- a -

• AA : protocols::optimize_weights
• Ab_TemplateInfoCOP : protocols::antibody2
• Ab_TemplateInfoOP : protocols::antibody2
• 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
• 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::util
• ABEGOManagerOP : core::util
• 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
• AbstractArchiveBaseCOP : protocols::jd2::archive
• AbstractArchiveBaseOP : protocols::jd2::archive
• AbstractRotamerTrieCOP : core::conformation
• AbstractRotamerTrieOP : core::conformation
• 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
• AddHydrogenCOP : protocols::ligand_docking
• AddHydrogenOP : protocols::ligand_docking
• AddHydrogensCOP : protocols::ligand_docking
• AddHydrogensOP : protocols::ligand_docking
• AddLigandMotifRotamersCOP : protocols::enzdes
• AddLigandMotifRotamersOP : protocols::enzdes
• Address : protocols::canonical_sampling::mc_convergence_checks
• AddRigidBodyLigandConfsCOP : protocols::enzdes
• AddRigidBodyLigandConfsOP : protocols::enzdes
• AddSearchPatternRotSetOpCOP : protocols::hotspot_hashing
• AddSearchPatternRotSetOpOP : protocols::hotspot_hashing
• AdductMap : core::chemical
• AdductOP : core::chemical
• Align_RmsdEvaluatorCOP : protocols::comparative_modeling
• Align_RmsdEvaluatorOP : protocols::comparative_modeling
• Align_RotamerEvaluatorCOP : protocols::comparative_modeling
• Align_RotamerEvaluatorOP : protocols::comparative_modeling
• 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
• all_water_weights_iterator : core::scoring::geometric_solvation
• AllowedSeqposForGeomCstCOP : protocols::toolbox::match_enzdes_util
• AllowedSeqposForGeomCstOP : protocols::toolbox::match_enzdes_util
• AllowInsertOP : protocols::toolbox
• AllowPdbIdFilterCOP : protocols::frag_picker
• AllowPdbIdFilterOP : protocols::frag_picker
• AmberPeriodicFuncCOP : core::scoring::constraints
• AmberPeriodicFuncOP : core::scoring::constraints
• 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
• 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
• Angle : core
• AngleConstraintCOP : core::scoring::constraints
• AngleConstraintOP : core::scoring::constraints
• AngleVector : core::pack::dunbrack
• AnnotatedFragDataCOP : core::fragment
• AnnotatedFragDataOP : core::fragment
• AntibodyInfoCOP : protocols::antibody2
• AntibodyInfoOP : protocols::antibody2
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody2
• AntibodyModelerProtocolOP : protocols::antibody2
• 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
• 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
• AssembleLinkerMoverCOP : protocols::domain_assembly
• AssembleLinkerMoverOP : protocols::domain_assembly
• 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::kinematics::tree
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCAP : core::kinematics::tree
• AtomChain : core::io::pdb
• AtomCOP : core::chemical , core::kinematics::tree
• AtomCOPs : 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_Mask : core::id
• AtomIndices : core::chemical
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• AtomNeighbors : core::scoring
• AtomOP : core::chemical , core::kinematics::tree
• AtomOPs : core::chemical
• AtomPairConstraintCOP : core::scoring::constraints
• 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
• 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
• AtomTypeDatabaseIOCOP : core::chemical
• AtomTypeIndex : core::chemical
• AtomTypeSetAP : core::chemical
• AtomTypeSetCAP : core::chemical
• AtomTypeSetOP : core::chemical
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• AtomVDWCOP : core::scoring
• AtomVDWOP : core::scoring
• 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