- d -

• DaemonIndices : protocols::pack_daemon::DaemonSet
• DaemonList : protocols::pack_daemon::DaemonSet
• DaemonListIter : protocols::pack_daemon::DaemonSet
• DataccacheBoolDataOP : protocols::splice::Splice
• DataMap : core::pack::task::operation::TaskOperation , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::evolution::EvolutionaryDynamicsMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::moves::DsspMover , protocols::pose_creation::MakePolyXMover , protocols::pose_metric_calculators::FragQualCalculator , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter
• dbase_const_iterator : protocols::splice::Splice , protocols::splice::SpliceOut
• DC_lines : core::scoring::DipolarCoupling
• decoy_iterator : protocols::jd2::archive::ArchiveBase
• DefaultPackerPalette : core::pack::task::TaskFactory
• DefaultPackerPaletteOP : core::pack::task::TaskFactory
• DeNovoArchitect : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::StrandArchitect
• DeNovoArchitectOP : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::StrandArchitect
• DensePDInteractionGraphOP : protocols::pack_daemon::DenseIGRepacker
• DependencyEdge : protocols::forge::build::BuildManager
• DependencyEdges : protocols::forge::build::BuildManager
• DerivedNameFunction : protocols::parser::DataLoaderCreator
• DerivVectorPair : core::optimization::MinimizerMap
• DesignInfo : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• DesignMoverFoldTreePair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• DesignMoverRealPair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• DesignTaskOP : protocols::flxbb::FlxbbDesign
• DesignTaskSet : protocols::flxbb::FlxbbDesign
• DestructionEvent : core::pose::Pose
• Difference : protocols::mean_field::jagged_array< T, A >
• difference_type : core::conformation::Conformation , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::RT , core::kinematics::tree::Atom , protocols::mean_field::jagged_array< T, A > , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• DigraphNodeForJobMap : protocols::jd3::job_distributors::JobExtractor
• Dihedrals : protocols::constraint_generator::HydrogenBondingAtom
• DimerPairing : protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet
• DimerPairings : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::StrandPairingSet
• DinucleotideStrand : core::pose::rna::BasePairStep
• DinucleotideStrandSequence : core::import_pose::libraries::BasePairStepSequence
• Distance : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• DistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• DistanceSquared : protocols::flexpack::interaction_graph::OTFFlexbbNode
• DisulfideList : protocols::denovo_design::DisulfidizeMover
• DisulfTemplateList : protocols::jumping::DisulfPairingLibrary
• DisulfTemplateMap : protocols::jumping::DisulfPairingLibrary
• DnaDesignDefOP : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DnaDesignDefOPs : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DOF3 : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• DOF_ID : core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::pose::Pose , core::scoring::constraints::ConstraintSet
• DOF_ID_Map : core::kinematics::MoveMap
• DOF_ID_Mask : core::kinematics::AtomTree , core::kinematics::MoveMap , core::kinematics::tree::Atom
• DOF_IDs : core::conformation::symmetry::SymmetryInfo
• DOF_Map : core::id::DOF_ID_Map< T >
• DOF_Node : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• DOF_NodeOP : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• DOF_Nodes : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• DOF_TaskMap : protocols::minimization_packing::MinMover
• DOF_Type : core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::optimization::MinimizerMap
• DOF_TypeMap : core::kinematics::MoveMap
• DOFElemVect : protocols::environment::EnvClaimBroker
• DofPassportCOP : protocols::environment::ClientMover
• DomainMap : core::conformation::Conformation , core::scoring::Energies
• DoubleDensePDInteractionGraphOP : protocols::pack_daemon::DoubleDenseIGRepacker
• downstream_atom : core::conformation::carbohydrates::GlycanNode
• DownstreamHitSets : protocols::match::output::CloudPDBWriter
• Dssp : protocols::fldsgn::BluePrintBDR
• DunbrackRotamerSampleData : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinSCSampler , protocols::match::upstream::ProteinUpstreamBuilder
• DunbrackRotamerSampleDataVector : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinSCSampler , protocols::match::upstream::ProteinUpstreamBuilder