- a -

• A3BHbsMoverCOP : protocols::simple_moves::a3b_hbs
• A3BHbsMoverOP : protocols::simple_moves::a3b_hbs
• A3BHbsPatcherCOP : protocols::simple_moves::a3b_hbs
• A3BHbsPatcherOP : protocols::simple_moves::a3b_hbs
• A3BHbsRandomSmallMoverCOP : protocols::simple_moves::a3b_hbs
• A3BHbsRandomSmallMoverOP : protocols::simple_moves::a3b_hbs
• AA : protocols::optimize_weights
• AA_VariantsExceptions : core::chemical
• AACompositionConstraintCOP : core::scoring::aa_composition_energy
• AACompositionConstraintOP : core::scoring::aa_composition_energy
• AACompositionEnergyOP : core::scoring::aa_composition_energy
• AACompositionEnergySetupCOP : core::scoring::aa_composition_energy
• AACompositionEnergySetupOP : core::scoring::aa_composition_energy
• AACompositionPropertiesSetCOP : core::scoring::aa_composition_energy
• AACompositionPropertiesSetOP : core::scoring::aa_composition_energy
• AAFrequencyCOP : protocols::denovo_design::task_operations
• AAFrequencyOP : protocols::denovo_design::task_operations
• AAMatrixCOP : protocols::mean_field
• AAMatrixOP : protocols::mean_field
• AAProbabilities : protocols::antibody , protocols::toolbox::task_operations
• AARepeatEnergyOP : core::scoring::aa_repeat_energy
• Ab_TemplateInfoCOP : protocols::antibody
• Ab_TemplateInfoOP : protocols::antibody
• Abego : protocols::denovo_design::architects
• ABEGO_SS_MapCOP : protocols::frag_picker::quota
• ABEGO_SS_MapOP : protocols::frag_picker::quota
• ABEGO_SS_PoolCOP : protocols::frag_picker::quota
• ABEGO_SS_PoolOP : protocols::frag_picker::quota
• ABEGO_SS_ScoreCOP : protocols::frag_picker::scores
• ABEGO_SS_ScoreOP : protocols::frag_picker::scores
• AbegoCOP : core::scoring::methods
• ABEGOEvalAP : core::fragment::picking_old::vall::eval
• ABEGOEvalCAP : core::fragment::picking_old::vall::eval
• ABEGOEvalCOP : core::fragment::picking_old::vall::eval
• ABEGOEvalOP : core::fragment::picking_old::vall::eval
• ABEGOManagerCOP : core::sequence
• ABEGOManagerOP : core::sequence
• AbegoOP : core::scoring::methods
• AbinitioMoverWeightAP : protocols::topology_broker::weights
• AbinitioMoverWeightCAP : protocols::topology_broker::weights
• AbinitioMoverWeightCOP : protocols::topology_broker::weights
• AbinitioMoverWeightOP : protocols::topology_broker::weights
• AbrelaxMoverCOP : protocols::abinitio
• AbrelaxMoverOP : protocols::abinitio
• AbscriptLoopCloserCMCOP : protocols::abinitio::abscript
• AbscriptLoopCloserCMOP : protocols::abinitio::abscript
• AbscriptMoverCOP : protocols::abinitio::abscript
• AbscriptMoverOP : protocols::abinitio::abscript
• AbscriptStageMoverCOP : protocols::abinitio::abscript
• AbscriptStageMoverOP : protocols::abinitio::abscript
• AbstractArchiveBaseCOP : protocols::jd2::archive
• AbstractArchiveBaseOP : protocols::jd2::archive
• AbstractRotamerTrieCOP : core::conformation
• AbstractRotamerTrieOP : core::conformation
• AcceptanceCheckCOP : protocols::loop_modeling::utilities
• AcceptanceCheckOP : protocols::loop_modeling::utilities
• AcceptorAtomEIter : core::chemical
• AcceptorAtomGraph : core::chemical
• AcceptorAtomVIter : core::chemical
• AcceptorAtomVIterPair : core::chemical
• AccumulatorOP : core::scoring::packstat
• ActiveSiteGridCOP : protocols::match::downstream
• ActiveSiteGridOP : protocols::match::downstream
• AdaptiveScoreHistogramCOP : protocols::frag_picker::scores
• AdaptiveScoreHistogramOP : protocols::frag_picker::scores
• AddAssemblyConstraintsCOP : protocols::domain_assembly
• AddAssemblyConstraintsOP : protocols::domain_assembly
• AddBehaviorRLTOP : core::pack::task::operation
• AddCDRProfileSetsOperationCOP : protocols::antibody::task_operations
• AddCDRProfileSetsOperationOP : protocols::antibody::task_operations
• AddCDRProfilesOperationCOP : protocols::antibody::task_operations
• AddCDRProfilesOperationOP : protocols::antibody::task_operations
• AddChainMoverCOP : protocols::simple_moves
• AddChainMoverOP : protocols::simple_moves
• AddCompositionConstraintMoverCOP : protocols::aa_composition
• AddCompositionConstraintMoverOP : protocols::aa_composition
• AddConstraintsCOP : protocols::constraint_generator
• AddConstraintsOP : protocols::constraint_generator
• AddGood2BPairEnergyRotamersCOP : protocols::toolbox::rotamer_set_operations
• AddGood2BPairEnergyRotamersOP : protocols::toolbox::rotamer_set_operations
• AddHelixSequenceConstraintsMoverCOP : protocols::aa_composition
• AddHelixSequenceConstraintsMoverOP : protocols::aa_composition
• AddHydrogenCOP : protocols::ligand_docking
• AddHydrogenOP : protocols::ligand_docking
• AddHydrogensCOP : protocols::ligand_docking
• AddHydrogensOP : protocols::ligand_docking
• AddJobPairDataCOP : protocols::simple_moves
• AddJobPairDataOP : protocols::simple_moves
• AddLigandMotifRotamersCOP : protocols::enzdes
• AddLigandMotifRotamersOP : protocols::enzdes
• AddMembraneMoverCOP : protocols::membrane
• AddMembraneMoverOP : protocols::membrane
• AddMoverCreatorCOP : protocols::stepwise::monte_carlo::mover
• AddMoverCreatorOP : protocols::stepwise::monte_carlo::mover
• AddMoverOP : protocols::stepwise::monte_carlo::mover
• AddMPLigandMoverCOP : protocols::membrane
• AddMPLigandMoverOP : protocols::membrane
• AddOrDeleteMoverOP : protocols::stepwise::monte_carlo::mover
• Address : protocols::canonical_sampling::mc_convergence_checks
• AddRigidBodyLigandConfsCOP : protocols::enzdes
• AddRigidBodyLigandConfsOP : protocols::enzdes
• AddSearchPatternRotSetOpCOP : protocols::hotspot_hashing
• AddSearchPatternRotSetOpOP : protocols::hotspot_hashing
• AddSegmentDataMoverCOP : protocols::denovo_design::movers
• AddSegmentDataMoverOP : protocols::denovo_design::movers
• AdductMap : core::chemical
• AdductOP : core::chemical
• AddZincSiteConstraintsCOP : protocols::metal_interface
• AddZincSiteConstraintsOP : protocols::metal_interface
• AdjacentIter : core::chemical
• AdjacentIterPair : core::chemical
• AdjacentListOP : protocols::cluster::calibur
• AIDs : core::pose::motif
• AIVD : core::io::pose_from_sfr
• AliasMap : protocols::denovo_design::components
• Align_RmsdEvaluatorCOP : protocols::comparative_modeling
• Align_RmsdEvaluatorOP : protocols::comparative_modeling
• Align_RotamerEvaluatorCOP : protocols::comparative_modeling
• Align_RotamerEvaluatorOP : protocols::comparative_modeling
• AlignChainMoverCOP : protocols::simple_moves
• AlignChainMoverOP : protocols::simple_moves
• AlignedThreadOperationCOP : protocols::toolbox::task_operations
• AlignedThreadOperationOP : protocols::toolbox::task_operations
• AlignerCOP : core::sequence
• AlignerOP : core::sequence
• AlignEvaluatorCOP : protocols::evaluation
• AlignEvaluatorOP : protocols::evaluation
• AlignmentClusterCOP : protocols::comparative_modeling
• AlignmentClusteringCOP : protocols::comparative_modeling
• AlignmentClusteringOP : protocols::comparative_modeling
• AlignmentClusterOP : protocols::comparative_modeling
• AlignmentSetCOP : protocols::comparative_modeling
• AlignmentSetOP : protocols::comparative_modeling
• AlignPoseToInvrotTreeMoverCOP : protocols::toolbox::match_enzdes_util
• AlignPoseToInvrotTreeMoverOP : protocols::toolbox::match_enzdes_util
• AlignResiduesMoverCOP : protocols::denovo_design::movers
• AlignResiduesMoverOP : protocols::denovo_design::movers
• AlignRMSD_ScreenerCOP : protocols::stepwise::screener
• AlignRMSD_ScreenerOP : protocols::stepwise::screener
• all_water_weights_iterator : core::scoring::geometric_solvation
• AllowedSeqposForGeomCstCOP : protocols::toolbox::match_enzdes_util
• AllowedSeqposForGeomCstOP : protocols::toolbox::match_enzdes_util
• AllowedStrandBulges : protocols::denovo_design::architects
• AllowPdbIdFilterCOP : protocols::frag_picker
• AllowPdbIdFilterOP : protocols::frag_picker
• AltCodeMap : core::io
• AmberPeriodicFuncCOP : core::scoring::func
• AmberPeriodicFuncOP : core::scoring::func
• AmbiguousConstraintCOP : core::scoring::constraints
• AmbiguousConstraintOP : core::scoring::constraints
• AmbiguousMultiConstraintCOP : protocols::constraints_additional
• AmbiguousMultiConstraintOP : protocols::constraints_additional
• AmbiguousNMRConstraintCOP : core::scoring::constraints
• AmbiguousNMRConstraintOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintOP : core::scoring::constraints
• AnalyticEtableEvaluatorOP : core::scoring::etable
• AnalyzeLoopModelingCOP : protocols::pose_length_moves
• AnalyzeLoopModelingOP : protocols::pose_length_moves
• AnchorCOP : protocols::anchored_design
• AnchoredDesignMoverOP : protocols::anchored_design
• AnchoredGraftMoverAP : protocols::grafting
• AnchoredGraftMoverCAP : protocols::grafting
• AnchoredGraftMoverCOP : protocols::grafting
• AnchoredGraftMoverOP : protocols::grafting
• AnchoredPerturbMoverOP : protocols::anchored_design
• AnchoredRefineMoverOP : protocols::anchored_design
• AnchorMoversDataCOP : protocols::anchored_design
• AnchorMoversDataOP : protocols::anchored_design
• AnchorOP : protocols::anchored_design
• AnchorSugarScreenerCOP : protocols::stepwise::screener
• AnchorSugarScreenerOP : protocols::stepwise::screener
• AndJumpSelectorCOP : core::select::jump_selector
• AndJumpSelectorOP : core::select::jump_selector
• AndResidueSelectorCOP : core::select::residue_selector
• AndResidueSelectorOP : core::select::residue_selector
• Angle : core
• AngleConstraintCOP : core::scoring::constraints
• AngleConstraintOP : core::scoring::constraints
• AngleToVectorCOP : protocols::simple_filters
• AngleToVectorOP : protocols::simple_filters
• AngleVector : core::pack::dunbrack
• AnnealableGraphBaseCOP : core::pack::interaction_graph
• AnnealableGraphBaseOP : core::pack::interaction_graph
• AnnotatedFragDataCOP : core::fragment
• AnnotatedFragDataOP : core::fragment
• Annotation : core::io::rna
• AntibodyCDRGraftDesignOptions : protocols::antibody::design
• AntibodyCDRGrafterCOP : protocols::antibody
• AntibodyCDRGrafterOP : protocols::antibody
• AntibodyCDRSeqDesignOptions : protocols::antibody::design
• AntibodyCDRSetOptions : protocols::antibody
• AntibodyDatabaseManagerCOP : protocols::antibody
• AntibodyDatabaseManagerOP : protocols::antibody
• AntibodyDesignEnumManagerCOP : protocols::antibody::design
• AntibodyDesignEnumManagerOP : protocols::antibody::design
• AntibodyDesignMoverCOP : protocols::antibody::design
• AntibodyDesignMoverOP : protocols::antibody::design
• AntibodyDesignProtocolCOP : protocols::antibody::design
• AntibodyDesignProtocolOP : protocols::antibody::design
• AntibodyEnumManagerCOP : protocols::antibody
• AntibodyEnumManagerOP : protocols::antibody
• AntibodyFeaturesCOP : protocols::antibody
• AntibodyFeaturesOP : protocols::antibody
• AntibodyInfoAP : protocols::antibody
• AntibodyInfoCAP : protocols::antibody
• AntibodyInfoCOP : protocols::antibody
• AntibodyInfoOP : protocols::antibody
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody
• AntibodyModelerProtocolOP : protocols::antibody
• AntibodyNumberingConverterMoverCOP : protocols::antibody
• AntibodyNumberingConverterMoverOP : protocols::antibody
• AntibodyNumberingParserCOP : protocols::antibody
• AntibodyNumberingParserOP : protocols::antibody
• AntibodyRegionSelectorCOP : protocols::antibody::residue_selector
• AntibodyRegionSelectorOP : protocols::antibody::residue_selector
• AntibodySeqDesignTFCreatorCOP : protocols::antibody::design
• AntibodySeqDesignTFCreatorOP : protocols::antibody::design
• APBSConfigAP : core::scoring
• APBSConfigCAP : core::scoring
• APBSConfigCOP : core::scoring
• APBSConfigOP : core::scoring
• APBSResultAP : core::scoring
• APBSResultCAP : core::scoring
• APBSResultCOP : core::scoring
• APBSResultOP : core::scoring
• APBSWrapperAP : core::scoring
• APBSWrapperCAP : core::scoring
• APBSWrapperCOP : core::scoring
• APBSWrapperOP : core::scoring
• APClusterCOP : protocols::cluster
• APClusterOP : protocols::cluster
• APolarHydrogenEIter : core::chemical
• APolarHydrogenGraph : core::chemical
• APolarHydrogenVIter : core::chemical
• APolarHydrogenVIterPair : core::chemical
• AppendResidueRotamerSetOP : core::pack::task::operation
• AppendRotamerOP : core::pack::task::operation
• AppendRotamerSetOP : core::pack::task::operation
• ApplyRandomStoredRBConfCOP : protocols::enzdes
• ApplyRandomStoredRBConfOP : protocols::enzdes
• Arc : core::scoring::packstat
• ArchiveBaseCOP : protocols::jd2::archive
• ArchiveBaseOP : protocols::jd2::archive
• ArchiveManagerAP : protocols::jd2::archive
• ArchiveManagerCAP : protocols::jd2::archive
• ArchiveManagerCOP : protocols::jd2::archive
• ArchiveManagerOP : protocols::jd2::archive
• ArcIter : core::scoring::packstat
• Arcs : core::scoring::packstat
• AreaAccumulatorOP : core::scoring::packstat
• AreConnectablePredicateCOP : protocols::denovo_design::connection
• AreConnectablePredicateOP : protocols::denovo_design::connection
• AromaticAtomEIter : core::chemical
• AromaticAtomGraph : core::chemical
• AromaticAtomVIter : core::chemical
• AromaticAtomVIterPair : core::chemical
• AspartimidePenaltyEnergyAP : core::scoring::methods
• AspartimidePenaltyEnergyCAP : core::scoring::methods
• AspartimidePenaltyEnergyCOP : core::scoring::methods
• AspartimidePenaltyEnergyOP : core::scoring::methods
• AssembleLinkerMoverCOP : protocols::domain_assembly
• AssembleLinkerMoverOP : protocols::domain_assembly
• AssemblyConstraintsMoverCOP : protocols::sewing
• AssemblyConstraintsMoverOP : protocols::sewing
• AssemblyCOP : protocols::sewing
• AssemblyMoverCOP : protocols::sewing
• AssemblyMoverOP : protocols::sewing
• AssemblyOP : protocols::sewing
• AssemblyScoreFunctionCOP : protocols::sewing::scoring
• AssemblyScoreFunctionOP : protocols::sewing::scoring
• AssemblyScorerCOP : protocols::sewing::scoring
• AssemblyScorerOP : protocols::sewing::scoring
• AssignToClustersMoverCOP : protocols::cluster
• AssignToClustersMoverOP : protocols::cluster
• AsymFoldandDockClaimerAP : protocols::topology_broker
• AsymFoldandDockClaimerCAP : protocols::topology_broker
• AsymFoldandDockClaimerCOP : protocols::topology_broker
• AsymFoldandDockClaimerOP : protocols::topology_broker
• AsymFoldandDockMoveRbJumpMoverCOP : protocols::simple_moves::asym_fold_and_dock
• AsymFoldandDockMoveRbJumpMoverOP : protocols::simple_moves::asym_fold_and_dock
• ATOM_RADIUS : core::scoring::sc
• AtomAngleSecMatchRPECOP : protocols::match::downstream
• AtomAngleSecMatchRPEOP : protocols::match::downstream
• AtomAP : core::chemical , core::kinematics::tree
• AtomAPs : core::chemical
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCAP : core::kinematics::tree
• AtomCoordinateCstMoverCOP : protocols::relax
• AtomCoordinateCstMoverOP : protocols::relax
• AtomCOP : core::chemical , core::kinematics::tree
• AtomCOPs : core::chemical
• AtomDatabaseIOCOP : core::chemical
• AtomDatabaseIOOP : core::chemical
• AtomDihedralSecMatchRPECOP : protocols::match::downstream
• AtomDihedralSecMatchRPEOP : protocols::match::downstream
• AtomDistanceSecMatchRPECOP : protocols::match::downstream
• AtomDistanceSecMatchRPEOP : protocols::match::downstream
• AtomDOFChangeSet : core::kinematics
• AtomGeometrySecMatchRPECOP : protocols::match::downstream
• AtomGeometrySecMatchRPEOP : protocols::match::downstream
• AtomGraph : core::conformation
• AtomGraphOP : core::conformation
• AtomGrps : protocols::noesy_assign
• AtomID_MapperCOP : protocols::toolbox
• AtomID_MapperOP : protocols::toolbox
• AtomID_Mask : core::id
• AtomIndex : core::chemical::sdf
• AtomIndices : core::chemical
• AtomInfoGraph : core::io::pose_from_sfr
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• AtomLevelDomainMapCOP : protocols::toolbox
• AtomLevelDomainMapOP : protocols::toolbox
• AtomMap : protocols::sewing
• AtomMemo : core::chemical
• AtomMemoOP : core::chemical
• AtomNeighbors : core::scoring
• AtomOP : core::chemical , core::kinematics::tree
• AtomOPs : core::chemical
• AtomPairConstraintCOP : core::scoring::constraints
• AtomPairConstraintGeneratorCOP : protocols::constraint_generator
• AtomPairConstraintGeneratorOP : protocols::constraint_generator
• AtomPairConstraintOP : core::scoring::constraints
• AtomPairConstraintsDataCOP : protocols::frag_picker::scores
• AtomPairConstraintsDataOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreCOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreOP : protocols::frag_picker::scores
• AtomPairEnergyTable : core::scoring
• AtomPairFuncListCOP : core::scoring::custom_pair_distance
• AtomPairFuncListOP : core::scoring::custom_pair_distance
• AtomPointer1D : core::kinematics
• AtomPointer2D : core::kinematics
• AtomPropertiesCOP : core::chemical
• AtomPropertiesOP : core::chemical
• Atoms : core::conformation
• AtomTreeAP : core::kinematics
• AtomTreeCAP : core::kinematics
• AtomTreeCollectionCOP : core::pack::scmin
• AtomTreeCollectionOP : core::pack::scmin
• AtomTreeCOP : core::kinematics
• AtomTreeDiffCOP : core::import_pose::atom_tree_diffs
• AtomTreeDiffJobInputterOP : protocols::jd2
• AtomTreeDiffJobOutputterCOP : protocols::jd2
• AtomTreeDiffJobOutputterOP : protocols::jd2
• AtomTreeDiffOP : core::import_pose::atom_tree_diffs
• AtomTreeMinimizerCOP : core::optimization
• AtomTreeMinimizerOP : core::optimization
• AtomTreeOP : core::kinematics
• AtomTreeSCMinMinimizerMapCOP : core::pack::scmin
• AtomTreeSCMinMinimizerMapOP : core::pack::scmin
• AtomTypeIndex : core::chemical
• AtomTypeSetAP : core::chemical
• AtomTypeSetCAP : core::chemical
• AtomTypeSetCOP : core::chemical
• AtomTypeSetOP : core::chemical
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• AtomVDWCOP : core::scoring
• AtomVDWOP : core::scoring
• AtomWeights : core::scoring::lkball
• AttachmentCOP : protocols::stepwise::monte_carlo::mover
• AttachmentOP : protocols::stepwise::monte_carlo::mover
• Attachments : protocols::stepwise::monte_carlo::mover
• AutoCutDataCOP : protocols::environment
• AutoCutDataOP : protocols::environment
• AutomorphismIteratorCOP : core::chemical
• AutomorphismIteratorOP : core::chemical
• AverageDegreeCountFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeCountFilterOP : protocols::protein_interface_design::filters
• AverageDegreeFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeFilterOP : protocols::protein_interface_design::filters
• AveragePathLengthFilterCOP : protocols::simple_filters
• AveragePathLengthFilterOP : protocols::simple_filters