Here is a list of all namespace members with links to the namespace documentation for each member:

- d -

• D : core::id
• d0 : protocols::hybridization
• D0_MIN : protocols::hybridization
• d0_out_ : protocols::hybridization
• d0_search : protocols::hybridization
• d0A : protocols::hybridization
• d0B : protocols::hybridization
• d2h_sa : core::scoring
• D2H_SA_EnergyCreator_registrator : core::init
• d2r() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• D_AA : core::chemical
• d_array_scale() : core::scoring::fiber_diffraction
• D_CHIRALITY : protocols::simple_moves::chiral
• D_RNA : core::chemical
• D_SUGAR : core::chemical
• dab_sasa : core::scoring
• dab_sev : core::scoring
• DaemonSetCOP : protocols::pack_daemon
• DaemonSetMessage : protocols::pack_daemon
• DaemonSetOP : protocols::pack_daemon
• DarcParticleSwarmMinimizerCOP : protocols::pockets
• DarcParticleSwarmMinimizerOP : protocols::pockets
• data_dim() : protocols::recces
• DATABASE : protocols::jd2::JobInputterInputSource
• 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
• Db : core::chemical::element
• DBREF : core::io::pdb
• DBREF1 : core::io::pdb
• DBREF2 : core::io::pdb
• DbTrajectoryReaderCOP : protocols::trajectory
• DbTrajectoryReaderOP : protocols::trajectory
• DbTrajectoryRecorderCOP : protocols::canonical_sampling
• DbTrajectoryRecorderOP : protocols::canonical_sampling
• DbTrajectoryWriterCOP : protocols::trajectory
• DbTrajectoryWriterOP : protocols::trajectory
• dc : core::scoring
• dcu0 : protocols::hybridization
• DCV_ALREADY_CYCLIZED : protocols::simple_moves
• DCV_CYCLIZABLE : protocols::simple_moves
• DCV_NOT_CYCLIZABLE : protocols::simple_moves
• dD_dv1() : protocols::pockets
• dD_dv2() : protocols::pockets
• dD_dv3() : protocols::pockets
• dD_dv4() : protocols::pockets
• dD_dv5() : protocols::pockets
• dD_dv6() : protocols::pockets
• ddG_bind_correlation : protocols::optimize_weights
• ddG_cycles() : protocols::protein_interface_design
• ddG_main() : protocols
• ddG_mutation_correlation : protocols::optimize_weights
• ddG_mutation_correlation_with_unfolded_energy : protocols::optimize_weights
• 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_
• DDPscoreCreator_registrator : core::init
• deallocation_msg_type : protocols::jd3::deallocation
• DeallocationMessageCOP : protocols::jd3::deallocation
• DeallocationMessageOP : protocols::jd3::deallocation
• debug : core::pack::interaction_graph
• debug_dump_pose() : protocols::anchored_design
• debug_dump_rotamers() : core::pack::rotamer_set
• debug_inaccurateG : core::optimization::symmetry
• DebuggingAnnealerOP : core::pack::annealer
• decide_on_beta_jumping_from_frags() : protocols::abinitio
• declare_chemical_bonds_at_cutpoints() : protocols::stepwise::modeler
• declare_cutpoint_chemical_bond() : core::pose
• 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
• decompose() : protocols::nonlocal
• DecomposeAndReweightEnergiesCalculatorCOP : protocols::pose_metric_calculators
• DecomposeAndReweightEnergiesCalculatorOP : protocols::pose_metric_calculators
• DecoySetEvaluationCOP : protocols::toolbox
• DecoySetEvaluationOP : protocols::toolbox
• DecoyStructOP : core::io::raw_data
• deep_copy() : core::chemical , core::chemical::rotamers , core::kinematics , core::pose , core::scoring , core::scoring::hbonds , protocols::antibody , protocols::antibody::design , protocols::loops
• 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
• DEEREnergyCreator_registrator : core::init
• 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
• default_jump_atom() : core::chemical::rna
• DEFAULT_LABEL : protocols::cyclic_peptide
• default_movemap_factory_attribute_name() : core::select::movemap
• DEFAULT_NCYCLES : protocols::hybridization
• default_stub : core::kinematics
• DEFAULT_t : core::chemical
• DEFAULT_TEMP : protocols::abinitio::abscript
• DefaultPackerPaletteCOP : core::pack::palette
• DefaultPackerPaletteOP : core::pack::palette
• define_chains() : core::import_pose
• define_cut_point_stochasticly() : protocols::seeded_abinitio
• define_extra_rotamers_sampling_level_restriction() : core::pack::task::operation
• define_local_frame() : core::scoring::nmr
• define_mg_water_map() : protocols::magnesium
• define_movemap_chains() : protocols::seeded_abinitio
• define_scorable_core_from_secondary_structure() : protocols::loops
• definite_terminal_root() : core::pose
• deflt_coords_ : core::scoring::epr_deer
• defs2allowedtypes() : protocols::motifs
• defs2map() : protocols::motifs
• defs2vector() : protocols::motifs
• DELETE : protocols::stepwise::monte_carlo::mover
• delete_carbohydrate_branch() : core::pose::carbohydrates
• delete_comment() : core::pose
• DELETE_DOWNSTREAM : protocols::indexed_structure_store
• DELETE_EDGE : protocols::legacy_sewing
• delete_edges_with_degree_zero() : core::pack::hbonds
• delete_leaf() : core::pose::carbohydrates
• DELETE_LOOP_RES : protocols::stepwise::monte_carlo::mover
• delete_non_protein_from_pose() : protocols::rna::denovo
• delete_overhang_residues() : protocols::grafting
• DELETE_PREVIOUS_ROTAMER : core::pack::rotamer_set
• delete_region() : protocols::grafting
• DELETE_ROTAMER : core::pack::rotamer_set
• delete_this_struct_id() : protocols::features::strand_assembly
• delete_this_sw_can_by_sh_id_from_sw_by_comp() : protocols::features::strand_assembly
• DELETE_UPSTREAM : protocols::indexed_structure_store
• delete_virtual_residues() : protocols::relax
• DeleteAllRotamerSetOperationCOP : core::pack::rotamer_set
• DeleteAllRotamerSetOperationOP : core::pack::rotamer_set
• DeleteBondOrder : core::chemical
• 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
• dellinte_dm() : core::scoring::rna::chemical_shift
• dellintk_dm() : core::scoring::rna::chemical_shift
• DELTA : core::chemical::rna , core::scoring::dna
• DELTA_ATOM : core::chemical
• delta_magnetic_anisotropy() : core::scoring::rna::chemical_shift
• delta_ring_current() : core::scoring::rna::chemical_shift
• delta_ring_current_term() : core::scoring::rna::chemical_shift
• DeltaFilterCOP : protocols::simple_filters
• DeltaFilterOP : protocols::simple_filters
• denom() : protocols::cryst
• 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
• DEOXY_O2PRIME : core::chemical
• DEOXY_SUGAR : core::chemical
• DEPROTONATED : core::chemical
• derive_sc_sc_restraints() : protocols::relax
• DerivedPeptideEntryCOP : protocols::peptide_deriver
• DerivedPeptideEntryOP : protocols::peptide_deriver
• DerivedSequenceMappingCOP : core::sequence
• DerivedSequenceMappingOP : core::sequence
• deserialize_db_listener_data() : protocols::features
• deserialize_xyz_coords() : protocols::features
• design_protocol_to_enum() : protocols::antibody::design
• design_protocol_to_string() : protocols::antibody::design
• design_residues_list() : protocols::dna
• 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
• DesignProtocolEnum_total : protocols::antibody::design
• DesignRepackMoverCOP : protocols::calc_taskop_movers
• DesignRepackMoverOP : protocols::calc_taskop_movers
• DesignRestrictionsCOP : core::pack::task::operation
• DesignRestrictionsCreator_registrator : core::init
• 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
• detect_base_contacts() : core::pose::rna
• detect_ld_chirality_from_polymer_residue() : core::chemical
• detect_phosphate_contacts() : core::pose::rna
• detect_sugar_contacts() : core::pose::rna
• DetectProteinLigandInterfaceAP : protocols::enzdes
• DetectProteinLigandInterfaceCAP : protocols::enzdes
• DetectProteinLigandInterfaceCOP : protocols::enzdes
• DetectProteinLigandInterfaceOP : protocols::enzdes
• DetectSymmetryMoverCOP : protocols::symmetry
• DetectSymmetryMoverOP : protocols::symmetry
• determinant() : protocols::simple_filters
• determinant_sign() : protocols::simple_filters
• determine_atom_level_edge_info() : core::pack::hbonds
• determine_atom_level_edge_info_for_all_edges() : core::pack::hbonds
• determine_atom_level_node_info() : core::pack::hbonds
• determine_atom_level_node_info_for_all_nodes() : core::pack::hbonds
• determine_core_heading_surface_heading_by_distance() : protocols::features::strand_assembly
• determine_file_type() : core::import_pose
• determine_frag_size() : protocols::abinitio::abscript
• determine_glycan_links() : core::io
• determine_heading_direction_by_vector() : protocols::features::strand_assembly
• determine_lo_and_hi_residues() : core::scoring::methods
• determine_num_for_partition() : protocols::jd3::dag_node_managers
• determine_residues_to_rebuild() : protocols::rna::movers
• determine_whether_point_is_buried() : core::select::util
• deterministic_graft : protocols::antibody::design
• dexponential() : core::scoring::constraints
• DFIRE : core::scoring , core::scoring::methods
• DFIRE_EnergyCreator_registrator : core::init
• dfour1_plan() : core::scoring::fiber_diffraction
• DFr : protocols::fldsgn::topology
• DFr_BAB : protocols::fldsgn::topology
• DFr_HPN : protocols::fldsgn::topology
• dG_binding_correlation : protocols::optimize_weights
• dgaussian() : core::scoring::constraints
• DGBindOptEDataCOP : protocols::optimize_weights
• DGBindOptEDataOP : protocols::optimize_weights
• DHR_Type : protocols::docking
• diagonal : core::sequence
• DIAMAGNETIC : core::chemical
• DID_NOT_ADD_STRUCTURE : protocols::optimize_weights
• different_resgroup() : core::pack::rotamer_set
• different_restype() : core::pack::rotamer_set
• dihedral_atom_set : core::chemical
• dihedral_bin() : core::scoring::dna
• dihedral_constraint : core::scoring
• dihedral_distance() : protocols::idealize
• dihedralA : protocols::jumping
• dihedralAB : protocols::jumping
• dihedralB : protocols::jumping
• DihedralConstraintCOP : core::scoring::constraints
• DihedralConstraintCreator_registrator : core::init
• 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
• DihedralPairConstraintCreator_registrator : core::init
• DihedralSet : core::pack::rotamer_set
• DIIODINATION : core::chemical
• dim3d_ : core::scoring::epr_deer
• DIM6 : protocols::evaluation , protocols::toolbox
• dimer_pairing_pointer_sorter() : core::scoring
• DimerPairingCOP : protocols::fldsgn::topology
• DimerPairingOP : core::scoring , protocols::fldsgn::topology
• DIMETHYLATED_CTERMINUS : core::chemical
• DIMETHYLATED_CTERMINUS_VARIANT : core::chemical
• DIMETHYLATION : core::chemical
• DipolarCouplingCOP : core::scoring
• DipolarCouplingEnergyCreator_registrator : core::init
• DipolarCouplingEnergyOP : core::energy_methods
• DipolarCouplingOP : core::scoring
• dir_jump : core::kinematics
• Direction : protocols::rigid
• DirectReadoutEnergyCreator_registrator : core::init
• DirectReadoutPotentialCOP : core::scoring::dna
• DirectReadoutPotentialOP : core::scoring::dna
• DirectSegmentLookupMoverCOP : protocols::indexed_structure_store::movers
• DirectSegmentLookupMoverOP : protocols::indexed_structure_store::movers
• dis_get_coordinate_system() : protocols::jumping
• dis_get_ncac() : protocols::jumping
• dis_RT_from_epos() : protocols::jumping
• disAB : protocols::jumping
• disable_conserved_framework_positions() : protocols::antibody::design
• disable_constraint_scoreterms() : protocols::enzdes::enzutil
• disable_design_antigen() : protocols::antibody::design
• disable_design_cdr() : protocols::antibody::design
• disable_design_cdrs() : protocols::antibody::design
• disable_design_framework() : protocols::antibody::design
• disable_design_region() : protocols::antibody::design
• disable_h3_stem_positions() : protocols::antibody::design
• DisableAntibodyRegionOperationCOP : protocols::antibody::task_operations
• DisableAntibodyRegionOperationOP : protocols::antibody::task_operations
• DisableCDRsOperationCOP : protocols::antibody::task_operations
• DisableCDRsOperationOP : protocols::antibody::task_operations
• DisallowIfNonnativeCreator_registrator : core::init
• DisallowIfNonnativeOP : core::pack::task::operation
• DisallowIfNonnativeRLTCreator_registrator : core::init
• DisallowIfNonnativeRLTOP : core::pack::task::operation
• discard_old_entity : protocols::pack_daemon
• discontinued_lower() : protocols::hybridization
• discontinued_upper() : protocols::hybridization
• DisplayPoseLabelsMoverCOP : protocols::fold_from_loops::movers
• DisplayPoseLabelsMoverOP : protocols::fold_from_loops::movers
• dist_score() : protocols::sic_dock
• Distance : core
• distance() : core::kinematics , core::kinematics::tree , protocols::mpi_refinement , protocols::multistage_rosetta_scripts::cluster
• distance_chainbreak : core::scoring
• distance_fast() : protocols::ligand_docking::ga_ligand_dock
• distance_from_line() : core::scoring::constraints
• distance_from_line2D() : core::membrane
• distance_internal() : protocols::ligand_docking::ga_ligand_dock
• distance_slow() : protocols::ligand_docking::ga_ligand_dock
• distance_squared() : core::kinematics::tree
• DistanceChainbreakEnergyCreator_registrator : core::init
• 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
• Distribution : protocols::ligand_docking
• DISULFIDE : core::chemical , core::pose::full_model_info
• DISULFIDE_BONDED : core::chemical
• disulfide_bonds() : core::conformation
• disulfide_matching_energy : core::scoring::methods
• DisulfideCyclizationViability : protocols::simple_moves
• DisulfideDerivativeAtom : core::scoring::disulfides
• 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
• DisulfideMatchingEnergyCreator_registrator : core::init
• 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
• divide() : protocols::mean_field
• DivideAndConquerorCOP : protocols::denovo_design::components
• DivideAndConquerorOP : protocols::denovo_design::components
• DMS : core::pose::rna
• DNA : core::chemical
• dna_aa_from_oneletter_code() : core::scoring::dna
• dna_base_distance : core::scoring
• dna_base_partner() : protocols::dna
• DNA_BaseEnergyCreator_registrator : core::init
• DNA_BasePotentialCOP : core::scoring::dna
• DNA_BasePotentialOP : core::scoring::dna
• dna_bb_torsion : core::scoring
• dna_bp : core::scoring
• dna_bs : core::scoring
• dna_chi : core::scoring
• dna_comp_name_str() : protocols::dna
• dna_deriv_atom() : core::energy_methods
• dna_dihedral_bb : core::scoring
• dna_dihedral_chi : core::scoring
• dna_dihedral_lr : core::scoring::methods
• dna_dihedral_sugar : core::scoring
• DNA_DihedralEnergyCreator_registrator : core::init
• DNA_DihedralPotentialCOP : core::scoring::dna
• DNA_DihedralPotentialOP : core::scoring::dna
• dna_dr : core::scoring
• dna_env : core::scoring
• DNA_EnvPairPotentialCOP : core::scoring::dna
• DNA_EnvPairPotentialOP : core::scoring::dna
• dna_full_name3() : protocols::dna
• DNA_INT_WTS : core::scoring
• DNA_INT_WTS_GB : core::scoring
• dna_pair : core::scoring
• dna_ref : core::scoring
• dna_sugar_close : core::scoring
• DNABFormPotentialCOP : core::scoring::dna
• DNABFormPotentialOP : core::scoring::dna
• DnaChainsCOP : protocols::dna
• DnaChainsOP : protocols::dna
• DNAChiEnergyCreator_registrator : core::init
• 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
• DNATorsionEnergyCreator_registrator : core::init
• DNATorsionEnergyOP : core::energy_methods
• DNATorsionPotentialCOP : core::scoring::dna
• DNATorsionPotentialOP : core::scoring::dna
• do_I_skip() : protocols::scoring::methods::pcs2
• do_not_edit_warning() : update_ResidueType_enum_files
• do_one_line() : protocols::frag_picker::scores
• do_scoring() : protocols::toolbox::sample_around
• do_set_xyz() : protocols::stepwise::sampler::protein
• do_xy_scan() : protocols::toolbox::sample_around
• DOCK_DOMAIN : core::pose::full_model_info
• dock_ens_conf : core::scoring
• DOCK_LOW_PATCH : core::scoring
• DOCK_PATCH : core::scoring
• dock_waters_to_atom() : protocols::pose_metric_calculators
• dock_with_hotspot_subsubtag_naming_func() : protocols::protein_interface_design::movers
• dock_with_hotspot_subtag_naming_func() : protocols::protein_interface_design::movers
• DockingEnsembleCOP : protocols::docking
• DockingEnsembleOP : protocols::docking
• DockingEnsemblePrepackProtocolCOP : protocols::docking
• DockingEnsemblePrepackProtocolOP : protocols::docking
• DockingHighResCOP : protocols::docking
• DockingHighResFilterCOP : protocols::docking
• DockingHighResFilterOP : protocols::docking
• DockingHighResLegacy : 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
• DockingPrepackProtocol : 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
• DOCKJUMP_TAG : protocols::rigid
• DockJumps : protocols::docking
• DockMCMCycleCOP : protocols::docking
• DockMCMCycleOP : protocols::docking
• DockMCMProtocol : protocols::docking
• DockMCMProtocolCOP : protocols::docking
• DockMCMProtocolOP : protocols::docking
• DockMinMover : protocols::docking
• DockMinMoverCOP : protocols::docking
• DockMinMoverOP : protocols::docking
• dockPoseIntoMap() : protocols::electron_density
• DockTaskFactoryCOP : protocols::docking
• DockTaskFactoryOP : protocols::docking
• DockWithHotspotMoverCOP : protocols::protein_interface_design::movers
• DockWithHotspotMoverOP : protocols::protein_interface_design::movers
• DOES_NOT_CONTROL : protocols::environment::claims
• DOF_bin_size() : protocols::stepwise::modeler::rna::rigid_body
• DOF_bin_value() : protocols::stepwise::modeler::rna::rigid_body
• dof_constraint : core::scoring
• 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_id_to_string() : protocols::environment
• DOF_Node_sorter() : core::optimization , core::optimization::symmetry
• DOF_NodeCOP : core::optimization
• DOF_NodeOP : core::optimization
• dof_type : core::conformation::symmetry
• DOF_Type : core::id
• DOF_type_is_rb() : core::id
• 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
• dofType : protocols::jumping
• DofUnlockCOP : protocols::environment
• DofUnlockOP : protocols::environment
• DomainInterfaceFilterCOP : protocols::simple_filters
• DomainInterfaceFilterOP : protocols::simple_filters
• DomainMap : core::kinematics
• DOT : core::scoring::sc
• DOUBLE_T_LOOP : core::scoring::rna
• DoubleBond : core::chemical
• DoubleBondOrder : core::chemical
• 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
• DOWN : protocols::denovo_design::components
• DownJumpSRFDCOP : core::fragment
• DownJumpSRFDOP : core::fragment
• downstream_centroid_by_jump() : protocols::geometry
• downstream_residues_from_jump() : protocols::hybridization
• 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
• Doxygen_info() : update_ResidueType_enum_files
• drop_constraints() : core::scoring::constraints
• dround() : core::scoring::rna::chemical_shift
• Ds : core::chemical::element
• dslf_ca_dih : core::scoring
• dslf_cbs_ds : core::scoring
• dslf_cs_ang : core::scoring
• dslf_fa13 : core::scoring
• dslf_fa13_ref : core::scoring
• dslf_ss_dih : core::scoring
• dslf_ss_dst : core::scoring
• dslfc_ang : core::scoring
• dslfc_bb_dih : core::scoring
• dslfc_cb_dih : core::scoring
• dslfc_cb_dst : core::scoring
• dslfc_cen_dst : core::scoring
• dslfc_rot : core::scoring
• dslfc_RT : core::scoring
• dslfc_trans : core::scoring
• dssp() : protocols::simple_filters
• DsspDesignOperationOP : protocols::task_operations
• dsspdo_group_name() : protocols::task_operations
• dsspdo_subelement_ct_name() : 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
• dualspace : protocols::antibody::design
• DUMMY_BOOL() : core::scoring::hbonds
• DUMMY_DERIV() : core::scoring::hbonds
• dummy_deriv_vector_ : core::energy_methods
• DUMMY_DERIVS : core::scoring::hbonds
• DUMMY_HBE : core::scoring::hbonds
• DUMMY_HBGEODIMTYPE : core::scoring::hbonds
• dummy_nodeop : core::pack::scmin
• dummy_score_type : core::scoring
• DUMMY_VECTOR : core::scoring::carbon_hbonds
• DummyClassCOP : protocols::toolbox
• DummyClassOP : protocols::toolbox
• dump_as_pdb() : protocols::toolbox
• dump_atom_tree_diff() : core::import_pose::atom_tree_diffs
• dump_atomtree_kinemage() : protocols::viewer
• dump_chis() : protocols::metal_interface
• dump_cif() : core::io::mmcif
• dump_comment_pdb() : core::pose
• dump_cutpoint_info() : protocols::anchored_design
• dump_debug_output() : protocols::cyclic_peptide
• dump_foldtree_kinemage() : protocols::viewer
• dump_frames_as_pdb() : core::fragment
• dump_graph() : core::chemical::sdf
• dump_gws() : core::io::carbohydrates
• dump_gws_chain() : core::io::carbohydrates
• dump_library() : core::pack::rotamers
• dump_loophash_linkers() : protocols::sic_dock
• dump_matrix() : protocols::evaluation , protocols::toolbox
• dump_matrix_no() : protocols::evaluation , protocols::toolbox
• dump_mmtf() : core::io::mmtf
• dump_movemap() : protocols::abinitio
• dump_multimodel_pdb() : core::io::pdb
• dump_pdb() : core::io::pdb
• dump_pdb_residue() : core::io::pdb
• dump_points_pdb() : protocols::sic_dock
• dump_pose_kinemage() : protocols::viewer
• dump_reference_pose() : core::import_pose::atom_tree_diffs
• dump_residue_kinemage() : protocols::viewer
• dump_score_line() : core::import_pose::atom_tree_diffs
• dump_stems() : core::import_pose
• dump_structure_kinemage() : protocols::viewer
• dump_tags_() : protocols::jumping
• dump_templates() : protocols::tcr
• dump_trajectory : core::scoring
• dump_vall_fasta() : protocols::frags
• dumpcgo() : protocols::kinmatch
• DumpPdbCOP : protocols::simple_moves
• DumpPdbOP : protocols::simple_moves
• DumpSingleResidueRotamersCOP : protocols::simple_moves
• DumpSingleResidueRotamersOP : protocols::simple_moves
• DumpTrajectoryEnergy_registrator : core::init
• DumpTrajectoryEnergyOP : core::energy_methods
• dunbrack_constraint : core::scoring
• DUNBRACK_FILE_DEFAULT_SCTOR : core::pack::dunbrack
• DUNBRACK_MAX_BBTOR : core::pack::dunbrack
• DUNBRACK_MAX_SCTOR : core::pack::dunbrack
• dunbrack_method : core::scoring::methods
• DunbrackConstraintCOP : core::pack::dunbrack
• DunbrackConstraintCreator_registrator : core::init
• DunbrackConstraintOP : core::pack::dunbrack
• DunbrackEnergyCreator_registrator : core::init
• DunbrackReal : core::pack::dunbrack
• DunbrackRotamerLibrarySpecificationCOP : core::chemical::rotamers
• DunbrackRotamerLibrarySpecificationCreator_registrator : core::init
• DunbrackRotamerLibrarySpecificationOP : core::chemical::rotamers
• DunbrackSCSamplerCOP : protocols::match::upstream
• DunbrackSCSamplerOP : protocols::match::upstream
• dup_residue() : core::pack::rotamer_set , core::pack::rotamers , protocols::matdes
• dxform_atr() : protocols::ligand_docking::ga_ligand_dock
• dxform_rep() : protocols::ligand_docking::ga_ligand_dock
• Dy : core::chemical::element
• DY3_COORDINATION : core::chemical
• DynamicAggregateFunctionCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverOP : protocols::pack_daemon
• DynamicAggregateFunctionOP : protocols::pack_daemon