- d -

• DaemonSetCOP : protocols::pack_daemon
• DaemonSetOP : protocols::pack_daemon
• DarcParticleSwarmMinimizerCOP : protocols::pockets
• DarcParticleSwarmMinimizerOP : protocols::pockets
• DatabaseEntryWorkUnitCOP : protocols::wum
• DatabaseEntryWorkUnitOP : protocols::wum
• DatabaseFilterCOP : protocols::features
• DatabaseFilterOP : protocols::features
• DatabaseJobInputterOP : protocols::features
• DatabaseJobOutputterOP : protocols::features
• DatabaseOccSolEneCOP : core::scoring::geometric_solvation
• DatabaseOccSolEneOP : core::scoring::geometric_solvation
• DatabaseThreadCOP : protocols::task_operations
• DatabaseThreadOP : protocols::task_operations
• DataccacheBoolDataOP : protocols::splice
• DataLoaderCOP : protocols::parser
• DataLoaderCreatorCOP : protocols::parser
• DataLoaderCreatorOP : protocols::parser
• DataLoaderOP : protocols::parser
• DbTrajectoryReaderCOP : protocols::trajectory
• DbTrajectoryReaderOP : protocols::trajectory
• DbTrajectoryRecorderCOP : protocols::canonical_sampling
• DbTrajectoryRecorderOP : protocols::canonical_sampling
• DbTrajectoryWriterCOP : protocols::trajectory
• DbTrajectoryWriterOP : protocols::trajectory
• DDGBindOptEDataOP : protocols::optimize_weights
• ddGCOP : protocols::simple_ddg
• DdGFeaturesCOP : protocols::features
• DdGFeaturesOP : protocols::features
• DdgFilterCOP : protocols::simple_ddg
• DdgFilterOP : protocols::simple_ddg
• ddGMoverCOP : protocols::ddg
• ddGMoverOP : protocols::ddg
• DDGMutationOptEDataOP : protocols::optimize_weights
• ddGOP : protocols::simple_ddg
• ddGs : protocols::ddg
• DdGScanCOP : protocols::simple_ddg
• DdGScanOP : protocols::simple_ddg
• DDPlookupCOP : core::scoring::interface_
• DDPlookupOP : core::scoring::interface_
• DeallocationMessageCOP : protocols::jd3::deallocation
• DeallocationMessageOP : protocols::jd3::deallocation
• DebuggingAnnealerOP : core::pack::annealer
• DeclareBondCOP : protocols::cyclic_peptide
• DeclareBondCOPs : protocols::cyclic_peptide
• DeclareBondOP : protocols::cyclic_peptide
• DeclareBondOPs : protocols::cyclic_peptide
• DeclareStructureDataCovalentBondMoverCOP : protocols::denovo_design::movers
• DeclareStructureDataCovalentBondMoverOP : protocols::denovo_design::movers
• DecomposeAndReweightEnergiesCalculatorCOP : protocols::pose_metric_calculators
• DecomposeAndReweightEnergiesCalculatorOP : protocols::pose_metric_calculators
• DecoySetEvaluationCOP : protocols::toolbox
• DecoySetEvaluationOP : protocols::toolbox
• DecoyStructOP : core::io::raw_data
• DEERChiSqMethodCOP : core::scoring::epr_deer::metrics
• DEERChiSqMethodOP : core::scoring::epr_deer::metrics
• DEERDataCacheCOP : core::scoring::epr_deer
• DEERDataCacheOP : core::scoring::epr_deer
• DEERDataCOP : core::scoring::epr_deer::metrics
• DEERDataOP : core::scoring::epr_deer::metrics
• DEERDecayDataCOP : core::scoring::epr_deer::metrics
• DEERDecayDataOP : core::scoring::epr_deer::metrics
• DEERDistanceBoundsCOP : core::scoring::epr_deer::metrics
• DEERDistanceBoundsOP : core::scoring::epr_deer::metrics
• DEERDistanceDistributionCOP : core::scoring::epr_deer::metrics
• DEERDistanceDistributionOP : core::scoring::epr_deer::metrics
• DEEREnergyCOP : core::energy_methods
• DEEREnergyOP : core::energy_methods
• DEERIOCOP : core::scoring::epr_deer
• DEERIOOP : core::scoring::epr_deer
• DEERJaccardMethodCOP : core::scoring::epr_deer::metrics
• DEERJaccardMethodOP : core::scoring::epr_deer::metrics
• DEERJSMethodCOP : core::scoring::epr_deer::metrics
• DEERJSMethodOP : core::scoring::epr_deer::metrics
• DEERMiscMethodCOP : core::scoring::epr_deer::metrics
• DEERMiscMethodOP : core::scoring::epr_deer::metrics
• DEEROverlapMethodCOP : core::scoring::epr_deer::metrics
• DEEROverlapMethodOP : core::scoring::epr_deer::metrics
• DefaultPackerPaletteCOP : core::pack::palette
• DefaultPackerPaletteOP : core::pack::palette
• DeleteAllRotamerSetOperationCOP : core::pack::rotamer_set
• DeleteAllRotamerSetOperationOP : core::pack::rotamer_set
• DeleteChainMoverCOP : protocols::simple_moves
• DeleteChainMoverOP : protocols::simple_moves
• DeleteChainsMoverCOP : protocols::simple_moves
• DeleteChainsMoverOP : protocols::simple_moves
• DeleteMoverCreatorCOP : protocols::stepwise::monte_carlo::mover
• DeleteMoverCreatorOP : protocols::stepwise::monte_carlo::mover
• DeleteMoverOP : protocols::stepwise::monte_carlo::mover
• DeleteRegionMoverCOP : protocols::grafting
• DeleteRegionMoverOP : protocols::grafting
• DeltaFilterCOP : protocols::simple_filters
• DeltaFilterOP : protocols::simple_filters
• DeNovoArchitectCOP : protocols::denovo_design::architects
• DeNovoArchitectCOPs : protocols::denovo_design::architects
• DeNovoArchitectCreatorCOP : protocols::denovo_design::architects
• DeNovoArchitectCreatorOP : protocols::denovo_design::architects
• DeNovoArchitectFactoryCOP : protocols::denovo_design::architects
• DeNovoArchitectFactoryOP : protocols::denovo_design::architects
• DeNovoArchitectOP : protocols::denovo_design::architects
• DeNovoArchitectOPs : protocols::denovo_design::architects
• DeNovoSilentFilePoseOutputterCOP : protocols::jd3::pose_outputters
• DeNovoSilentFilePoseOutputterOP : protocols::jd3::pose_outputters
• DenseEnergyContainerOP : core::scoring
• DenseIGRepackerCOP : protocols::pack_daemon
• DenseIGRepackerOP : protocols::pack_daemon
• DenseNeighborIteratorOP : core::scoring
• DenseNPDHBondInteractionGraph : core::pack::interaction_graph
• DenseNPDHBondInteractionGraphOP : core::pack::interaction_graph
• DensePDInteractionGraphCOP : core::pack::interaction_graph
• DensePDInteractionGraphOP : core::pack::interaction_graph
• DensityFitResidueSelectorCOP : core::select::residue_selector
• DensityFitResidueSelectorOP : core::select::residue_selector
• DensityScoringClaimerAP : protocols::topology_broker
• DensityScoringClaimerCAP : protocols::topology_broker
• DensityScoringClaimerCOP : protocols::topology_broker
• DensityScoringClaimerOP : protocols::topology_broker
• DensSkeletonCOP : protocols::loop_grower
• DensSkeletonOP : protocols::loop_grower
• DenyPdbIdFilterCOP : protocols::frag_picker
• DenyPdbIdFilterOP : protocols::frag_picker
• DerivedPeptideEntryCOP : protocols::peptide_deriver
• DerivedPeptideEntryOP : protocols::peptide_deriver
• DerivedSequenceMappingCOP : core::sequence
• DerivedSequenceMappingOP : core::sequence
• DesignableResiduesFilterCOP : protocols::protein_interface_design::filters
• DesignableResiduesFilterOP : protocols::protein_interface_design::filters
• DesignAroundOperationCOP : protocols::task_operations
• DesignAroundOperationOP : protocols::task_operations
• DesignInterfacesOperationCOP : protocols::splice
• DesignInterfacesOperationOP : protocols::splice
• DesignMeanFieldCOP : protocols::mean_field
• DesignMeanFieldOP : protocols::mean_field
• DesignRepackMoverCOP : protocols::calc_taskop_movers
• DesignRepackMoverOP : protocols::calc_taskop_movers
• DesignRestrictionsCOP : core::pack::task::operation
• DesignRestrictionsOP : core::pack::task::operation
• DesignTask_LayerOP : protocols::flxbb
• DesignTask_NormalOP : protocols::flxbb
• DesignTaskOP : protocols::flxbb
• DesignTaskSet : protocols::flxbb
• DesignTaskSetOP : protocols::flxbb
• DesignVsNativeComparisonOP : protocols::enzdes
• DetectProteinLigandInterfaceAP : protocols::enzdes
• DetectProteinLigandInterfaceCAP : protocols::enzdes
• DetectProteinLigandInterfaceCOP : protocols::enzdes
• DetectProteinLigandInterfaceOP : protocols::enzdes
• DetectSymmetryMoverCOP : protocols::symmetry
• DetectSymmetryMoverOP : protocols::symmetry
• DGBindOptEDataCOP : protocols::optimize_weights
• DGBindOptEDataOP : protocols::optimize_weights
• dihedral_atom_set : core::chemical
• DihedralConstraintCOP : core::scoring::constraints
• DihedralConstraintGeneratorCOP : protocols::constraint_generator
• DihedralConstraintGeneratorOP : protocols::constraint_generator
• DihedralConstraintOP : core::scoring::constraints
• DihedralConstraintsScoreCOP : protocols::frag_picker::scores
• DihedralConstraintsScoreOP : protocols::frag_picker::scores
• DihedralDistanceMetricCOP : core::simple_metrics::metrics
• DihedralDistanceMetricOP : core::simple_metrics::metrics
• DihedralSet : core::pack::rotamer_set
• DimerPairingCOP : protocols::fldsgn::topology
• DimerPairingOP : core::scoring , protocols::fldsgn::topology
• DipolarCouplingCOP : core::scoring
• DipolarCouplingEnergyOP : core::energy_methods
• DipolarCouplingOP : core::scoring
• DirectReadoutPotentialCOP : core::scoring::dna
• DirectReadoutPotentialOP : core::scoring::dna
• DirectSegmentLookupMoverCOP : protocols::indexed_structure_store::movers
• DirectSegmentLookupMoverOP : protocols::indexed_structure_store::movers
• DisableAntibodyRegionOperationCOP : protocols::antibody::task_operations
• DisableAntibodyRegionOperationOP : protocols::antibody::task_operations
• DisableCDRsOperationCOP : protocols::antibody::task_operations
• DisableCDRsOperationOP : protocols::antibody::task_operations
• DisallowIfNonnativeOP : core::pack::task::operation
• DisallowIfNonnativeRLTOP : core::pack::task::operation
• DisplayPoseLabelsMoverCOP : protocols::fold_from_loops::movers
• DisplayPoseLabelsMoverOP : protocols::fold_from_loops::movers
• Distance : core
• DistanceConstraintGeneratorCOP : protocols::constraint_generator
• DistanceConstraintGeneratorOP : protocols::constraint_generator
• DistanceFuncAP : core::scoring::custom_pair_distance
• DistanceFuncCAP : core::scoring::custom_pair_distance
• DistanceFuncCOP : core::scoring::custom_pair_distance
• DistanceFuncOP : core::scoring::custom_pair_distance
• DistanceHistogramCOP : core::scoring::saxs
• DistanceHistogramOP : core::scoring::saxs
• DistanceMap : protocols::noesy_assign
• DistanceResidueNetworkCOP : protocols::toolbox
• DistanceResidueNetworkOP : protocols::toolbox
• DistanceScoreMoverAP : protocols::noesy_assign
• DistanceScoreMoverCAP : protocols::noesy_assign
• DistanceScoreMoverCOP : protocols::noesy_assign
• DistanceScoreMoverOP : protocols::noesy_assign
• DistanceSquared : core
• DisulfideEntropyFilterCOP : protocols::simple_filters
• DisulfideEntropyFilterOP : protocols::simple_filters
• DisulfideInsertionMoverCOP : protocols::simple_moves
• DisulfideInsertionMoverCreatorCOP : protocols::simple_moves
• DisulfideInsertionMoverCreatorOP : protocols::simple_moves
• DisulfideInsertionMoverOP : protocols::simple_moves
• DisulfideMatchingEnergyContainerAP : core::scoring::disulfides
• DisulfideMatchingEnergyContainerCAP : core::scoring::disulfides
• DisulfideMatchingEnergyContainerCOP : core::scoring::disulfides
• DisulfideMatchingEnergyContainerOP : core::scoring::disulfides
• DisulfideMatchingEnergyCOP : core::energy_methods
• DisulfideMatchingEnergyOP : core::energy_methods
• DisulfideMatchingPotentialAP : core::scoring::disulfides
• DisulfideMatchingPotentialCAP : core::scoring::disulfides
• DisulfideMatchingPotentialCOP : core::scoring::disulfides
• DisulfideMatchingPotentialOP : core::scoring::disulfides
• DisulfideOptimizationMoverCOP : protocols::minimization_packing
• DisulfideOptimizationMoverOP : protocols::minimization_packing
• DisulfidizerMoverAP : protocols::denovo_design
• DisulfidizerMoverCAP : protocols::denovo_design
• DisulfidizerMoverCOP : protocols::denovo_design
• DisulfidizerMoverOP : protocols::denovo_design
• DisulfJumpClaimerAP : protocols::topology_broker
• DisulfJumpClaimerCAP : protocols::topology_broker
• DisulfJumpClaimerCOP : protocols::topology_broker
• DisulfJumpClaimerOP : protocols::topology_broker
• DisulfMinDataCOP : core::energy_methods
• DisulfMinDataOP : core::energy_methods
• DisulfPairingList : protocols::jumping
• DisulfPairingsList : protocols::jumping
• DiversifyStoredRBConfsCOP : protocols::enzdes
• DiversifyStoredRBConfsOP : protocols::enzdes
• DivideAndConquerorCOP : protocols::denovo_design::components
• DivideAndConquerorOP : protocols::denovo_design::components
• DNA_BasePotentialCOP : core::scoring::dna
• DNA_BasePotentialOP : core::scoring::dna
• DNA_DihedralPotentialCOP : core::scoring::dna
• DNA_DihedralPotentialOP : core::scoring::dna
• DNA_EnvPairPotentialCOP : core::scoring::dna
• DNA_EnvPairPotentialOP : core::scoring::dna
• DNABFormPotentialCOP : core::scoring::dna
• DNABFormPotentialOP : core::scoring::dna
• DnaChainsCOP : protocols::dna
• DnaChainsOP : protocols::dna
• DNAClashCheckFilterCOP : protocols::dna_dock
• DNAClashCheckFilterOP : protocols::dna_dock
• DnaDesignDefCOP : protocols::dna
• DnaDesignDefOP : protocols::dna
• DnaDesignDefOPs : protocols::dna
• DnaDesignDefs : protocols::dna
• DnaInterfaceFinderCOP : protocols::dna
• DnaInterfaceFinderOP : protocols::dna
• DnaInterfaceMinMoverCOP : protocols::dna
• DnaInterfaceMinMoverOP : protocols::dna
• DnaInterfaceMultiStateDesignCOP : protocols::dna
• DnaInterfaceMultiStateDesignOP : protocols::dna
• DnaInterfacePackerCOP : protocols::dna
• DnaInterfacePackerOP : protocols::dna
• DNAMethyltransferaseMoverCOP : protocols::enzymatic_movers
• DNAMethyltransferaseMoverOP : protocols::enzymatic_movers
• DnaNeighbors : protocols::dna
• DNAParametersCOP : protocols::dna
• DNAParametersOP : protocols::dna
• DnaPositions : protocols::dna
• DNATorsionEnergyCOP : core::energy_methods
• DNATorsionEnergyOP : core::energy_methods
• DNATorsionPotentialCOP : core::scoring::dna
• DNATorsionPotentialOP : core::scoring::dna
• DockingEnsembleCOP : protocols::docking
• DockingEnsembleOP : protocols::docking
• DockingEnsemblePrepackProtocolCOP : protocols::docking
• DockingEnsemblePrepackProtocolOP : protocols::docking
• DockingHighResCOP : protocols::docking
• DockingHighResFilterCOP : protocols::docking
• DockingHighResFilterOP : protocols::docking
• DockingHighResLegacyCOP : protocols::docking
• DockingHighResLegacyOP : protocols::docking
• DockingHighResOP : protocols::docking
• DockingInitialPerturbationCOP : protocols::docking
• DockingInitialPerturbationOP : protocols::docking
• DockingLowResCOP : protocols::docking
• DockingLowResEnsembleCOP : protocols::docking
• DockingLowResEnsembleOP : protocols::docking
• DockingLowResFilterCOP : protocols::docking
• DockingLowResFilterOP : protocols::docking
• DockingLowResOP : protocols::docking
• DockingPrepackProtocolCOP : protocols::docking
• DockingPrepackProtocolOP : protocols::docking
• DockingProtocolOP : protocols::docking
• DockingScoreFunctionCOP : core::scoring
• DockingScoreFunctionOP : core::scoring
• DockingSetupMoverOP : protocols::docking
• DockingSlideIntoContactCOP : protocols::docking
• DockingSlideIntoContactOP : protocols::docking
• DockIntoDensityMoverOP : protocols::electron_density
• DockJumps : protocols::docking
• DockMCMCycleCOP : protocols::docking
• DockMCMCycleOP : protocols::docking
• DockMCMProtocolCOP : protocols::docking
• DockMCMProtocolOP : protocols::docking
• DockMinMoverCOP : protocols::docking
• DockMinMoverOP : protocols::docking
• DockTaskFactoryCOP : protocols::docking
• DockTaskFactoryOP : protocols::docking
• DockWithHotspotMoverCOP : protocols::protein_interface_design::movers
• DockWithHotspotMoverOP : protocols::protein_interface_design::movers
• DOF_ConstraintCOP : core::scoring::constraints
• DOF_ConstraintCOPs : core::scoring::constraints
• DOF_ConstraintOP : core::scoring::constraints
• DOF_ConstraintOPs : core::scoring::constraints
• DOF_ID : core::optimization::symmetry
• DOF_ID_Mask : core::id
• DOF_NodeCOP : core::optimization
• DOF_NodeOP : core::optimization
• DofClaimAP : protocols::topology_broker::claims
• DofClaimCAP : protocols::topology_broker::claims
• DofClaimCOP : protocols::topology_broker::claims
• DofClaimOP : protocols::topology_broker::claims
• DofClaims : protocols::topology_broker::claims
• DOFElements : protocols::environment::claims
• DofPassportCOP : core::environment
• DofPassportOP : core::environment
• DofUnlockCOP : protocols::environment
• DofUnlockOP : protocols::environment
• DomainInterfaceFilterCOP : protocols::simple_filters
• DomainInterfaceFilterOP : protocols::simple_filters
• DomainMap : core::kinematics
• DOT : core::scoring::sc
• DoubleDenseIGRepackerCOP : protocols::pack_daemon
• DoubleDenseIGRepackerOP : protocols::pack_daemon
• DoubleDensePDInteractionGraphCOP : core::pack::interaction_graph
• DoubleDensePDInteractionGraphOP : core::pack::interaction_graph
• DoubleLayerKinematicAbinitioCOP : protocols::abinitio
• DoubleLayerKinematicAbinitioOP : protocols::abinitio
• DoubleLazyInteractionGraphCOP : core::pack::interaction_graph
• DoubleLazyInteractionGraphOP : core::pack::interaction_graph
• DownJumpSRFDCOP : core::fragment
• DownJumpSRFDOP : core::fragment
• DownstreamAlgorithmCOP : protocols::match::downstream
• DownstreamAlgorithmOP : protocols::match::downstream
• DownstreamBuilderCOP : protocols::match::downstream
• DownstreamBuilderOP : protocols::match::downstream
• DownstreamCoordinateKinemageWriterCOP : protocols::match::output
• DownstreamCoordinateKinemageWriterOP : protocols::match::output
• DownstreamRMSEvaluatorCOP : protocols::match::output
• DownstreamRMSEvaluatorOP : protocols::match::output
• DsspDesignOperationOP : protocols::task_operations
• DsspMoverOP : protocols::moves
• DsspSpecificLengthRequirementCOP : protocols::sewing::requirements
• DsspSpecificLengthRequirementCreatorCOP : protocols::sewing::requirements
• DsspSpecificLengthRequirementCreatorOP : protocols::sewing::requirements
• DsspSpecificLengthRequirementOP : protocols::sewing::requirements
• DualMonteCarloCOP : protocols::moves
• DualMonteCarloOP : protocols::moves
• DummyClassCOP : protocols::toolbox
• DummyClassOP : protocols::toolbox
• DumpPdbCOP : protocols::simple_moves
• DumpPdbOP : protocols::simple_moves
• DumpSingleResidueRotamersCOP : protocols::simple_moves
• DumpSingleResidueRotamersOP : protocols::simple_moves
• DumpTrajectoryEnergyOP : core::energy_methods
• DunbrackConstraintCOP : core::pack::dunbrack
• DunbrackConstraintOP : core::pack::dunbrack
• DunbrackReal : core::pack::dunbrack
• DunbrackRotamerLibrarySpecificationCOP : core::chemical::rotamers
• DunbrackRotamerLibrarySpecificationOP : core::chemical::rotamers
• DunbrackSCSamplerCOP : protocols::match::upstream
• DunbrackSCSamplerOP : protocols::match::upstream
• DynamicAggregateFunctionCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverOP : protocols::pack_daemon
• DynamicAggregateFunctionOP : protocols::pack_daemon