- a -

• AA : protocols::optimize_weights
• AAProbabilities : protocols::antibody::design
• Ab_TemplateInfoCOP : protocols::antibody
• Ab_TemplateInfoOP : protocols::antibody
• 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
• 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
• AcceptanceCheckCOP : protocols::loop_modeling::utilities
• AcceptanceCheckOP : protocols::loop_modeling::utilities
• access_ptr_bool : protocols::jd2::utility::pointer
• access_ptr_char : protocols::jd2::utility::pointer
• access_ptr_double : protocols::jd2::utility::pointer
• access_ptr_float : protocols::jd2::utility::pointer
• access_ptr_int : protocols::jd2::utility::pointer
• access_ptr_long : protocols::jd2::utility::pointer
• access_ptr_longdouble : protocols::jd2::utility::pointer
• access_ptr_schar : protocols::jd2::utility::pointer
• access_ptr_short : protocols::jd2::utility::pointer
• access_ptr_size_t : protocols::jd2::utility::pointer
• access_ptr_uchar : protocols::jd2::utility::pointer
• access_ptr_uint : protocols::jd2::utility::pointer
• access_ptr_ulong : protocols::jd2::utility::pointer
• access_ptr_ushort : protocols::jd2::utility::pointer
• 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
• AddChainMoverCOP : protocols::simple_moves
• AddChainMoverOP : protocols::simple_moves
• 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
• AddMoverOP : protocols::stepwise::monte_carlo::rna
• AddOrDeleteMoverOP : protocols::stepwise::monte_carlo::rna
• Address : protocols::canonical_sampling::mc_convergence_checks
• AddRigidBodyLigandConfsCOP : protocols::enzdes
• AddRigidBodyLigandConfsOP : protocols::enzdes
• AddSearchPatternRotSetOpCOP : protocols::hotspot_hashing
• AddSearchPatternRotSetOpOP : protocols::hotspot_hashing
• AddZincSiteConstraintsCOP : protocols::metal_interface
• AddZincSiteConstraintsOP : protocols::metal_interface
• 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
• 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
• AllowedSeqposForGeomCstCOP : protocols::toolbox::match_enzdes_util
• AllowedSeqposForGeomCstOP : protocols::toolbox::match_enzdes_util
• AllowInsertOP : protocols::toolbox
• AllowPdbIdFilterCOP : protocols::frag_picker
• AllowPdbIdFilterOP : protocols::frag_picker
• AmbiguousMultiConstraintCOP : protocols::constraints_additional
• AmbiguousMultiConstraintOP : protocols::constraints_additional
• 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
• AntibodyCDRDesignerCOP : protocols::antibody::design
• AntibodyCDRDesignerOP : protocols::antibody::design
• AntibodyDatabaseManagerCOP : protocols::antibody::design
• AntibodyDatabaseManagerOP : protocols::antibody::design
• AntibodyDesignModelerCOP : protocols::antibody::design
• AntibodyDesignModelerOP : protocols::antibody::design
• AntibodyDesignMoverCOP : protocols::antibody::design
• AntibodyDesignMoverOP : protocols::antibody::design
• AntibodyEnumManagerCOP : protocols::antibody
• AntibodyEnumManagerOP : protocols::antibody
• AntibodyGraftDesignerCOP : protocols::antibody::design
• AntibodyGraftDesignerOP : protocols::antibody::design
• AntibodyInfoAP : protocols::antibody
• AntibodyInfoCAP : protocols::antibody
• AntibodyInfoCOP : protocols::antibody
• AntibodyInfoOP : protocols::antibody
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody
• AntibodyModelerProtocolOP : protocols::antibody
• AntibodyNumberingParserCOP : protocols::antibody
• AntibodyNumberingParserOP : protocols::antibody
• APClusterCOP : protocols::cluster
• APClusterOP : protocols::cluster
• ApplyRandomStoredRBConfCOP : protocols::enzdes
• ApplyRandomStoredRBConfOP : protocols::enzdes
• ArchiveBaseCOP : protocols::jd2::archive
• ArchiveBaseOP : protocols::jd2::archive
• ArchiveManagerAP : protocols::jd2::archive
• ArchiveManagerCAP : protocols::jd2::archive
• ArchiveManagerCOP : protocols::jd2::archive
• ArchiveManagerOP : protocols::jd2::archive
• 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
• AtomAngleSecMatchRPECOP : protocols::match::downstream
• AtomAngleSecMatchRPEOP : protocols::match::downstream
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCoordinateCstMoverCOP : protocols::relax
• AtomCoordinateCstMoverOP : protocols::relax
• AtomDihedralSecMatchRPECOP : protocols::match::downstream
• AtomDihedralSecMatchRPEOP : protocols::match::downstream
• AtomDistanceSecMatchRPECOP : protocols::match::downstream
• AtomDistanceSecMatchRPEOP : protocols::match::downstream
• AtomGeometrySecMatchRPECOP : protocols::match::downstream
• AtomGeometrySecMatchRPEOP : protocols::match::downstream
• AtomGrps : protocols::noesy_assign
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• AtomPairConstraintsDataCOP : protocols::frag_picker::scores
• AtomPairConstraintsDataOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreCOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreOP : protocols::frag_picker::scores
• AtomTreeDiffJobInputterOP : protocols::jd2
• AtomTreeDiffJobOutputterCOP : protocols::jd2
• AtomTreeDiffJobOutputterOP : protocols::jd2
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• AtrRepCheckerCOP : protocols::stepwise::sampling::rna::checker
• AtrRepCheckerOP : protocols::stepwise::sampling::rna::checker
• AtrRepScreenerCOP : protocols::stepwise::screener
• AtrRepScreenerOP : protocols::stepwise::screener
• AttachmentCOP : protocols::stepwise::monte_carlo
• AttachmentOP : protocols::stepwise::monte_carlo
• Attachments : protocols::stepwise::monte_carlo
• AutoCutDataCOP : protocols::environment
• AutoCutDataOP : protocols::environment
• 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