- 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
DataLoaderCOP : protocols::jd2::parser
DataLoaderCreatorCOP : protocols::jd2::parser
DataLoaderCreatorOP : protocols::jd2::parser
DataLoaderOP : protocols::jd2::parser
DDGBindOptEDataOP : protocols::optimize_weights
ddGCOP : protocols::simple_moves
DdgFilterCOP : protocols::simple_filters
DdgFilterOP : protocols::simple_filters
DDGMutationOptEDataOP : protocols::optimize_weights
ddGOP : protocols::simple_moves
ddGs : protocols::ddg
DDPlookupCOP : core::scoring::interface
DDPlookupOP : core::scoring::interface
DebuggingAnnealerOP : core::pack::annealer
DecomposeAndReweightEnergiesCalculatorCOP : protocols::toolbox::pose_metric_calculators
DecomposeAndReweightEnergiesCalculatorOP : protocols::toolbox::pose_metric_calculators
DecoySetEvaluationCOP : protocols::toolbox
DecoySetEvaluationOP : protocols::toolbox
DecoyStructOP : core::io::raw_data
DelphiElectrostaticsCOP : protocols::pockets
DelphiElectrostaticsOP : protocols::pockets
DeltaFilterCOP : protocols::simple_filters
DeltaFilterOP : protocols::simple_filters
DenseEnergyContainerOP : core::scoring
DenseIGRepackerCOP : protocols::pack_daemon
DenseIGRepackerOP : protocols::pack_daemon
DenseNeighborIteratorOP : core::scoring
DensePDInteractionGraphCOP : core::pack::interaction_graph
DensePDInteractionGraphOP : core::pack::interaction_graph
DensityScoringClaimerAP : protocols::topology_broker
DensityScoringClaimerCAP : protocols::topology_broker
DensityScoringClaimerCOP : protocols::topology_broker
DensityScoringClaimerOP : protocols::topology_broker
DenyPdbIdFilterCOP : protocols::frag_picker
DenyPdbIdFilterOP : protocols::frag_picker
DerivedSequenceMappingCOP : core::sequence
DerivedSequenceMappingOP : core::sequence
DesignableResiduesFilterCOP : protocols::protein_interface_design::filters
DesignableResiduesFilterOP : protocols::protein_interface_design::filters
DesignAroundOperationCOP : protocols::toolbox::task_operations
DesignAroundOperationOP : protocols::toolbox::task_operations
DesignRepackMoverCOP : protocols::simple_moves
DesignRepackMoverOP : protocols::simple_moves
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::simple_moves::symmetry
DetectSymmetryMoverOP : protocols::simple_moves::symmetry
DGBindOptEDataCOP : protocols::optimize_weights
DGBindOptEDataOP : protocols::optimize_weights
dihedral_atom_set : core::chemical
DihedralConstraintCOP : core::scoring::constraints
DihedralConstraintOP : core::scoring::constraints
DihedralConstraintsScoreCOP : protocols::frag_picker::scores
DihedralConstraintsScoreOP : protocols::frag_picker::scores
DihedralSet : core::pack::rotamer_set
DimerPairingCOP : protocols::fldsgn::topology
DimerPairingOP : core::scoring , protocols::fldsgn::topology
DipolarCouplingCOP : core::scoring
DipolarCouplingEnergyOP : core::scoring::methods
DipolarCouplingOP : core::scoring
DirectReadoutPotentialCOP : core::scoring::dna
DirectReadoutPotentialOP : core::scoring::dna
DisallowIfNonnativeOP : core::pack::task::operation
DisallowIfNonnativeRLTOP : core::pack::task::operation
Distance : core
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
DistanceScoreMoverAP : protocols::noesy_assign
DistanceScoreMoverCAP : protocols::noesy_assign
DistanceScoreMoverCOP : protocols::noesy_assign
DistanceScoreMoverOP : protocols::noesy_assign
DistanceSquared : core
DisulfideMatchingEnergyContainerAP : core::scoring::disulfides
DisulfideMatchingEnergyContainerCAP : core::scoring::disulfides
DisulfideMatchingEnergyContainerCOP : core::scoring::disulfides
DisulfideMatchingEnergyContainerOP : core::scoring::disulfides
DisulfideMatchingEnergyCOP : core::scoring::disulfides
DisulfideMatchingEnergyOP : core::scoring::disulfides
DisulfideMatchingPotentialAP : core::scoring::disulfides
DisulfideMatchingPotentialCAP : core::scoring::disulfides
DisulfideMatchingPotentialCOP : core::scoring::disulfides
DisulfideMatchingPotentialOP : core::scoring::disulfides
DisulfJumpClaimerAP : protocols::topology_broker
DisulfJumpClaimerCAP : protocols::topology_broker
DisulfJumpClaimerCOP : protocols::topology_broker
DisulfJumpClaimerOP : protocols::topology_broker
DisulfMinDataCOP : core::scoring::disulfides
DisulfMinDataOP : core::scoring::disulfides
DisulfPairingList : protocols::jumping
DisulfPairingsList : protocols::jumping
DiversifyStoredRBConfsCOP : protocols::enzdes
DiversifyStoredRBConfsOP : protocols::enzdes
DNA_BasePotentialCOP : core::scoring::dna
DNA_BasePotentialOP : core::scoring::dna
DNABFormPotentialCOP : core::scoring::dna
DNABFormPotentialOP : core::scoring::dna
DnaChainsCOP : protocols::dna
DnaChainsOP : protocols::dna
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
DnaNeighbors : protocols::dna
DNAParametersCOP : protocols::dna
DNAParametersOP : protocols::dna
DnaPositions : protocols::dna
DNATorsionEnergyCOP : core::scoring::dna
DNATorsionEnergyOP : core::scoring::dna
DockDesignFilterFactoryCOP : protocols::protein_interface_design
DockDesignFilterFactoryOP : protocols::protein_interface_design
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::symmetry
DockingScoreFunctionOP : core::scoring::symmetry
DockingSetupMoverOP : protocols::docking
DockingSlideIntoContactCOP : protocols::docking
DockingSlideIntoContactOP : protocols::docking
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
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
DofClaimCAP : protocols::topology_broker
DofClaimCOP : protocols::topology_broker
DofClaimOP : protocols::topology_broker
DofClaims : protocols::topology_broker
DomainMap : core::kinematics
DOT : core::scoring::sc
DoubleD1 : protocols::sparta
DoubleD2 : protocols::sparta
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
DsspMoverOP : protocols::moves
DummyClassAP : protocols::toolbox
DummyClassCAP : protocols::toolbox
DummyClassCOP : protocols::toolbox
DummyClassOP : protocols::toolbox
DunbrackConstraintCOP : core::pack::dunbrack
DunbrackConstraintOP : core::pack::dunbrack
DunbrackReal : core::pack::dunbrack
DunbrackSCSamplerCOP : protocols::match::upstream
DunbrackSCSamplerOP : protocols::match::upstream
DynamicAggregateFunctionCOP : protocols::pack_daemon
DynamicAggregateFunctionOP : protocols::pack_daemon