmsdFromResidueSelectorFilterCreator (protocols::fold_from_loops::filters); RMSDMetric (core::simple_metrics::metrics); RMSDMetricCreator (core::simple_metrics::metrics); RMSDReporter (protocols::pose_reporters); RMSDReporterCreator (protocols::pose_reporters); RmsdSimpleFilter (protocols::protein_interface_design::filters); RmsdSimpleFilterCreator (protocols::protein_interface_design::filters); RmsdTargetEvaluatorCreator (protocols::simple_filters); RMSVallData (protocols::frags); RNA_AddDeleteMonteCarlo (protocols::stepwise::monte_carlo::rna); RNA_AnalyticLoopCloser (protocols::stepwise::legacy::modeler::rna); RNA_AtomVDW (core::scoring::rna); RNA_AtrRepChecker (protocols::stepwise::modeler::rna::checker); RNA_AtrRepScreener (protocols::stepwise::legacy::screener); RNA_BaseCentroidChecker (protocols::stepwise::modeler::rna::checker); RNA_BasePairHandler (core::import_pose); RNA_BasicOptions (core::import_pose::options); RNA_BulgeEnergy (core::energy_methods); RNA_BulgeEnergyCreator (core::energy_methods); RNA_CentroidInfo (core::scoring::rna); RNA_ChainClosableGeometryChecker (protocols::stepwise::modeler::rna::checker); RNA_ChainClosableGeometryResidueBasedScreener (protocols::stepwise::screener); RNA_ChainClosableGeometryScreener (protocols::stepwise::screener); RNA_ChainClosableGeometryStubBasedScreener (protocols::stepwise::screener); RNA_ChainClosureChecker (protocols::stepwise::modeler::rna::checker); RNA_ChainClosureScreener (protocols::stepwise::screener); RNA_ChemicalMappingEnergy (core::energy_methods); RNA_ChemicalMappingEnergyCreator (core::energy_methods); RNA_ChemicalShiftEnergy (core::energy_methods); RNA_ChemicalShiftEnergyCreator (core::energy_methods); RNA_ChemicalShiftPotential (core::scoring::rna::chemical_shift); RNA_ChiStepWiseSampler (protocols::stepwise::sampler::rna); RNA_ChunkLibrary (core::import_pose::libraries); RNA_CoarseDistEnergy (core::energy_methods); RNA_CoarseDistEnergyCreator (core::energy_methods); RNA_Coarsify (protocols::rna::movers); RNA_CoarsifyCreator (protocols::rna::movers); RNA_CS_parameters (core::scoring::rna::chemical_shift); RNA_CS_residue_parameters (core::scoring::rna::chemical_shift); RNA_CSA_JobDistributor (protocols::rna::setup); RNA_DataBackboneEnergy (core::energy_methods); RNA_DataBackboneEnergyCreator (core::energy_methods); RNA_DataInfo (core::pose::rna); RNA_DataReader (core::io::rna); RNA_Datum (core::pose::rna); RNA_Decoarsify (protocols::rna::movers); RNA_DecoarsifyCreator (protocols::rna::movers); RNA_DeNovoJobOutputter (protocols::jd2); RNA_DeNovoJobOutputterCreator (protocols::jd2); RNA_DeNovoMasterMover (protocols::rna::denovo::movers); RNA_DeNovoOptimizer (protocols::rna::movers); RNA_DeNovoParameters (core::import_pose); RNA_DeNovoPoseInitializer (protocols::rna::denovo); RNA_DeNovoProtocol (protocols::rna::denovo); RNA_DeNovoProtocolCreator (protocols::rna::denovo); RNA_DeNovoProtocolMover (protocols::rna::denovo::movers); RNA_DeNovoProtocolMoverCreator (protocols::rna::denovo::movers); RNA_DeNovoProtocolOptions (core::import_pose::options); RNA_DeNovoSetup (core::import_pose); RNA_DMS_LowResolutionPotential (core::scoring::rna::data); RNA_DMS_Potential (core::scoring::rna::data); RNA_EnergyMethodOptions (core::scoring::rna); RNA_FA_ElecEnergy (core::energy_methods); RNA_FA_ElecEnergyCreator (core::energy_methods); RNA_FilteredBaseBaseInfo (core::pose::rna); RNA_FittedTorsionInfo (core::chemical::rna); RNA_FragmentHomologyExclusion (core::fragment::rna); RNA_FragmentMonteCarlo (protocols::rna::denovo); RNA_FragmentMonteCarloOptions (core::import_pose::options); RNA_FragmentMonteCarloOutputter (protocols::rna::denovo::output); RNA_FragmentMover (protocols::rna::denovo::movers); RNA_Fragments (core::fragment::rna); RNA_FullAtomStackingEnergy (core::energy_methods); RNA_FullAtomStackingEnergyCreator (core::energy_methods); RNA_FullAtomVDW_BasePhosphate (core::energy_methods); RNA_FullAtomVDW_BasePhosphateCreator (core::energy_methods); RNA_HelixAssembler (core::import_pose); RNA_HelixMover (protocols::rna::denovo::movers); RNA_IdealCoord (core::pose::rna); RNA_Info (core::chemical::rna); RNA_JobDistributor (protocols::rna::setup); RNA_JR_SuiteEnergy (core::energy_methods); RNA_JR_SuiteEnergyCreator (core::energy_methods); RNA_JumpLibrary (core::import_pose::libraries); RNA_JumpMover (core::import_pose); RNA_KIC_Sampler (protocols::stepwise::sampler::rna); RNA_KinematicCloser (protocols::stepwise::sampler::rna); RNA_LibraryManager (core::import_pose::libraries); RNA_LJ_BaseEnergy (core::energy_methods); RNA_LJ_BaseEnergyCreator (core::energy_methods); RNA_LoopCloser (protocols::rna::movers); RNA_LowResolutionPotential (core::scoring::rna); RNA_LowResolutionPotentialCreator (core::scoring::rna); RNA_MgPointEnergy (core::energy_methods); RNA_MgPointEnergyCreator (core::energy_methods); RNA_Minimizer (protocols::rna::denovo::movers); RNA_MinimizerOptions (core::import_pose::options); RNA_MonteCarloJobDistributor (protocols::rna::setup); RNA_Motif (core::scoring::rna); RNA_Motifs (core::scoring::rna); RNA_NucleosideStepWiseSampler (protocols::stepwise::sampler::rna); RNA_O2PrimeMover (protocols::stepwise::monte_carlo::rna); RNA_PairingTemplate (core::import_pose::libraries); RNA_PairwiseLowResolutionEnergy (core::energy_methods); RNA_PairwiseLowResolutionEnergyCreator (core::energy_methods); RNA_PartitionEnergy (core::energy_methods); RNA_PartitionEnergyCreator (core::energy_methods); RNA_RawBaseBaseInfo (core::pose::rna); RNA_Reactivity (core::pose::rna); RNA_Relaxer (protocols::rna::denovo::movers); RNA_ResidueLevelTask (core::pack::task::rna); RNA_ScoringInfo (core::scoring::rna); RNA_SecStruct (core::pose::rna); RNA_SecStructLegacyInfo (core::pose::rna::secstruct_legacy); RNA_SilentStruct (core::io::silent); RNA_SilentStructCreator (core::io::silent); RNA_StubCoordinateEnergy (core::energy_methods); RNA_StubCoordinateEnergyCreator (core::energy_methods); RNA_SugarCloseEnergy (core::energy_methods); RNA_SugarCloseEnergyCreator (core::energy_methods); RNA_SugarStepWiseSampler (protocols::stepwise::sampler::rna); RNA_SuiteAssignment (core::pose::rna); RNA_SuiteEnergy (core::energy_methods); RNA_SuiteEnergyCreator (core::energy_methods); RNA_SuiteInfo (core::pose::rna); RNA_SuiteName (core::pose::rna); RNA_SuitePotential (core::scoring::rna); RNA_SuiteStepWiseSampler (protocols::stepwise::sampler::rna); RNA_TorsionEnergy (core::energy_methods); RNA_TorsionEnergyCreator (core::energy_methods); RNA_TorsionMover (protocols::stepwise::monte_carlo::rna); RNA_TorsionPotential (core::scoring::rna); RNA_TorsionScreener (protocols::stepwise::sampler::screener); RNA_VDW_BinChecker (protocols::stepwise::modeler::rna::checker); RNA_VDW_Energy (core::energy_methods); RNA_VDW_EnergyCreator (core::energy_methods); RNAIdealizeMover (protocols::rna::movers); RNAIdealizeMoverCreator (protocols::rna::movers); RNAThreadAndMinimizeMover (protocols::rna::movers); RNAThreadAndMinimizeMoverCreator (protocols::rna::movers); RNP_HighResMover (protocols::rna::denovo::movers); RNP_LowResEnergy (core::energy_methods); RNP_LowResEnergyCreator (core::energy_methods); RNP_LowResPairDistEnergy (core::energy_methods); RNP_LowResPairDistEnergyCreator (core::energy_methods); RNP_LowResPairDistPotential (core::scoring::rna); RNP_LowResPotential (core::scoring::rna); RNP_LowResStackData (core::scoring::rna); RNP_LowResStackEnergy (core::energy_methods); RNP_LowResStackEnergyCreator (core::energy_methods); RollMover (protocols::rigid); RollMoverCreator (protocols::rigid); RootData (core::chemical::carbohydrates); Rose (protocols::sic_dock); RosettaScriptsJobQueen (protocols::rosetta_scripts); RosettaScriptsParser (protocols::rosetta_scripts); RosettaScriptsSchemaValidator (protocols::rosetta_scripts); RosettaTensorflowProtocolBase (basic::tensorflow_manager); ROT (protocols::splice); RotamerAssigningAnnealer (core::pack::annealer); RotamerBoltzCalculator (protocols::pose_metric_calculators); RotamerBoltzmannWeight (protocols::calc_taskop_filters); RotamerBoltzmannWeight2 (protocols::calc_taskop_filters); RotamerBoltzmannWeight2Creator (protocols::calc_taskop_filters); RotamerBoltzmannWeightEvaluator (protocols::toolbox); RotamerBoltzmannWeightFeatures (protocols::features); RotamerBoltzmannWeightFeaturesCreator (protocols::features); RotamerBoltzmannWeightFilterCreator (protocols::calc_taskop_filters); RotamerBuildingData (core::pack::dunbrack); RotamerConstraint (core::pack::dunbrack); RotamerCouplings (core::pack::rotamer_set); RotamerDescriptor (core::scoring::trie); RotamerDescriptorAtom (core::scoring::trie); RotamerDNAHBondFilter (protocols::dna); RotamerDots (core::pack::interaction_graph); RotamerDotsCache (core::pack::interaction_graph); RotamerDotsRadiusData (core::pack::interaction_graph); RotamerDumpMover (protocols::RotamerDump); RotamerExplosion (core::pack::task::operation); RotamerExplosionCreator (core::pack::task::operation); RotamerFeatures (protocols::features); RotamerFeaturesCreator (protocols::features); RotamericData (core::pack::dunbrack); RotamericSingleResidueDunbrackLibrary (core::pack::dunbrack); RotamericSingleResidueDunbrackLibraryParser (core::pack::dunbrack); RotamerInitializer (protocols::features); RotamerizeMover (protocols::minimization_packing); RotamerLibrary (core::pack::dunbrack); RotamerLibraryInterpolationScratch (core::pack::dunbrack); RotamerLibraryScratchSpace (core::pack::dunbrack); RotamerLibrarySpecification (core::chemical::rotamers); RotamerLibrarySpecificationCreator (core::chemical::rotamers); RotamerLibrarySpecificationFactory (core::chemical::rotamers); RotamerLibrarySpecificationRegistrator (core::chemical::rotamers); RotamerLinks (core::pack::rotamer_set); RotamerOperation (core::pack::rotamer_set); RotamerPairEnergies (protocols::ligand_docking::ga_ligand_dock); RotamerRecovery (protocols::pose_metric_calculators); RotamerRecovery (protocols::rotamer_recovery); RotamerRecoveryFactory (protocols::rotamer_recovery); RotamerRecoveryFeatures (protocols::features); RotamerRecoveryFeaturesCreator (protocols::features); RotamerRecoveryMover (protocols::rotamer_recovery); RotamerRecoveryMoverCreator (protocols::rotamer_recovery); RotamerRecoveryRegistrator (protocols::rotamer_recovery); RotamerRotamerHasher (core::pack::guidance_scoreterms::sap); RotamerSet (core::pack::rotamer_set); RotamerSet_ (core::pack::rotamer_set); RotamerSetBase (core::conformation); RotamerSetFactory (core::pack::rotamer_set); RotamerSetOperation (core::pack::rotamer_set); RotamerSets (core::pack::rotamer_set); RotamerSetsBase (core::pack_basic); RotamerSetsFactory (core::pack::rotamer_set); RotamerSetsOperation (core::pack::rotamer_set); RotamerSubset (core::pack::rotamer_set); RotamerSubsetRepacker (protocols::pack_daemon); RotamerSubsets (core::pack::rotamer_set); RotamerTrialsMinMover (protocols::minimization_packing); RotamerTrialsMinMoverCreator (protocols::minimization_packing); RotamerTrialsMover (protocols::minimization_packing); RotamerTrialsMoverCreator (protocols::minimization_packing); RotamerTrialsRefiner (protocols::loop_modeling::refiners); RotamerTrialsRefinerCreator (protocols::loop_modeling::refiners); RotamerTrie (core::scoring::trie); RotamerTrieBase (core::scoring::trie); Rotate (protocols::ligand_docking); Rotate_info (protocols::ligand_docking); RotateCreator (protocols::ligand_docking); RotateJumpAxisMover (protocols::rigid); Rotates (protocols::ligand_docking); RotatesCreator (protocols::ligand_docking); RotateSegmentMover (protocols::denovo_design::movers); RotateSegmentMoverCreator (protocols::denovo_design::movers); RotationMover (protocols::membrane); RotationMoverCreator (protocols::membrane); RotationRange (protocols::denovo_design::movers); RotationSearchPattern (protocols::hotspot_hashing); RotData (protocols::make_rot_lib); RotLibdb (protocols::splice); RotLibOut (protocols::splice); RotLibOutCreator (protocols::splice); RotMatrix (protocols::mean_field); RotProb (protocols::mean_field); RotSub (core::pack::annealer); RouletteSelector (protocols::ligand_evolution); RPM_FilterStats (core::scoring::motif); RRComparer (protocols::rotamer_recovery); RRComparerAutomorphicRMSD (protocols::rotamer_recovery); RRComparerAutomorphicRMSDCreator (protocols::rotamer_recovery); RRComparerChiDiff (protocols::rotamer_recovery); RRComparerChiDiffCreator (protocols::rotamer_recovery); RRComparerCreator (protocols::rotamer_recovery); RRComparerElecDensDiff (protocols::rotamer_recovery); RRComparerElecDensDiffCreator (protocols::rotamer_recovery); RRComparerRotBins (protocols::rotamer_recovery); RRComparerRotBinsCreator (protocols::rotamer_recovery); RRProtocol (protocols::rotamer_recovery); RRProtocolCreator (protocols::rotamer_recovery); RRProtocolMinPack (protocols::rotamer_recovery); RRProtocolMinPackCreator (protocols::rotamer_recovery); RRProtocolMover (protocols::rotamer_recovery); RRProtocolMoverCreator (protocols::rotamer_recovery); RRProtocolPackRotamers (protocols::rotamer_recovery); RRProtocolPackRotamersCreator (protocols::rotamer_recovery); RRProtocolReferenceStructure (protocols::rotamer_recovery); RRProtocolReferenceStructureCreator (protocols::rotamer_recovery); RRProtocolRelax (protocols::rotamer_recovery); RRProtocolRelaxCreator (protocols::rotamer_recovery); RRProtocolRotamerTrials (protocols::rotamer_recovery); RRProtocolRotamerTrialsCreator (protocols::rotamer_recovery); RRProtocolRTMin (protocols::rotamer_recovery); RRProtocolRTMinCreator (protocols::rotamer_recovery); RRReporter (protocols::rotamer_recovery); RRReporterCreator (protocols::rotamer_recovery); RRReporterHuman (protocols::rotamer_recovery); RRReporterHumanCreator (protocols::rotamer_recovery); RRReporterSimple (protocols::rotamer_recovery); RRReporterSimpleCreator (protocols::rotamer_recovery); RRReporterSQLite (protocols::rotamer_recovery); RRReporterSQLiteCreator (protocols::rotamer_recovery); RT (core::kinematics); RT_helper (core::scoring::disulfides); RTConstraint (core::scoring::constraints); RTMin (core::pack); running_average_pair (protocols::make_rot_lib); RunSimpleMetricsMover (protocols::analysis::simple_metrics); RunSimpleMetricsMoverCreator (protocols::analysis::simple_metrics); RuntimeFeatures (protocols::features); RuntimeFeaturesCreator (protocols::features)

S: SA_Energy (core::energy_methods); SA_EnergyCreator (core::energy_methods); SaltBridgeCalculator (protocols::pose_metric_calculators); SaltBridgeFeatures (protocols::features); SaltBridgeFeaturesCreator (protocols::features); SameChiBinComboGrouper (protocols::match::output); SameRotamerComboGrouper (protocols::match::output); SameSequenceAndDSPositionGrouper (protocols::match::output); SameSequenceGrouper (protocols::match::output); SameStrand (protocols::jumping); SampleApplier (protocols::stepwise::screener); SampleFarnesylMover (protocols::farnesyl); SampleFarnesylMoverCreator (protocols::farnesyl); SampleGrid (protocols::magnesium); SampleRotamersFromPDB (protocols::splice); SampleRotamersFromPDB_RotamerSetOperation (protocols::splice); SampleRotamersFromPDBCreator (protocols::splice); SamplerPlusPlus (protocols::toolbox); SampleSequenceFromProbabilities (protocols::simple_moves); SampleSequenceFromProbabilitiesCreator (protocols::simple_moves); SampleStrategyData (protocols::match::upstream); SampleTiltAngles (protocols::membrane::benchmark); SampleTiltAnglesCreator (protocols::membrane::benchmark); SandwichFeatures (protocols::features::strand_assembly); SandwichFeaturesCreator (protocols::features::strand_assembly); SandwichFragment (protocols::features::strand_assembly); SaneDockingProtocol (protocols::docking::stateless); SaneMinMover (protocols::minimization_packing); SaneMinMoverCreator (protocols::minimization_packing); SAnode (core::scoring::power_diagram); SAnode (core::scoring); SapConstraint (core::pack::guidance_scoreterms::sap); SapConstraintEnergy (core::pack::guidance_scoreterms::sap); SapConstraintEnergyCreator (core::pack::guidance_scoreterms::sap); SapConstraintHelper (core::pack::guidance_scoreterms::sap); SapConstraintOptions (core::pack::guidance_scoreterms::sap); SapDatabase (core::pack::guidance_scoreterms::sap); SapMathConstraint (core::pack::guidance_scoreterms::sap); SapParameterOptions (core::pack::guidance_scoreterms::sap); SapScoreMetric (core::pack::guidance_scoreterms::sap); SapScoreMetricCreator (core::pack::guidance_scoreterms::sap); SasaCalc (core::scoring::sasa); SasaCalculator2 (core::pose::metrics::simple_calculators); SasaCalculatorLegacy (core::pose::metrics::simple_calculators); SASAEnergy (core::energy_methods); SASAEnergyCreator (core::energy_methods); SasaMethod (core::scoring::sasa); SasaMetric (core::simple_metrics::metrics); SasaMetricCreator (core::simple_metrics::metrics); SasaOptions (core::scoring::packstat); SASAPotential (core::scoring); SasaResult (core::scoring::packstat); SAScoreData (protocols::drug_design); SAScoreFilter (protocols::drug_design); SAScoreFilterCreator (protocols::drug_design); SaveAndRetrieveSidechains (protocols::protein_interface_design::movers); SaveAndRetrieveSidechainsCreator (protocols::protein_interface_design::movers); SavePDBInfoMover (protocols::fold_from_loops::movers); SavePDBInfoMoverCreator (protocols::fold_from_loops::movers); SavePoseConstraintToFileFilter (protocols::constraint_filters); SavePoseConstraintToFileFilterCreator (protocols::constraint_filters); SavePoseMover (protocols::rosetta_scripts); SavePoseMoverCreator (protocols::rosetta_scripts); SaveProbabilitiesMetricMover (protocols::simple_moves); SaveProbabilitiesMetricMoverCreator (protocols::simple_moves); SaveResfileToDiskFilter (protocols::simple_filters); SaveResfileToDiskFilterCreator (protocols::simple_filters); SaveSequenceToCommentsMover (protocols::simple_moves); SaveSequenceToCommentsMoverCreator (protocols::simple_moves); SAXSEnergy (core::energy_methods); SAXSEnergyCEN (core::energy_methods); SAXSEnergyCreator (core::energy_methods); SAXSEnergyCreatorCEN (core::energy_methods); SAXSEnergyCreatorFA (core::energy_methods); SAXSEnergyFA (core::energy_methods); SAXSScoreFilter (protocols::simple_filters); SC_BB_EnergyInvoker (core::scoring::etable); SC_SC_EnergyInvoker (core::scoring::etable); SC_Whole_EnergyInvoker (core::scoring::etable); ScaffoldBuildPoint (protocols::match::upstream); ScalarWeightedFunc (core::scoring::func); ScaleAnnealerTemperatureOperation (protocols::optimize_weights); ScaleMapIntensities (protocols::electron_density); ScaleMapIntensitiesCreator (protocols::electron_density); SCAN (core::pack::task); Scheduler (protocols::mpi_refinement); SchemePlaceMotifsMover (protocols::matdes); SchemePlaceMotifsMoverCreator (protocols::matdes); SCMinMinimizerMap (core::pack::scmin); SCMinMultifunc (core::pack::scmin); ScoreCache (core::energy_methods); ScoreCutoffFilter (protocols::score_filters); ScoreCutoffFilterCreator (protocols::score_filters); ScoredBridgingWater (core::scoring::lkball); ScoreEValuator (protocols::frag_picker::scores); ScoreEvaluator (protocols::simple_filters); ScoreFileData (core::io::raw_data); ScoreFileOutputSpecification (protocols::jd3::pose_outputters); ScoreFileOutputter (protocols::jd3::pose_outputters); ScoreFileOutputterCreator (protocols::jd3::pose_outputters); ScoreFileSilentStruct (core::io::silent); ScoreFileSilentStructCreator (core::io::silent); ScoreFunction (core::scoring); ScoreFunctionFactory (core::scoring); ScoreFunctionFeatures (protocols::features); ScoreFunctionFeaturesCreator (protocols::features); ScoreFunctionInfo (core::scoring); ScoreFunctionKey (core::scoring); ScoreFunctionLoader (protocols::parser); ScoreFunctionLoaderCreator (protocols::parser); ScoreJumpFileSilentStruct (core::io::silent); ScoreJumpFileSilentStructCreator (core::io::silent); ScoreLessThanComparator (core::import_pose::atom_tree_diffs); ScoreMap (core::io::raw_data); ScoreMover (protocols::simple_moves); ScoreMoverCreator (protocols::simple_moves); ScoreNormalization (protocols::qsar::scoring_grid); ScoreOnlyJobOutputter (protocols::jd2); ScoreOnlyJobOutputterCreator (protocols::jd2); ScorePoseSegmentFromResidueSelectorFilter (protocols::fold_from_loops::filters); ScorePoseSegmentFromResidueSelectorFilterCreator (protocols::fold_from_loops::filters); Scorer (protocols::ligand_evolution); Scorer (protocols::stepwise::screener); ScoreRmsPoint (protocols::toolbox); ScoreRmsPoints (protocols::toolbox); ScoreStructJSON (core::io::raw_data); ScoreStructText (core::io::raw_data); ScoreTermValueBasedSelector (core::select::residue_selector); ScoreTermValueBasedSelectorCreator (core::select::residue_selector); ScoreTypeFeatures (protocols::features); ScoreTypeFeaturesCreator (protocols::features); ScoreTypeFilter (protocols::score_filters); ScoreTypeFilterCreator (protocols::score_filters); ScoreTypeManager (core::scoring); ScoringGridLoader (protocols::qsar::scoring_grid); ScoringGridLoaderCreator (protocols::qsar::scoring_grid); ScoringManager (core::scoring); ScoringScheme (core::sequence); ScoringSchemeFactory (core::sequence); ScoringSecMatchRPE (protocols::match::downstream); ScreeningFeatures (protocols::features); ScreeningFeaturesCreator (protocols::features); ScreeningJobInputter (protocols::jd2); ScreeningJobInputterCreator (protocols::jd2); ModuleType1::screw_construct_struct (core::kinematics::jacobian); ScriptCM (protocols::environment); ScriptCMCreator (protocols::environment); sd_index (core::io::mmtf); SDFParser (core::chemical::sdf); SealFoldTreeMover (protocols::denovo_design::movers); SealFoldTreeMoverCreator (protocols::denovo_design::movers); SearchPattern (protocols::hotspot_hashing); SearchPatternExpansion (protocols::hotspot_hashing); SearchPatternRotSetOp (protocols::hotspot_hashing); SearchPatternTransform (protocols::hotspot_hashing); SecMatchEvaluatorFactory (protocols::match::downstream); SecMatchResiduePairEvaluator (protocols::match::downstream); SecondaryIdentity (protocols::frag_picker::scores); SecondaryMatcherToDownstreamResidue (protocols::match::downstream); SecondaryMatcherToUpstreamResidue (protocols::match::downstream); SecondaryMatchProtocol (protocols::enzdes); SecondaryMatchUpstreamResProcessor (protocols::match::downstream); SecondaryPoseOutputter (protocols::jd3::pose_outputters); SecondaryPoseOutputterCreator (protocols::jd3::pose_outputters); SecondaryPoseOutputterRegistrator (protocols::jd3::pose_outputters); SecondarySimilarity (protocols::frag_picker::scores); SecondaryStructure (core::fragment); SecondaryStructureCountFilter (protocols::fldsgn::filters); SecondaryStructureCountFilterCreator (protocols::fldsgn::filters); SecondaryStructureEnergy (core::energy_methods); SecondaryStructureEnergyCreator (core::energy_methods); SecondaryStructureFilter (protocols::fldsgn::filters); SecondaryStructureFilterCreator (protocols::fldsgn::filters); SecondaryStructureHasResidueFilter (protocols::fldsgn::filters); SecondaryStructureHasResidueFilterCreator (protocols::fldsgn::filters); SecondaryStructureMetric (core::simple_metrics::metrics); SecondaryStructureMetricCreator (core::simple_metrics::metrics); SecondaryStructureMPM (protocols::match); SecondaryStructurePool (protocols::frag_picker::quota); SecondaryStructurePotential (core::scoring); SecondaryStructureSegment (protocols::features); SecondaryStructureSegmentFeatures (protocols::features); SecondaryStructureSegmentFeaturesCreator (protocols::features); SecondaryStructureSelector (core::select::residue_selector); SecondaryStructureSelectorCreator (core::select::residue_selector); SecondaryStructureWeights (core::scoring); SecretionOptimizationMover (protocols::protein_interface_design::movers); SecretionOptimizationMoverCreator (protocols::protein_interface_design::movers); SecretionPredictionFilter (protocols::simple_filters); SecretionPredictionFilterCreator (protocols::simple_filters); SecStructFinder (protocols::ncbb); SecStructFinderCreator (protocols::ncbb); SecStructGen (core::fragment::picking_old::vall::gen); SecStructInfo (protocols::denovo_design::architects); SecStructMinimizeMover (protocols::ncbb); SecStructMinimizeMoverCreator (protocols::ncbb); SecStructMinimizeMultiFunc (protocols::ncbb); SecstructSRFD (core::fragment); SeedFoldTree (protocols::seeded_abinitio); SeedFoldTreeCreator (protocols::seeded_abinitio); SeedSettings (protocols::pose_sewing::movers); SeedSetupMover (protocols::seeded_abinitio); SeedSetupMoverCreator (protocols::seeded_abinitio); Segment (protocols::denovo_design::components); Segment (protocols::features); Segment (protocols::forge::remodel); segment (protocols::legacy_sewing); SegmentContactOrderScorer (protocols::sewing::scoring); SegmentContactOrderScorerCreator (protocols::sewing::scoring); SegmentCounts (protocols::denovo_design::components); SegmentedAtomPairConstraintGenerator (protocols::fold_from_loops::constraint_generator); SegmentedAtomPairConstraintGeneratorCreator (protocols::fold_from_loops::constraint_generator); SegmentEnvelope (protocols::pose_sewing::data_storage); SegmentGraph (protocols::legacy_sewing); SegmentHybridizer (protocols::seeded_abinitio); SegmentHybridizerCreator (protocols::seeded_abinitio); SegmentInsert (protocols::forge::build); SegmentPairing (protocols::denovo_design::components); SegmentPairSet (protocols::denovo_design::components); SegmentRebuild (protocols::forge::build); SegmentSequenceProfile (protocols::indexed_structure_store); SegmentSequenceProfileConfig (protocols::indexed_structure_store); SegmentSequenceProfileMover (protocols::indexed_structure_store::movers); SegmentSequenceProfileMoverCreator (protocols::indexed_structure_store::movers); SegmentSequenceProfileResult (protocols::indexed_structure_store); SegmentSpec (protocols::seeded_abinitio); SegmentSwap (protocols::forge::build); SegmentVector (protocols::sewing::hashing); SelectByDeltaScoreOperation (protocols::task_operations); SelectByDeltaScoreOperationCreator (protocols::task_operations); SelectByDensityFitOperation (protocols::task_operations); SelectByDensityFitOperationCreator (protocols::task_operations); SelectBySASAOperation (protocols::task_operations); SelectBySASAOperationCreator (protocols::task_operations); SelectDensityPointsOptions (protocols::electron_density); SelectedResidueCountMetric (core::simple_metrics::metrics); SelectedResidueCountMetricCreator (core::simple_metrics::metrics); SelectedResiduesMetric (core::simple_metrics::metrics); SelectedResiduesMetricCreator (core::simple_metrics::metrics); SelectedResiduesPyMOLMetric (core::simple_metrics::metrics); SelectedResiduesPyMOLMetricCreator (core::simple_metrics::metrics); SelectedResPredicate (core::scoring); SelectGdtEvaluator (protocols::simple_filters); SelectMaxsubEvaluator (protocols::simple_filters); Selector (protocols::ligand_evolution); Selector_AA (core::chemical); Selector_BASENAME (core::chemical); Selector_CMDFLAG (core::chemical); Selector_HAS_ATOMS (core::chemical); Selector_MATCH_VARIANTS (core::chemical); Selector_NAME1 (core::chemical); Selector_NAME3 (core::chemical); Selector_NO_VARIANTS (core::chemical); Selector_PROPERTY (core::chemical); Selector_UPPER_ATOM (core::chemical); Selector_VARIANT_TYPE (core::chemical); SelectorLogicParser (core::select::residue_selector); SelectRDC_Evaluator (protocols::simple_filters); SelectResiduesByLayer (core::select::util); SelectResiduesWithinChainOperation (protocols::task_operations); SelectResiduesWithinChainOperationCreator (protocols::task_operations); SelectRmsdEvaluator (protocols::simple_filters); SemiExplicitWaterUnsatisfiedPolarsCalculator (protocols::pose_metric_calculators); SemiRotamericSingleResidueDunbrackLibrary (core::pack::dunbrack); SeparateDnaFromNonDna (protocols::dna); SeparateDnaFromNonDnaCreator (protocols::dna); SeqprofConsensusOperation (protocols::task_operations); SeqprofConsensusOperationCreator (protocols::task_operations); SeqSymmAnnealerSetup (core::pack::annealer); Sequence (core::sequence); SequenceAlignment (core::sequence); SequenceAlignmentHasher (core::sequence); SequenceAnnotation (core::environment); SequenceClaim (protocols::topology_broker::claims); SequenceClaimer (protocols::topology_broker); SequenceComparison (protocols::pose_metric_calculators); SequenceConstraint (core::scoring::aa_composition_energy); SequenceCoupling (core::sequence); SequenceCoupling1BDConstraint (protocols::constraints_additional); SequenceCoupling1BDConstraintCreator (protocols::constraints_additional); SequenceCouplingConstraint (protocols::constraints_additional); SequenceCouplingConstraintCreator (protocols::constraints_additional); SequenceCouplingCreator (core::sequence); SequenceCreator (core::sequence); SequenceDependentRefEnergy (core::energy_methods); SequenceDependentRefEnergyCreator (core::energy_methods); SequenceDistance (protocols::simple_filters); SequenceDistanceFilterCreator (protocols::simple_filters); SequenceFactory (core::sequence); SequenceIdentity (protocols::frag_picker::scores); SequenceMapping (core::id); SequenceMetric (core::simple_metrics::metrics); SequenceMetric (protocols::multistage_rosetta_scripts::cluster::metrics); SequenceMetricCreator (core::simple_metrics::metrics); SequenceMetricCreator (protocols::multistage_rosetta_scripts::cluster::metrics); SequenceMotifTaskOperation (protocols::task_operations); SequenceMotifTaskOperationCreator (protocols::task_operations); SequenceMover (protocols::moves); SequenceMoverCreator (protocols::moves); SequenceNumberResolver (protocols::topology_broker); SequenceProfile (core::sequence); SequenceProfileConstraint (core::scoring::constraints); SequenceProfileConstraintCreator (core::scoring::constraints); SequenceProfileCreator (core::sequence); SequenceProfileMover (protocols::simple_moves); SequenceProfileMoverCreator (protocols::simple_moves); SequenceRecoveryFilter (protocols::protein_interface_design::filters); SequenceRecoveryFilterCreator (protocols::protein_interface_design::filters); SequenceRecoveryMetric (protocols::analysis::simple_metrics); SequenceRecoveryMetricCreator (protocols::analysis::simple_metrics); SequenceRegistrator (core::sequence); SequenceShiftMover (protocols::rbsegment_relax); SequenceSimilarityMetric (core::simple_metrics::metrics); SequenceSimilarityMetricCreator (core::simple_metrics::metrics); SequenceSpecification (protocols::pdbinfo_manipulations); SequenceSymmetricAnnealer (core::pack::annealer); SequentialSymmetrySlider (protocols::symmetry); Serial_Refine (protocols::mpi_refinement); SerializedLoop (protocols::loops); SerializedPoseJobInputter (protocols::jd2); SerializedPoseJobInputterCreator (protocols::jd2); SerializedPoseJobOutputter (protocols::jd2); SerializedPoseJobOutputterCreator (protocols::jd2); SeriesJacobians (core::kinematics::jacobian); NetworkQueue::ServerAddress (protocols::network); Set_AA (core::chemical); SetAACompositionPotential (protocols::fldsgn::potentials); SetAACompositionPotentialCreator (protocols::fldsgn::potentials); SetAACreator (core::chemical); SetAllAtomsRepulsive (core::chemical); SetAllAtomsRepulsiveCreator (core::chemical); SetAncestorCreator (core::chemical); SetAtomicCharge (core::chemical); SetAtomicChargeCreator (core::chemical); SetAtomTree (protocols::protein_interface_design::movers); SetAtomTreeCreator (protocols::protein_interface_design::movers); SetAtomType (core::chemical); SetAtomTypeCreator (core::chemical); SetBackboneHeavyatom (core::chemical); SetBackboneHeavyatomCreator (core::chemical); SetBaseName (core::chemical); SetBaseNameCreator (core::chemical); SetCatalyticResPackBehavior (protocols::enzdes); SetCatalyticResPackBehaviorCreator (protocols::enzdes); SetChiMover (protocols::simple_moves::sidechain_moves); SetChiMoverCreator (protocols::simple_moves::sidechain_moves); SetCrystWeightMover (protocols::cryst); SetCrystWeightMoverCreator (protocols::cryst); SetDisulfideAtomName (core::chemical); SetDisulfideAtomNameCreator (core::chemical); SetFormalCharge (core::chemical); SetFormalChargeCreator (core::chemical); SetICoor (core::chemical); SetICOORCreator (core::chemical); SetIGTypeOperation (protocols::task_operations); SetIGTypeOperationCreator (protocols::task_operations); SetInterchangeabilityGroup_String (core::chemical); SetInterchangeabilityGroupCreator (core::chemical); SetIO_String (core::chemical); SetIOStringCreator (core::chemical); SetMembraneCenterMover (protocols::membrane); SetMembraneCenterMoverCreator (protocols::membrane); SetMembraneNormalMover (protocols::membrane); SetMembraneNormalMoverCreator (protocols::membrane); SetMembranePositionMover (protocols::membrane); SetMembranePositionMoverCreator (protocols::membrane); SetMMAtomType (core::chemical); SetMMAtomTypeCreator (core::chemical); SetNbrAtom (core::chemical); SetNbrAtomCreator (core::chemical); SetNbrRadius (core::chemical); SetNbrRadiusCreator (core::chemical); SetNetFormalCharge (core::chemical); SetNetFormalChargeCreator (core::chemical); SetOrientAtom (core::chemical); SetOrientAtomCreator (core::chemical); SetPolymerConnectAtom (core::chemical); SetPolymerConnectCreator (core::chemical); SetPoseSecstructFromStructureDataMover (protocols::denovo_design::movers); SetRefinementOptionsMover (protocols::cryst); SetRefinementOptionsMoverCreator (protocols::cryst); SetResidueAliasMover (protocols::denovo_design::movers); SetResidueAliasMoverCreator (protocols::denovo_design::movers); SetReturningPackRotamersMover (protocols::minimization_packing); SetRotamerCouplings (core::pack::task::operation); SetRotamerCouplingsCreator (core::pack::task::operation); SetRotamerLinks (core::pack::task::operation); SetRotamerLinksCreator (core::pack::task::operation); SetSecStructEnergies (protocols::fldsgn::potentials); SetSecStructEnergiesCreator (protocols::fldsgn::potentials); SetTemperatureFactor (protocols::protein_interface_design::movers); SetTemperatureFactorCreator (protocols::protein_interface_design::movers); SetTorsion (protocols::simple_moves); SetTorsionCreator (protocols::simple_moves); SetupForDensityScoringMover (protocols::electron_density); SetupForDensityScoringMoverCreator (protocols::electron_density); SetupForFibrilMover (protocols::fibril); SetupForSequenceSymmetryMover (protocols::symmetry); SetupForSequenceSymmetryMoverCreator (protocols::symmetry); SetupForSymmetryMover (protocols::symmetry); SetupForSymmetryMoverCreator (protocols::symmetry); SetupHotspotConstraintsLoopsMover (protocols::protein_interface_design::movers); SetupHotspotConstraintsLoopsMoverCreator (protocols::protein_interface_design::movers); SetupHotspotConstraintsMover (protocols::protein_interface_design::movers); SetupHotspotConstraintsMoverCreator (protocols::protein_interface_design::movers); SetupMetalsMover (protocols::simple_moves); SetupMetalsMoverCreator (protocols::simple_moves); SetupNCSMover (protocols::symmetry); SetupNCSMoverCreator (protocols::symmetry); SetupPoissonBoltzmannPotential (protocols::pb_potential); SetupPoissonBoltzmannPotentialCreator (protocols::pb_potential); SetVirtualShadow (core::chemical); SetVirtualShadowCreator (core::chemical); SewAnythingAddMover (protocols::pose_sewing::movers); SewAnythingAddMoverCreator (protocols::pose_sewing::movers); SewAtom (protocols::legacy_sewing); SewGraph (protocols::legacy_sewing); SewResidue (protocols::legacy_sewing); SewSegment (protocols::legacy_sewing); SF_Replica (protocols::toolbox); SG_Dist_Func (core::scoring::disulfides); SGSG_Dihedral_Func (core::scoring::disulfides); ShakeStructureMover (protocols::simple_moves); ShapeComplementarityCalculator (core::scoring::sc); ShapeComplementarityCalculatorException (core::scoring::sc); ShapeComplementarityFilter (protocols::simple_filters); ShapeComplementarityFilterCreator (protocols::simple_filters); ShapeGrid (protocols::qsar::scoring_grid); ShapeGridCreator (protocols::qsar::scoring_grid); ShapeSimilarityCalculator (core::scoring::sc); ShapeSimilarityMetric (core::simple_metrics::metrics); ShapeSimilarityMetricCreator (core::simple_metrics::metrics); SharedSilentData (core::io::silent); ShearFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers); ShearMinCCDTrial (protocols::loops::loop_mover::refine); ShearMinCCDTrialCreator (protocols::loops::loop_mover::refine); ShearMover (protocols::simple_moves); ShearMoverCreator (protocols::simple_moves); Sheet (protocols::fldsgn::topology); SheetBuilder (protocols::jumping); SheetConstraintGenerator (protocols::fldsgn); SheetConstraintGeneratorCreator (protocols::fldsgn); SheetDB (protocols::denovo_design::components); SheetFilter (protocols::simple_filters); SheetFoldTypeManager (protocols::fldsgn::topology); SHEETInformation (core::io); SheetPositions (protocols::loop_grower); SheetRemodelConstraintGenerator (protocols::fldsgn); SheetRemodelConstraintGeneratorCreator (protocols::fldsgn); SheetSampler (protocols::loop_grower); SheetSet (protocols::fldsgn::topology); SheetTopologyFilter (protocols::fldsgn::filters); SheetTopologyFilterCreator (protocols::fldsgn::filters); SheetTranslate (protocols::nonlocal); SHOBuriedUnsatisfiedPolarsCalculator (protocols::pose_metric_calculators); ShortBackrubMover (protocols::simple_moves); ShortBackrubMoverCreator (protocols::simple_moves); ShortestPathInFoldTree (core::kinematics); ShortLoopClosure (protocols::loops::loop_closure::ccd); ShortRangeTwoBodyEnergy (core::scoring::methods); ShoveResidueMover (protocols::protein_interface_design::movers); ShoveResidueMoverCreator (protocols::protein_interface_design::movers); ShowConstraintsFilter (protocols::constraint_filters); ShowConstraintsFilterCreator (protocols::constraint_filters); ShowViolation (protocols::abinitio); ShuffleFileSystemJobDistributor (protocols::jd2); SICFast (protocols::sic_dock); SICPatternAtTransform (protocols::hotspot_hashing); SidechainContactDistCutoff (protocols::frag_picker); SideChainCopier (protocols::stepwise::modeler::packer); SidechainMCMover (protocols::simple_moves::sidechain_moves); SidechainMCMoverCreator (protocols::simple_moves::sidechain_moves); SidechainMetropolisHastingsMover (protocols::canonical_sampling); SidechainMetropolisHastingsMoverCreator (protocols::canonical_sampling); SidechainMinMover (protocols::docking); SidechainMover (protocols::simple_moves::sidechain_moves); SidechainMoverBase (protocols::simple_moves::sidechain_moves); SidechainMoverCreator (protocols::simple_moves::sidechain_moves); SidechainNeighborCountMetric (core::simple_metrics::per_residue_metrics); SidechainNeighborCountMetricCreator (core::simple_metrics::per_residue_metrics); SidechainRmsdFilter (protocols::simple_filters); SidechainRmsdFilterCreator (protocols::simple_filters); SidechainStateAssignment (core::pack::scmin); Sigmoid (protocols::calc_taskop_filters); SigmoidFilterCreator (protocols::calc_taskop_filters); SigmoidFunc (core::scoring::func); SigmoidWeightedCenList (core::scoring); SilentEnergy (core::io::silent); SilentFileData (core::io::silent); SilentFileFullModelInputter (protocols::jd3::full_model_inputters); SilentFileFullModelInputterCreator (protocols::jd3::full_model_inputters); SilentFileJobInputter (protocols::jd2); SilentFileJobInputterCreator (protocols::jd2); SilentFileJobOutputter (protocols::jd2); SilentFileJobOutputterCreator (protocols::jd2); SilentFileOptions (core::io::silent); SilentFilePoseInputStream (core::import_pose::pose_stream); SilentFilePoseInputter (protocols::jd3::pose_inputters); SilentFilePoseInputterCreator (protocols::jd3::pose_inputters); SilentFilePoseOutputSpecification (protocols::jd3::pose_outputters); SilentFilePoseOutputter (protocols::jd3::pose_outputters); SilentFilePoseOutputterCreator (protocols::jd3::pose_outputters); SilentObserver (protocols::viewer); SilentStruct (core::io::silent); SilentStructCreator (core::io::silent); SilentStructFactory (core::io::silent); SilentStructRegistrator (core::io::silent); SilentStructStore (protocols::wum); SilentStructureStoreBackend (protocols::indexed_structure_store); SilentTrajectoryRecorder (protocols::canonical_sampling); SilentTrajectoryRecorderCreator (protocols::canonical_sampling); SimAnnealerBase (core::pack::annealer); SimPDB (protocols::cluster::calibur); Simple; SimpleCycpepPredictApplication (protocols::cyclic_peptide_predict); SimpleDerivCheckResult (core::optimization); SimpleEdge (core::pack::interaction_graph); SimpleGlycosylateMover (protocols::carbohydrates); SimpleGlycosylateMoverCreator (protocols::carbohydrates); SimpleHbondsToAtomFilter (protocols::simple_filters); SimpleHbondsToAtomFilterCreator (protocols::simple_filters); SimpleInteractionGraph (core::pack::interaction_graph); SimpleMetric (core::simple_metrics); SimpleMetricCreator (core::simple_metrics); SimpleMetricData (core::simple_metrics); SimpleMetricFactory (core::simple_metrics); SimpleMetricFeatures (protocols::features); SimpleMetricFeaturesCreator (protocols::features); SimpleMetricFilter (protocols::simple_filters); SimpleMetricFilterCreator (protocols::simple_filters); SimpleMetricLoader (protocols::parser); SimpleMetricLoaderCreator (protocols::parser); SimpleMetricRegistrator (core::simple_metrics); SimpleMetricSelector (core::select::residue_selector); SimpleMetricSelectorCreator (core::select::residue_selector); SimpleMetricStruct (core::simple_metrics); SimpleNode (core::pack::interaction_graph); SimpleNodeManager (protocols::jd3::dag_node_managers); SimplePDB (core::scoring::packstat); SimplePDB_Atom (core::scoring::packstat); SimplePoseSelection (protocols::stepwise::legacy::screener); SimpleRMSD_Screener (protocols::stepwise::legacy::screener); SimpleScoringScheme (core::sequence); SimpleSequenceCreator (core::sequence); SimpleSequenceData (core::io::silent); SimpleThreadingMover (protocols::simple_moves); SimpleThreadingMoverCreator (protocols::simple_moves); SimpleTreeBuilder (protocols::nonlocal); Simulated4PDEERTrace (core::scoring::epr_deer); Simulated4PDEERTraceFactory (core::scoring::epr_deer); SimulatedTempering (protocols::canonical_sampling); SimulatedTempering (protocols::moves); SimulatedTemperingCreator (protocols::canonical_sampling); SingleBasicRotamerLibrary (core::pack::rotamers); SingleBasicRotamerLibraryCreator (core::pack::rotamers); SingleConstraint (protocols::toolbox::match_enzdes_util); SingleDownstreamResidueWriter (protocols::match::output); SingleFileBuffer (protocols::jd2); SingleFragmentMover (protocols::nonlocal); SingleFragmentMoverCreator (protocols::nonlocal); SingleGrid (protocols::qsar::scoring_grid); SingleLigandRotamerLibrary (core::pack::rotamers); SingleLigandRotamerLibraryCreator (core::pack::rotamers); SingleMotif (protocols::motifs); SingleNCAARotamerLibraryCreator (core::pack::rotamers); SingleQueryExecutor (protocols::indexed_structure_store::search); SingleQuerySummaryStatistics (protocols::indexed_structure_store::search); SingleResidueCenrotLibrary (core::pack::dunbrack::cenrot); SingleResidueCenrotLibraryCreator (core::pack::dunbrack::cenrot); SingleResidueDunbrackLibrary (core::pack::dunbrack); SingleResidueDunbrackLibraryConcrete (core::pack::dunbrack); SingleResidueDunbrackLibraryCreator (core::pack::dunbrack); SingleResidueFragData (core::fragment); SingleResidueInvrotTarget (protocols::toolbox::match_enzdes_util); SingleResidueMultifunc (core::optimization); SingleResidueRotamerLibrary (core::pack::rotamers); SingleResidueRotamerLibraryCreator (core::pack::rotamers); SingleResidueRotamerLibraryFactory (core::pack::rotamers); SingleResidueRotamerLibraryRegistrator (core::pack::rotamers); SingleResidueTorsionFragmentLibrary (protocols::frags); SingleState (protocols::multistate_design); SingleStateEntityData (protocols::multistate_design); SingleStateFitnessFunction (protocols::multistate_design); SingleStructureData (protocols::optimize_weights); SingleValuePoseEvaluator (protocols::evaluation); SingleValuePoseEvaluator_Size (protocols::evaluation); SingleValuePoseEvaluator_SSize (protocols::evaluation); SingResCnlCrea (protocols::constel); SinXOverX (core::scoring::saxs); SiteConstraint (core::scoring::constraints); SiteConstraintCreator (core::scoring::constraints); SiteConstraintResidues (core::scoring::constraints); SiteConstraintResiduesCreator (core::scoring::constraints); SiteGrid (protocols::qsar::scoring_grid); SiteGridCreator (protocols::qsar::scoring_grid); SixDoFGridDockMover (protocols::simple_moves); SixDoFGridDockMoverCreator (protocols::simple_moves); SixDTransRotPotential (core::scoring::loop_graph::evaluator); SixDTransRotPotentialEvaluator (core::scoring::loop_graph::evaluator); SizeInSegmentsRequirement (protocols::sewing::requirements); SizeInSegmentsRequirementCreator (protocols::sewing::requirements); SizeValuedParameter (core::conformation::parametric); SizeVectorValuedParameter (core::conformation::parametric); SkipViolFunc (core::scoring::func); Slab (core::conformation::membrane::membrane_geometry); Slice (core::scoring::packstat); SlicedPoseWorkingParameters (protocols::stepwise::legacy::modeler::rna); SliceResidueSelector (core::select::residue_selector); SliceResidueSelectorCreator (core::select::residue_selector); SliceToMiniProteinMover (protocols::pose_creation); SliceToMiniProteinMoverCreator (protocols::pose_creation); SlideIntoContact (protocols::docking); SlideTogether (protocols::ligand_docking); SlideTogetherCreator (protocols::ligand_docking); SlidingWindowLoopClosure (protocols::loops::loop_closure::ccd); SmallAtNb (core::scoring); SmallBBSampler (protocols::simple_moves::bb_sampler); SmallFragWeight (protocols::topology_broker::weights); SmallMinCCDTrial (protocols::loops::loop_mover::refine); SmallMinCCDTrialCreator (protocols::loops::loop_mover::refine); SmallMol (protocols::pockets); SmallMover (protocols::simple_moves); SmallMoverCreator (protocols::simple_moves); SmartAssembly (protocols::sewing::data_storage); SmartFixbbSimAnnealer (core::pack::annealer); SmartSegment (protocols::sewing::data_storage); SmartSewingResidue (protocols::sewing::data_storage); SmoothCenPairEnergy (core::energy_methods); SmoothCenPairEnergyCreator (core::energy_methods); SmoothEnvEnergy (core::energy_methods); SmoothEnvEnergyCreator (core::energy_methods); SmoothEnvPairPotential (core::scoring); SmoothFragmentMover (protocols::simple_moves); SmoothFragWeight (protocols::topology_broker::weights); SmoothPolicy (protocols::nonlocal); SmoothScoreTermCoeffs (core::scoring); SmoothStepFunc (core::scoring::func); SmoothSymmetricFragmentMover (protocols::simple_moves); SmotifFeatures (protocols::features); SmotifFeaturesCreator (protocols::features); SnugDock (protocols::antibody::snugdock); SnugDockCreator (protocols::antibody::snugdock); SnugDockProtocol (protocols::antibody::snugdock); SoedingFunc (core::scoring::func); SOGFunc (core::scoring::func); SOGFunc_Impl (core::scoring::func); SolutionPicker (protocols::kinematic_closure::solution_pickers); SolutionPredicate (protocols::denovo_design::components); SolutionSorter (protocols::denovo_design::components); SolvationGrid (protocols::qsar::scoring_grid); SolvationGridCreator (protocols::qsar::scoring_grid); SolvationMetaGrid (protocols::qsar::scoring_grid); SolvationMetaGridCreator (protocols::qsar::scoring_grid); SolventAccessibility (protocols::frag_picker::scores); sort_pred (core::optimization); sort_SilentStructOPs (protocols::wum); SortByLowEnergy (protocols::multistage_rosetta_scripts); SortPredicate (protocols::jd2::archive); SourcePositions (protocols::rna::denovo::coarse); Spacegroup (protocols::cryst); Span (core::conformation::membrane); SpanInfo (protocols::membrane); SpanningTopology (core::conformation::membrane); SpanTopologyMatchPoseFilter (protocols::simple_filters); SpanTopologyMatchPoseFilterCreator (protocols::simple_filters); SparseMatrixIndex (core::pack::interaction_graph); Sparta (protocols::sparta); Sparta::SpartaLib (protocols::sparta); SpecialRotamerEnergy (protocols::scoring::methods); SpecialRotamerEnergyCreator (protocols::scoring::methods); SpecialRotamerRSO (protocols::toolbox::rotamer_set_operations); SpecialSegmentsObserver (core::pose::datacache); SpecificGeometryLibrary (protocols::jumping); SpecificResiduesNearInterfaceFilter (protocols::protein_interface_design::filters); SpecificResiduesNearInterfaceFilterCreator (protocols::protein_interface_design::filters); Sphere (core::scoring::packstat); spherical_coor_triplet (protocols::pockets); SphericalRotationSearchPattern (protocols::hotspot_hashing); CrossPeak::Spin (protocols::noesy_assign); SpinAroundPartnerMover (protocols::membrane); SpinAroundPartnerMoverCreator (protocols::membrane); SpinlabelDatabaseEntry (core::io::nmr); SpinlabelDatabaseHandler (core::io::nmr); SpinMover (protocols::protein_interface_design::movers); SpinMoverCreator (protocols::protein_interface_design::movers); Splice (protocols::splice); SpliceCreator (protocols::splice); SpliceIn (protocols::splice); SpliceInAntibody (protocols::splice); SpliceInAntibodyCreator (protocols::splice); SpliceInCreator (protocols::splice); SpliceInTail (protocols::splice); SpliceInTailCreator (protocols::splice); SpliceManager (protocols::splice); SpliceOut (protocols::splice); SpliceOutAntibody (protocols::splice); SpliceOutAntibodyCreator (protocols::splice); SpliceOutCreator (protocols::splice); SpliceOutTail (protocols::splice); SpliceOutTailCreator (protocols::splice); SpliceSegment (protocols::splice); SplineFunc (core::scoring::func); SplitAndMixPoseMover (protocols::fold_from_loops::movers); SplitAndMixPoseMoverCreator (protocols::fold_from_loops::movers); SplitUnfoldedTwoBodyEnergy (core::energy_methods); SplitUnfoldedTwoBodyEnergyCreator (core::energy_methods); SplitUnfoldedTwoBodyPotential (core::scoring); SpringParams (core::scoring); SquarePlanarMetal_Helper (protocols::cyclic_peptide::crosslinker); SquarePyramidalMetal_Helper (protocols::cyclic_peptide::crosslinker); SquareWell2Func (core::scoring::func); SquareWellFunc (core::scoring::func); SRelaxPose (protocols::relax); SS_Base (protocols::fldsgn::topology); SS_Info (core::scoring); SS_Info2 (protocols::fldsgn::topology); SS_Killhairpins_Info (core::scoring); SS_predictor (protocols::ss_prediction); SSamountFilter (protocols::protein_interface_design::filters); SSamountFilterCreator (protocols::protein_interface_design::filters); SSBondInformation (core::io); SSElementSelector::SSElement (core::select::residue_selector); SliceToMiniProteinMover::SSElement (protocols::pose_creation); SSElementBisectddGFilter (protocols::simple_ddg); SSElementBisectddGFilterCreator (protocols::simple_ddg); SSElementLengthFilter (protocols::simple_filters); SSElementLengthFilterCreator (protocols::simple_filters); SSElementMotifContactEnergy (core::energy_methods); SSElementMotifContactEnergyCreator (core::energy_methods); SSElementMotifContactFilter (protocols::simple_filters); SSElementMotifContactFilterCreator (protocols::simple_filters); SSElementSelector (core::select::residue_selector); SSElementSelectorCreator (core::select::residue_selector); SSFeature (protocols::comparative_modeling::features); SSHashedFragmentStore (protocols::indexed_structure_store); SSManager (core::sequence); SSMotifFinder (protocols::simple_filters); SSMotifFinderFilterCreator (protocols::simple_filters); SSPairPotential (protocols::fldsgn::potentials::sspot); SSPredictionFilter (protocols::denovo_design::filters); SSPredictionFilterCreator (protocols::denovo_design::filters); SSShapeComplementarityFilter (protocols::denovo_design::filters); SSShapeComplementarityFilterCreator (protocols::denovo_design::filters); SSWeightParameters (core::scoring::hbonds); StackElecEnergy (core::energy_methods); StackElecEnergyCreator (core::energy_methods); Stage1Sampler (protocols::abinitio); StagePreparer (protocols::abinitio::abscript); AbscriptMover::StageTracker (protocols::abinitio::abscript); StandardDisulfPairingLibrary (protocols::jumping); StandardInnerLarvalJob (protocols::jd3::standard); StandardJobQueen (protocols::jd3::standard); StandardPairingLibrary (protocols::jumping); StandardPivots (protocols::kinematic_closure::pivot_pickers); StandardPoseJobSummary (protocols::jd3::job_summaries); StarAbinitio (protocols::star); StartFrom (protocols::ligand_docking); StartFromCreator (protocols::ligand_docking); StartingNodeMotifScorer (protocols::sewing::scoring); StartingNodeMotifScorerCreator (protocols::sewing::scoring); StarTreeBuilder (protocols::nonlocal); StartStructClaimer (protocols::topology_broker); StateAccumulatingMatchFilter (protocols::match::output); StealLigandMover (protocols::comparative_modeling); StealSideChainsMover (protocols::comparative_modeling); StemFinder (protocols::simple_filters); StemFinderFilterCreator (protocols::simple_filters); StepWiseBasicModelerOptions (protocols::stepwise::modeler::options); StepWiseBasicOptions (protocols::stepwise::options); StepWiseBasicWorkingParameters (protocols::stepwise::modeler::working_parameters); StepWiseClusterer (protocols::stepwise::modeler::align); StepWiseConnectionSampler (protocols::stepwise::modeler); StepWiseLegacyClusterer (protocols::stepwise::modeler::align); StepWiseLegacyClustererSilentBased (protocols::stepwise::modeler::align); StepWiseMasterMover (protocols::stepwise::monte_carlo::mover); StepWiseMasterPacker (protocols::stepwise::modeler::packer); StepWiseMinimizer (protocols::stepwise::modeler); StepWiseModeler (protocols::stepwise::modeler); StepWiseModelerOptions (protocols::stepwise::modeler::options); StepWiseMonteCarlo (protocols::stepwise::monte_carlo); StepWiseMonteCarloOptions (protocols::stepwise::monte_carlo::options); StepWiseMove (protocols::stepwise::monte_carlo::mover); StepWiseMoveSelector (protocols::stepwise::monte_carlo::mover); StepWiseMoveSelectorOptions (protocols::stepwise::monte_carlo::mover::options); StepWisePacker (protocols::stepwise::modeler::packer); StepWisePoseAligner (protocols::stepwise::modeler::align); StepWiseProteinBackboneSampler (protocols::stepwise::modeler::protein); StepWiseProteinCCD_Closer (protocols::stepwise::modeler::protein::loop_close); StepWiseProteinCCD_MultiPoseCloser (protocols::stepwise::modeler::protein::loop_close); StepWiseProteinKIC_LoopBridger (protocols::stepwise::modeler::protein::loop_close); StepWiseProteinMinimizer (protocols::stepwise::legacy::modeler::protein); StepWiseProteinModelerOptions (protocols::stepwise::modeler::options); StepWiseProteinPoseSetup (protocols::stepwise::legacy::modeler::protein); StepWiseResiduePairScreener (protocols::stepwise::screener); StepWiseRNA_Clusterer (protocols::stepwise::legacy::modeler::rna); StepWiseRNA_CombineLongLoopFilterer (protocols::stepwise::modeler::rna); StepWiseRNA_CountStruct (protocols::stepwise::modeler::rna); StepWiseRNA_ModelerOptions (protocols::stepwise::modeler::options); StepWiseRNA_PoseSelection (protocols::stepwise::legacy::modeler::rna); StepWiseRNA_PoseSetup (protocols::stepwise::legacy::modeler::rna); StepWiseSampleAndScreen (protocols::stepwise); StepWiseSampler (protocols::stepwise::sampler); StepWiseSamplerComb (protocols::stepwise::sampler); StepWiseSamplerOneDOF (protocols::stepwise::sampler); StepWiseSamplerOneTorsion (protocols::stepwise::sampler); StepWiseSamplerOneValue (protocols::stepwise::sampler); StepWiseSamplerOneValueComb (protocols::stepwise::sampler); StepWiseSamplerRingConformer (protocols::stepwise::sampler); StepWiseSamplerSized (protocols::stepwise::sampler); StepWiseSamplerSizedAny (protocols::stepwise::sampler); StepWiseSamplerSizedComb (protocols::stepwise::sampler); StepWiseScreener (protocols::stepwise::screener); StepWiseWorkingParameters (protocols::stepwise::modeler::working_parameters); StepWiseWorkingParametersSetup (protocols::stepwise::legacy::modeler::rna); STMStoredTask (protocols::task_operations); StochasticFilter (protocols::filters); StochasticFilterCreator (protocols::filters); StoreCombinedStoredTasksMover (protocols::task_operations); StoreCombinedStoredTasksMoverCreator (protocols::task_operations); StoreCompoundTaskMover (protocols::task_operations); StoreCompoundTaskMoverCreator (protocols::task_operations); StoredResidueSubsetSelector (protocols::residue_selectors); StoredResidueSubsetSelectorCreator (protocols::residue_selectors); StoredRotamerLibraryCreator (core::pack::rotamers); StoredRotamerLibrarySpecification (core::chemical::rotamers); StoredRotamerLibrarySpecificationCreator (core::chemical::rotamers); StorePoseSnapshot (protocols::simple_moves); StorePoseSnapshotCreator (protocols::simple_moves); StoreResidueSubsetMover (protocols::residue_selectors); StoreResidueSubsetMoverCreator (protocols::residue_selectors); StoreTaskMover (protocols::task_operations); StoreTaskMoverCreator (protocols::task_operations); Strand (protocols::fldsgn::topology); StrandArchitect (protocols::denovo_design::architects); StrandArchitectCreator (protocols::denovo_design::architects); StrandBundleFeatures (protocols::features::strand_assembly); StrandBundleFeaturesCreator (protocols::features::strand_assembly); StrandConstraints (protocols::abinitio); StrandCurvatureByLevels (protocols::fldsgn::filters); StrandCurvatureByLevelsCreator (protocols::fldsgn::filters); StrandFragment (protocols::features::strand_assembly); StrandHelixGeometryFilter (protocols::fldsgn::filters); StrandHelixGeometryFilterCreator (protocols::fldsgn::filters); StrandPairing (core::scoring::dssp); StrandPairing (protocols::fldsgn::topology); StrandPairing (protocols::denovo_design::components); StrandPairingSet (core::scoring::dssp); StrandPairingSet (protocols::fldsgn::topology); Strands (core::scoring); StrandTwistingMover (protocols::rbsegment_relax); StringMetric (core::simple_metrics); StrongWolfeLineMinimization (core::optimization); Stru (protocols::cluster::calibur); StructAvrgMover (protocols::mpi_refinement); StructFileReaderOptions (core::io); StructFileRep (core::io); StructFileRepOptions (core::io); StructFragmentMover (protocols::struct_fragment); StructFragmentMoverCreator (protocols::struct_fragment); StructInfo (protocols::ligand_docking::ga_ligand_dock); StructInfoComp (protocols::ligand_docking::ga_ligand_dock); StructInfoCompdH (protocols::ligand_docking::ga_ligand_dock); StructPerturberCM (protocols::abinitio::abscript); StructPerturberCMCreator (protocols::abinitio::abscript); StructProfileMover (protocols::simple_moves); StructProfileMoverCreator (protocols::simple_moves); StructuralSimilarityEvaluator (protocols::simple_filters); StructureArchitect (protocols::denovo_design::architects); StructureData (protocols::denovo_design::components); StructureData (protocols::indexed_structure_store::search); StructureDatabase (protocols::indexed_structure_store::search); StructureDataCreator (protocols::denovo_design::components); StructureDataFactory (protocols::denovo_design::components); StructureDataObserver (protocols::denovo_design::components); StructureDataPerturber (protocols::denovo_design::components); StructureDependentCalculator (core::pose::metrics); StructureDependentPeakCalibrator (protocols::noesy_assign); StructureEntry (protocols::indexed_structure_store); StructureFeatures (protocols::features); StructureFeaturesCreator (protocols::features); StructureFileNames (protocols::pack_daemon); StructureIndependentPeakCalibrator (protocols::noesy_assign); StructurePairQuery (protocols::indexed_structure_store::search); StructurePairQueryResult (protocols::indexed_structure_store::search); StructureRecord (protocols::indexed_structure_store); StructureRestrictor (protocols::moves); StructureScoresFeatures (protocols::features); StructureScoresFeaturesCreator (protocols::features); StructureSimilarityEvaluatorCreator (protocols::simple_filters); StructureSingleQuery (protocols::indexed_structure_store::search); StructureSingleQueryResult (protocols::indexed_structure_store::search); StructureSlice (protocols::denovo_design::components); StructureSlicePredicate (protocols::denovo_design::components); StructureStore (protocols::abinitio); StructureStore (protocols::indexed_structure_store); StructureStoreManager (protocols::indexed_structure_store); StructureStoreProvider (protocols::indexed_structure_store); Stub (core::kinematics); StubApplier (protocols::stepwise::screener); StubDistanceScreener (protocols::stepwise::screener); StubGenerator (protocols::hotspot_hashing); StubID (core::id); StubScoreFilter (protocols::protein_interface_design::filters); StubScoreFilterCreator (protocols::protein_interface_design::filters); StubScoreLoopsFilter (protocols::protein_interface_design::filters); StubScoreLoopsFilterCreator (protocols::protein_interface_design::filters); SubMotifInfo (core::pose::full_model_info); SubMotifLibrary (protocols::stepwise::monte_carlo::submotif); SubroutineMover (protocols::protein_interface_design::movers); SubroutineMoverCreator (protocols::protein_interface_design::movers); SubsetPartnerMotifScorer (protocols::sewing::scoring); SubsetPartnerMotifScorerCreator (protocols::sewing::scoring); SubstituentReplace (protocols::drug_design); SubstituentReplaceCreator (protocols::drug_design); SubstructureReplace (protocols::drug_design); SubstructureReplaceCreator (protocols::drug_design); SuckerEnergy (core::energy_methods); SuckerEnergyCreator (core::energy_methods); SugarBackboneEnergy (core::energy_methods); SugarBackboneEnergyCreator (core::energy_methods); SugarBBSampler (protocols::simple_moves::bb_sampler); SugarInstantiateMover (protocols::stepwise::modeler::rna::sugar); SugarInstantiator (protocols::stepwise::screener); SugarModeling (protocols::stepwise::modeler::rna::sugar); SugarModificationsNomenclatureTableRow (core::chemical::carbohydrates); SugarVirtualizeMover (protocols::stepwise::modeler::rna::sugar); SuggestValueMessage (protocols::topology_broker); SumFunc (core::scoring::func); Supercharge (protocols::design_opt); SuperimposeMover (protocols::simple_moves); SuperimposeMoverCreator (protocols::simple_moves); SurfaceBackgroundEdge (core::pack::interaction_graph); SurfaceBackgroundNode (core::pack::interaction_graph); SurfaceCalculator (protocols::pose_metric_calculators); SurfaceDockingProtocol (protocols::surface_docking); SurfaceEdge (core::pack::interaction_graph); SurfaceEnergies (core::scoring::solid_surface); SurfaceEnergy (core::pack::interaction_graph); SurfaceEnergyCreator (core::pack::interaction_graph); SurfaceInteractionGraph (core::pack::interaction_graph); SurfaceNode (core::pack::interaction_graph); SurfaceOrientMover (protocols::surface_docking); SurfaceParameters (protocols::surface_docking); SurfacePotential (core::pack::interaction_graph); SurfaceSearchPattern (protocols::hotspot_hashing); SurfaceVectorLoader (protocols::surface_docking); SurfaceVectorLoaderCreator (protocols::surface_docking); SurfEnergy (core::energy_methods); SurfEnergyCreator (core::energy_methods); SurfVol (core::scoring::packing); SurfVolDeriv (core::scoring::packing); SurfVolEnergy (core::energy_methods); SurfVolEnergyCreator (core::energy_methods); SurrogateVariableExpression (protocols::pack_daemon); SurroundingSS (protocols::denovo_design::task_operations); SWAligner (core::sequence); SwapSegment (protocols::seeded_abinitio); SwapSegmentCreator (protocols::seeded_abinitio); SwitchChainOrderMover (protocols::simple_moves); SwitchChainOrderMoverCreator (protocols::simple_moves); SwitchMover (protocols::moves); SwitchMoverCreator (protocols::moves); SwitchResidueTypeSetMover (protocols::simple_moves); SwitchResidueTypeSetMoverCreator (protocols::simple_moves); SymAtomTreeMinimizer (core::optimization::symmetry); SymAtomTreeMultifunc (core::optimization::symmetry); SymDockBaseProtocol (protocols::symmetric_docking); SymDockingHiRes (protocols::symmetric_docking); SymDockingInitialPerturbation (protocols::symmetry); SymDockingLowRes (protocols::symmetric_docking); SymDockingSlideIntoContact (protocols::symmetry); SymDockProtocol (protocols::symmetric_docking); SymDockProtocolCreator (protocols::symmetric_docking); SymDof (core::conformation::symmetry); SymDofMover (protocols::matdes); SymDofMoverCreator (protocols::matdes); SymDofMoverSampler (protocols::matdes); symECreator (core::scoring::sym_e); symEnergy (core::scoring::sym_e); SymEnergyCutRotamerTrialsMover (protocols::minimization_packing::symmetry); SymFoldandDockMoveRbJumpMover (protocols::symmetric_docking); SymFoldandDockMoveRbJumpMoverCreator (protocols::symmetric_docking); SymFoldandDockRbTrialMover (protocols::symmetric_docking); SymFoldandDockRbTrialMoverCreator (protocols::symmetric_docking); SymFoldandDockSlideTrialMover (protocols::symmetric_docking); SymFoldandDockSlideTrialMoverCreator (protocols::symmetric_docking); SymInterfaceSidechainMinMover (protocols::symmetric_docking); SymmData (core::conformation::symmetry); SymmDataLoader (core::conformation::symmetry); SymmDataLoaderCreator (core::conformation::symmetry); SymmetricAddMembraneMover (protocols::membrane::symmetry); SymmetricAddMembraneMoverCreator (protocols::membrane::symmetry); SymmetricalResidueSelector (core::select::residue_selector); SymmetricalResidueSelectorCreator (core::select::residue_selector); SymmetricConformation (core::conformation::symmetry); SymmetricCycpepAlign (protocols::cyclic_peptide); SymmetricCycpepAlignCreator (protocols::cyclic_peptide); SymmetricEnergies (core::scoring::symmetry); SymmetricFragmentMover (protocols::simple_moves); SymmetricLigandEnergy (core::energy_methods); SymmetricLigandEnergyCreator (core::energy_methods); SymmetricMotifFilter (protocols::simple_filters); SymmetricMotifFilterCreator (protocols::simple_filters); SymmetricRmsdEvaluator (protocols::simple_filters); SymmetricRMSMover (protocols::symmetry); SymmetricRotamerSet_ (core::pack::rotamer_set::symmetry); SymmetricRotamerSets (core::pack::rotamer_set::symmetry); SymmetricScoreFunction (core::scoring::symmetry); SymmetryClaim (protocols::topology_broker::claims); SymmetryClaimer (protocols::topology_broker); SymmetryInfo (core::conformation::symmetry); SymmetrySlider (protocols::symmetry); SymmetryTransform (core::conformation::symmetry); SymMinimizerMap (core::optimization::symmetry); SymMinMover (protocols::minimization_packing::symmetry); SymMinMoverCreator (protocols::minimization_packing::symmetry); SymmLinearMemEdge (core::pack::interaction_graph); SymmLinearMemNode (core::pack::interaction_graph); SymmLinearMemoryInteractionGraph (core::pack::interaction_graph); SymmMinimalistEdge (core::pack::interaction_graph); SymmMinimalistInteractionGraph (core::pack::interaction_graph); SymmMinimalistNode (core::pack::interaction_graph); SymmOnTheFlyEdge (core::pack::interaction_graph); SymmOnTheFlyInteractionGraph (core::pack::interaction_graph); SymmOnTheFlyNode (core::pack::interaction_graph); SymPackRotamersMover (protocols::minimization_packing::symmetry); SymPackRotamersMoverCreator (protocols::minimization_packing::symmetry); SymRestrictTaskForDocking (protocols::symmetric_docking); SymRotamerTrialsMover (protocols::minimization_packing::symmetry); SymRotamerTrialsMoverCreator (protocols::minimization_packing::symmetry); SymShakeStructureMover (protocols::symmetry); SymSidechainMinMover (protocols::symmetric_docking); SymSlideInfo (core::conformation::symmetry); SymUnsatHbondFilter (protocols::matdes); SymUnsatHbondFilterCreator (protocols::matdes)

T: tableID (core::scoring); TableLookupEtableEnergy (core::scoring::etable); TableLookupEvaluator (core::scoring::etable); TabooSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); TagDefinition (protocols::stepwise::screener); TagManager (protocols::multistage_rosetta_scripts); TagPoseWithRefinementStatsMover (protocols::cryst); TagPoseWithRefinementStatsMoverCreator (protocols::cryst); TailSegmentMover (protocols::splice); TailSegmentMoverCreator (protocols::splice); TailsScoreMover (protocols::simple_moves); TalosSSSimilarity (protocols::frag_picker::scores); TARGET (core::pack::task); TargetClashEnergy (protocols::scoring::methods); TargetClashEnergyCreator (protocols::scoring::methods); TargetPocketGrid (protocols::pockets); TargetRotamerCoords (protocols::match::downstream); TaskAwareCsts (protocols::protein_interface_design::movers); TaskAwareCstsCreator (protocols::protein_interface_design::movers); TaskAwareMinMover (protocols::minimization_packing); TaskAwareMinMoverCreator (protocols::minimization_packing); TaskAwareSASAFilter (protocols::simple_filters); TaskAwareSASAFilterCreator (protocols::simple_filters); TaskAwareScoreTypeFilter (protocols::simple_filters); TaskAwareScoreTypeFilterCreator (protocols::simple_filters); TaskAwareSymMinMover (protocols::minimization_packing::symmetry); TaskAwareSymMinMoverCreator (protocols::minimization_packing::symmetry); TaskFactory (core::pack::task); TaskOperationFeatures::Taskop_id_name_factory_ (protocols::features); TaskOperation (core::pack::task::operation); TaskOperationCreator (core::pack::task::operation); TaskOperationFactory (core::pack::task::operation); TaskOperationFeatures (protocols::features); TaskOperationFeaturesCreator (protocols::features); TaskOperationLoader (protocols::parser); TaskOperationLoaderCreator (protocols::parser); TaskOperationMPM (protocols::match); TaskOperationRegistrator (core::pack::task::operation); TaskSelector (protocols::residue_selectors); TaskSelectorCreator (protocols::residue_selectors); TautomerizeAnomerMover (protocols::carbohydrates); TautomerizeAnomerMoverCreator (protocols::carbohydrates); TBMB_Helper (protocols::cyclic_peptide::crosslinker); TCRmodel (protocols::tcr); TCRmodel::tcrtmplts (protocols::tcr); TemperatureController (protocols::canonical_sampling); TemperedDocking (protocols::docking); TemperedDockingCreator (protocols::docking); TemperingBase (protocols::canonical_sampling); Template (protocols::abinitio); TemplateFragmentClaimer (protocols::topology_broker); TemplateHistory (protocols::hybridization); TemplateJumpClaimer (protocols::topology_broker); TemplateJumpSetup (protocols::abinitio); Templates (protocols::abinitio); TenANeighborEdge (core::scoring); TenANeighborGraph (core::scoring); TenANeighborNode (core::scoring); TensorsOptimizer (protocols::scoring::methods::pcs2); TensorsOptimizer (protocols::scoring::methods::pcs); TensorsOptimizer_Ts1 (protocols::scoring::methods::pcsTs1); TensorsOptimizer_Ts2 (protocols::scoring::methods::pcsTs2); TensorsOptimizer_Ts3 (protocols::scoring::methods::pcsTs3); TensorsOptimizer_Ts4 (protocols::scoring::methods::pcsTs4); TensorsOptimizerFix (protocols::scoring::methods::pcs2); TensorsOptimizerSvd (protocols::scoring::methods::pcs2); TerminalDSSPSortedPoseVector (protocols::pose_sewing::data_storage); TerminiConstraintGenerator (protocols::constraint_generator); TerminiConstraintGeneratorCreator (protocols::constraint_generator); TerminusDistanceFilter (protocols::simple_filters); TerminusDistanceFilterCreator (protocols::simple_filters); TerminusMotifScorer (protocols::sewing::scoring); TerminusMotifScorerCreator (protocols::sewing::scoring); TestCompositeRealMetric (core::simple_metrics); TestCompositeRealMetricCreator (core::simple_metrics); TestCompositeStringMetric (core::simple_metrics); TestCompositeStringMetricCreator (core::simple_metrics); TestPattern (protocols::hotspot_hashing); TestPerResidueProbabilitiesMetric (core::simple_metrics); TestPerResidueProbabilitiesMetricCreator (core::simple_metrics); TestPerResidueRealMetric (core::simple_metrics); TestPerResidueRealMetricCreator (core::simple_metrics); TestPerResidueStringMetric (core::simple_metrics); TestPerResidueStringMetricCreator (core::simple_metrics); TestRealMetric (core::simple_metrics); TestRealMetricCreator (core::simple_metrics); TestStringMetric (core::simple_metrics); TestStringMetricCreator (core::simple_metrics); TetherLigand (protocols::ligand_docking); TetrahedralMetal_Helper (protocols::cyclic_peptide::crosslinker); TheozymeInvrotTree (protocols::toolbox::match_enzdes_util); ThermalMinimizer (protocols::recces::scratch); ThermalMinimizerCreator (protocols::recces::scratch); ThermalSamplingMover (protocols::recces::scratch); ThermalSamplingMoverCreator (protocols::recces::scratch); ThermodynamicData (protocols::simple_moves); ThermodynamicMover (protocols::canonical_sampling); ThermodynamicObserver (protocols::canonical_sampling); Thermostat (protocols::md); Thioether_Helper (protocols::cyclic_peptide::crosslinker); ThreadingJob (protocols::comparative_modeling); ThreadingJobInputter (protocols::comparative_modeling); ThreadingJobInputterCreator (protocols::comparative_modeling); ThreadingMover (protocols::comparative_modeling); ThreadSequenceOperation (protocols::task_operations); ThreadSequenceOperationCreator (protocols::task_operations); TiltMover (protocols::membrane); TiltMoverCreator (protocols::membrane); TimeEvaluator (protocols::evaluation); TimeFilter (protocols::filters); TimeFilterCreator (protocols::filters); Timer (protocols::checkpoint); TimingProfileMetric (core::simple_metrics::metrics); TimingProfileMetricCreator (core::simple_metrics::metrics); SecretionOptimizationMover::tm_region (protocols::protein_interface_design::movers); SecretionPredictionFilter::tm_region (protocols::simple_filters); TMA_Helper (protocols::cyclic_peptide::crosslinker); TMalign (protocols::hybridization); TMHTopologySamplerClaimer (protocols::topology_broker); TCRmodel::tmpltinfo (protocols::tcr); TMsAACompFilter (protocols::simple_filters); TMsAACompFilterCreator (protocols::simple_filters); TMscore (core::scoring); TMscoreStore (core::scoring); TMsSpanMembraneFilter (protocols::simple_filters); TMsSpanMembraneFilterCreator (protocols::simple_filters); TNA_SuiteEnergy (core::energy_methods); TNA_SuiteEnergyCreator (core::energy_methods); TNA_SuitePotential (core::scoring::rna); ToolboxKeys (protocols::loop_modeling); TopCountOfAllInputs (protocols::features); TopCountOfEachInput (protocols::features); TopEntitySet (protocols::pack_daemon); TopNByProperty (protocols::pose_selectors); TopNByPropertyCreator (protocols::pose_selectors); TopNMotifScorer (protocols::sewing::scoring); TopNMotifScorerCreator (protocols::sewing::scoring); TopologyBroker (protocols::topology_broker); TopologyBrokerMover (protocols::protein_interface_design::movers); TopologyBrokerMoverCreator (protocols::protein_interface_design::movers); TopologyClaimer (protocols::topology_broker); TopologyClaimerFactory (protocols::topology_broker); TopOutFunc (core::scoring::func); TopPercentOfAllInputs (protocols::features); TopPercentOfEachInput (protocols::features); Torsion (protocols::protein_interface_design::filters); Torsion_Info (protocols::stepwise::modeler::rna); TorsionBinIO (protocols::frag_picker); TorsionBinSimilarity (protocols::frag_picker::scores); TorsionClaim (protocols::environment::claims); TorsionCreator (protocols::protein_interface_design::filters); TorsionDistrParams (protocols::ligand_docking::ga_ligand_dock); TorsionDOFMover (protocols::simple_moves); TorsionEnergy (core::pack::rotamers); TorsionFeature (protocols::comparative_modeling::features); TorsionFourierComponent (core::scoring::dna); TorsionFragment (protocols::frags); TorsionFragmentLibrary (protocols::frags); TorsionFragmentMover (protocols::frags); TorsionID (core::id); TorsionID_Range (core::id); TorsionParams (core::scoring); TorsionRange (protocols::make_rot_lib); TorsionRestrictedKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); torsions (core::fragment); TorsionSampler (protocols::ligand_docking::ga_ligand_dock); TorsionSamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); TorsionSet (core::fragment::rna); TorsionSetMover (protocols::simple_moves); TorsionSpec (protocols::canonical_sampling); TorsionSweepingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); TorsionType (protocols::ligand_docking::ga_ligand_dock); TotalEnergyMetric (core::simple_metrics::metrics); TotalEnergyMetricCreator (core::simple_metrics::metrics); TotalSasaFilter (protocols::simple_filters); TotalSasaFilterCreator (protocols::simple_filters); TotalScoreFeatures (protocols::features); TotalScoreFeaturesCreator (protocols::features); TournamentSelector (protocols::ligand_evolution); trace (core::scoring::packstat); TrajectoryLogger (protocols::loop_modeling::utilities); TrajectoryMapFeatures (protocols::features); TrajectoryMapFeaturesCreator (protocols::features); TrajectoryRecorder (protocols::canonical_sampling); TrajectoryReportToDB (protocols::features); TrajectoryReportToDBCreator (protocols::features); Transform (protocols::ligand_docking); Transform_info (protocols::ligand_docking); Transformation (protocols::protein_interface_design); Transformation; TransformCreator (protocols::ligand_docking); TransformEnsemble (protocols::ligand_docking); TransformEnsemble_info (protocols::ligand_docking); TransformEnsembleCreator (protocols::ligand_docking); TransformIntoMembraneMover (protocols::membrane); TransformIntoMembraneMoverCreator (protocols::membrane); TransientCutpointHandler (protocols::stepwise::monte_carlo::mover); Translate (protocols::ligand_docking); Translate_info (protocols::ligand_docking); TranslateCreator (protocols::ligand_docking); TranslationFreePeptideMover (protocols::backbone_moves::local_backbone_mover::free_peptide_movers); TranslationMover (protocols::membrane); TranslationMoverCreator (protocols::membrane); TranslationRotationMover (protocols::membrane); TranslationRotationMoverCreator (protocols::membrane); TreeBuilder (protocols::nonlocal); TreeBuilderFactory (protocols::nonlocal); TreeVizBuilder (core::kinematics); Trial; TrialCounter (protocols::moves); TrialCounterObserver (protocols::canonical_sampling); TrialCounterObserverCreator (protocols::canonical_sampling); TrialMover (protocols::moves); triangle (protocols::viewer); triangleIterator (protocols::viewer); TriazolamerMover (protocols::simple_moves::triazolamer); TriazolamerRandomSmallMover (protocols::simple_moves::triazolamer); TrieCollection (core::scoring::trie); TrieCountPair1BC3 (core::scoring::etable::etrie); TrieCountPair1BC4 (core::scoring::etable::etrie); TrieCountPairAll (core::scoring::etable::etrie); TrieCountPairBase (core::scoring::trie); TrieCountPairGeneric (core::scoring::etable::etrie); TrieCountPairNone (core::scoring::etable::etrie); TrieNode (core::scoring::trie); TrieVsTrieCachedDataContainerBase (core::scoring::trie); TrigonalPlanarMetal_Helper (protocols::cyclic_peptide::crosslinker); TrigonalPyramidalMetal_Helper (protocols::cyclic_peptide::crosslinker); triplet_and_originnum (protocols::pockets); TripletID (protocols::fldsgn::topology); TrisBpyScore (protocols::sic_dock::scores); trRosettaConstraintGenerator (protocols::trRosetta_protocols::constraint_generators); trRosettaConstraintGeneratorCreator (protocols::trRosetta_protocols::constraint_generators); trRosettaOutputs_v1 (protocols::trRosetta); trRosettaOutputsBase (protocols::trRosetta); trRosettaProtocol_v1 (protocols::trRosetta); trRosettaProtocolBase (protocols::trRosetta); trRosettaProtocolMover (protocols::trRosetta_protocols::movers); trRosettaProtocolMoverCreator (protocols::trRosetta_protocols::movers); TrueFalseFilter (protocols::filters); TrueFalseFilterCreator (protocols::filters); TrueFilter (protocols::filters); TrueFilterCreator (protocols::filters); TrueResidueSelector (core::select::residue_selector); TrueResidueSelectorCreator (core::select::residue_selector); TruncatedScoreEvaluator (protocols::simple_filters); TryDisulfPermutations (protocols::cyclic_peptide); TryDisulfPermutationsCreator (protocols::cyclic_peptide); TryRotamers (protocols::protein_interface_design::movers); TryRotamersCreator (protocols::protein_interface_design::movers); Tumble (protocols::simple_moves); TumbleCreator (protocols::simple_moves); TwelveANeighborEdge (core::scoring); TwelveANeighborGraph (core::scoring); TwelveANeighborNode (core::scoring); TwoBodyEnergy (core::scoring::methods)

U: ubi_e2c_modeler (protocols::ub_e2c); UBQ_GTPaseMover (protocols::chemically_conjugated_docking); UBQ_GTPaseMoverCreator (protocols::chemically_conjugated_docking); UDPSocketClient (protocols::moves); UIMover (protocols::network); UIObserver (protocols::network); UltraLightResidue (core::conformation); UnaryExpression (numeric::expression_parser); UnboundRotamersOperation (core::pack::rotamer_set); UnconstrainedTorsionsMover (protocols::ligand_docking); UnfoldedStateEnergy (core::energy_methods); UnfoldedStateEnergyCalculatorJobDistributor (protocols::unfolded_state_energy_calculator); UnfoldedStateEnergyCalculatorMover (protocols::unfolded_state_energy_calculator); UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (protocols::unfolded_state_energy_calculator); UnfoldedStateEnergyCreator (core::energy_methods); UnfoldedStatePotential (core::scoring); UniformPerturber (protocols::kinematic_closure::perturbers); UniformPolicy (protocols::nonlocal); UniformRigidBodyCM (protocols::rigid); UniformRigidBodyCMCreator (protocols::rigid); UniformRigidBodyMover (protocols::rigid); UniformRigidBodyMoverCreator (protocols::rigid); UniformRotationMover (protocols::simple_moves); UniformSphereTransMover (protocols::rigid); UniformTranslationMover (protocols::simple_moves); UnionEdge (protocols::pockets); UnrecognizedAtomFeatures (protocols::features); UnrecognizedAtomFeaturesCreator (protocols::features); UnrecognizedAtomRecord (core::pose); unsafe_nonpod_npy_format_descriptor (pybind11::detail); UnsatCorrectionOptions (core::pack::guidance_scoreterms::approximate_buried_unsat_penalty); UnsatSelector (protocols::hbnet); UnsatSelectorCreator (protocols::hbnet); UpdateCrystInfo (protocols::cryst); UpdateCrystInfoCreator (protocols::cryst); UpdateEnzdesHeaderMover (protocols::enzdes); UpdateEnzdesHeaderMoverCreator (protocols::enzdes); UpdateSolventMover (protocols::cryst); UpdateSolventMoverCreator (protocols::cryst); UpJumpSRFD (core::fragment); upstream_hit (protocols::match); UpstreamBuilder (protocols::match::upstream); UpstreamCollisionFilter (protocols::match::output); UpstreamDownstreamCollisionFilter (protocols::match::output); UpstreamHitCacher (protocols::match::output); UpstreamResidueProcessor (protocols::match::upstream); UpstreamResTypeGeometry (protocols::match::upstream); us_secmatch_hit_compare (protocols::match::downstream); USE_INPUT_SC (core::pack::task); UseMultiCoolAnnealer (core::pack::task::operation); UseMultiCoolAnnealerCreator (core::pack::task::operation); UserDefinedGroupDiscriminator (protocols::minimization_packing); USOGFunc (core::scoring::func); UDPSocketClient::UUID (protocols::moves)

V: V; VallChunk (protocols::frag_picker); VallChunkFilter (protocols::frag_picker); VallData (protocols::frags); VallFragmentEval (core::fragment::picking_old::vall::eval); VallFragmentGen (core::fragment::picking_old::vall::gen); VallFragmentScore (core::fragment::picking_old::vall::scores); VallLibrarian (core::fragment::picking_old::vall); VallLibrary (core::fragment::picking_old::vall); VallProvider (protocols::frag_picker); VallResidue (core::fragment::picking_old::vall); VallResidue (protocols::frag_picker); VallResidues (core::fragment::picking_old::vall); VallSection (core::fragment::picking_old::vall); VallSections (core::fragment::picking_old::vall); Value (core::pack::annealer); ValueEvaluator (protocols::enzdes); VanillaJobDistributor (protocols::jd3::job_distributors); VariableExpression (numeric::expression_parser); VariableSubstitutionPair (protocols::relax); VariableVectorExpression (protocols::pack_daemon); VarianceStatisticsArchive (protocols::jd2::archive); VarLengthBuild (protocols::forge::components); VarSolDistSasaCalculator (protocols::vardist_solaccess); VarSolDRotamerDots (protocols::vardist_solaccess); VaryLoopLengthMover (protocols::stepwise::monte_carlo::mover); VDDistanceMatrix (core::chemical); VDW_BinScreener (protocols::stepwise::screener); VDW_CachedRepScreenInfo (protocols::scoring); VDW_Energy (core::scoring::vdwaals); VDW_EnergyCreator (core::scoring::vdwaals); VDW_Grid (core::pose::rna); VDW_GridEnergy (protocols::scoring); VDW_GridEnergyCreator (protocols::scoring); VDW_RepScreenInfo (core::pose::rna); VDWAtom (core::scoring::vdwaals); VdwGrid (protocols::qsar::scoring_grid); VdwGridCreator (protocols::qsar::scoring_grid); VdWTinkerEnergy (core::energy_methods); VdWTinkerEnergyCreator (core::energy_methods); VdWTinkerPoseInfo (core::scoring); VdWTinkerPotential (core::scoring); VdWTinkerResidueInfo (core::scoring); VdWTinkerResPairMinData (core::energy_methods); VdWTinkerRotamerSetInfo (core::scoring); VDWTrieCountPair1B (core::scoring::vdwaals); VDWTrieEvaluator (core::scoring::vdwaals); Vec1Hash (protocols::genetic_algorithm); Vec3 (protocols::sic_dock); VectorCacheUnit (core::fragment); VectorExpression (protocols::pack_daemon); VectorExpressionCreator (protocols::pack_daemon); VectorFunction (protocols::pack_daemon); VectorFunction2 (protocols::pack_daemon); VectorPair (protocols::hotspot_hashing); VectorPoseFilter (protocols::filters); VectorPoseJobDistributor (protocols::jd2); VectorPoseMover (protocols::moves); VectorSelector (protocols::denovo_design::components); Vesicle (core::conformation::membrane::membrane_geometry); VicinityPerturber (protocols::kinematic_closure::perturbers); VicinitySamplingKinematicPerturber (protocols::loops::loop_closure::kinematic_closure); VIP_Mover (protocols::vip); VIP_Report (protocols::vip); VirtResClaim (protocols::environment::claims); VirtualCoordinate (core::conformation::symmetry); VirtualizeAll (core::chemical); VirtualizeAllCreator (core::chemical); VirtualizeSidechain (core::chemical); VirtualizeSidechainCreator (core::chemical); VirtualResidueSelector (core::select::residue_selector); VirtualResidueSelectorCreator (core::select::residue_selector); VirtualRootMover (protocols::simple_moves); VirtualRootMoverCreator (protocols::simple_moves); VirtualSugarJustInTimeInstantiator (protocols::stepwise::modeler::rna::sugar); VirtualSugarSampler (protocols::stepwise::modeler::rna::sugar); VirtualSugarSamplerFromStringList (protocols::stepwise::modeler::rna::sugar); VisualizeEmbeddingMover (protocols::membrane::visualize); VisualizeEmbeddingMoverCreator (protocols::membrane::visualize); VisualizeMembraneMover (protocols::membrane::visualize); VisualizeMembraneMoverCreator (protocols::membrane::visualize); VLB (protocols::protein_interface_design::movers); VLBCreator (protocols::protein_interface_design::movers); VLBInstruction (protocols::protein_interface_design::movers); VLBProtected (protocols::denovo_design::components); VMax (protocols::pack_daemon); VMaxBy (protocols::pack_daemon); VMin (protocols::pack_daemon); VMinBy (protocols::pack_daemon); VoidsPenaltyEnergy (core::pack::guidance_scoreterms::voids_penalty_energy); VoidsPenaltyEnergyCreator (core::pack::guidance_scoreterms::voids_penalty_energy); VoidsPenaltyVoxelGrid (core::pack::guidance_scoreterms::voids_penalty_energy); volumepixel (core::scoring::atomic_depth); voxel (core::scoring::atomic_depth); voxel2 (core::scoring::atomic_depth); VoxelGridPoint (core::scoring::nmr); VoxelGridPoint_AA (core::scoring::nmr); VoxelSetIterator (protocols::match); VoxelSpacingMultifunc (protocols::electron_density); VoxelSpacingRefinementMover (protocols::electron_density); VoxelSpacingRefinementMoverCreator (protocols::electron_density)

W: WalkingBondAnglePerturber (protocols::kinematic_closure::perturbers); WalkingPerturber (protocols::kinematic_closure::perturbers); WallpaperGroup (protocols::cryst); WaterAdductHBondEnergy (core::energy_methods); WaterAdductHBondEnergyCreator (core::energy_methods); WaterAdductHBondPotential (core::scoring); WaterAdductIntraEnergy (core::energy_methods); WaterAdductIntraEnergyCreator (core::energy_methods); WaterAnchorInfo (core::pack::rotamer_set); WaterBuilder (core::scoring::lkball); WaterBuilderForRestype (core::scoring::lkball); WaterFeatures (protocols::features); WaterFeaturesCreator (protocols::features); WaterMediatedHbondMetric (core::simple_metrics::per_residue_metrics); WaterMediatedHbondMetricCreator (core::simple_metrics::per_residue_metrics); WaterPackingInfo (core::pack::rotamer_set); WaterRot (protocols::simple_moves); WaterRotsDB (protocols::simple_moves); WaterSpecificEnergy (core::energy_methods); WaterSpecificEnergyCreator (core::energy_methods); WaterWeightGridSet (core::energy_methods); WatsonCrickResidueMatcher (core::conformation); WatsonCrickRotamerCouplings (protocols::dna); WatsonCrickRotamerCouplingsCreator (protocols::dna); weight_triple (core::scoring::elec); WeightedFragmentSmoothTrialMover (protocols::hybridization); WeightedFragmentTrialMover (protocols::hybridization); WeightRangeConstraint (protocols::optimize_weights); WhileMover (protocols::moves); WholeBodyRotationMover (protocols::rigid); WholeBodyTranslationMover (protocols::rigid); WholeStructureEnergy (core::scoring::methods); WholeWholeEnergyInvoker (core::scoring::etable); WidgetFactory (utility::factory); WidgetRegistrator (utility::factory); WidthFirstSlidingWindowLoopClosure (protocols::loops::loop_closure::ccd); WindowPoseCompMotifMetric (protocols::pose_sewing::simple_metrics); WindowPoseCompMotifMetricCreator (protocols::pose_sewing::simple_metrics); WobbleMover (protocols::simple_moves); NetworkQueue::WorkUnit (protocols::network); WorkUnit_BatchRelax (protocols::relax); WorkUnit_BatchRelax_and_PostRescore (protocols::relax); WorkUnit_bbGauss (protocols::mpi_refinement); WorkUnit_CombinePose (protocols::mpi_refinement); WorkUnit_FragInsert (protocols::mpi_refinement); WorkUnit_KicCloser (protocols::mpi_refinement); WorkUnit_LoopHash (protocols::loophash); WorkUnit_LoopHash (protocols::mpi_refinement); WorkUnit_MD (protocols::mpi_refinement); WorkUnit_MoverWrapper (protocols::wum); WorkUnit_NormalMode (protocols::mpi_refinement); WorkUnit_PartialAbinitio (protocols::mpi_refinement); WorkUnit_RamaPerturber (protocols::mpi_refinement); WorkUnit_Relax (protocols::mpi_refinement); WorkUnit_Sampler (protocols::mpi_refinement); WorkUnit_SilentStructStore (protocols::wum); WorkUnit_Wait (protocols::wum); WorkUnitBase (protocols::wum); WorkUnitList (protocols::wum); WorkUnitManager (protocols::wum); WorkUnitQueue (protocols::wum); WorkUnitQueue_Swapped (protocols::wum); Worst9merFilter (protocols::simple_filters); Worst9merFilterCreator (protocols::simple_filters); WrappedBaseChemistry (protocols::chemistries); WrappedOptEExpressionCreator (protocols::optimize_weights); WrapperOptEMultifunc (protocols::optimize_weights); WriteableCacheableData (basic::datacache); WriteableCacheableDataCreator (basic::datacache); WriteFileSFB (protocols::jd2); WriteFiltersToPose (protocols::simple_moves); WriteFiltersToPoseCreator (protocols::simple_moves); WriteKinemageOutputter (protocols::match::output); WriteLigandMolFile (protocols::ligand_docking); WriteLigandMolFileCreator (protocols::ligand_docking); WriteOut_MpiFileBuffer (protocols::jd2); WriteSSEMover (protocols::simple_moves); WriteSSEMoverCreator (protocols::simple_moves); WriteUpstreamCoordinateKinemage (protocols::match::output); WriteUpstreamHitKinemage (protocols::match::output); WTEBiasEnergy (protocols::canonical_sampling); WorkUnitBase::WU_Header (protocols::wum); wwPDBJobOutputter (protocols::jd2)

Y: YHHPlanarityEnergy (core::energy_methods); YHHPlanarityEnergyCreator (core::energy_methods)

Z: ZincHeterodimerMover (protocols::metal_interface); ZincSiteFinder (protocols::metal_interface)