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

- d -

• D2LChiralData : protocols::simple_moves::chiral
• D2LChiralMap() : protocols::simple_moves::chiral
• D_CHIRALITY : protocols::simple_moves::chiral
• DaemonSetCOP : protocols::pack_daemon
• DaemonSetMessage : protocols::pack_daemon
• DaemonSetOP : protocols::pack_daemon
• DarcParticleSwarmMinimizerCOP : protocols::pockets
• DarcParticleSwarmMinimizerOP : protocols::pockets
• DATABASE : protocols::jd2::JobInputterInputSource
• DatabaseEntryWorkUnitCOP : protocols::wum
• DatabaseEntryWorkUnitOP : protocols::wum
• DatabaseFilterCOP : protocols::features
• DatabaseFilterOP : protocols::features
• DatabaseJobInputterOP : protocols::features
• DatabaseJobOutputterOP : protocols::features
• DatabaseThreadCOP : protocols::toolbox::task_operations
• DatabaseThreadOP : protocols::toolbox::task_operations
• DataLoaderCOP : protocols::jd2::parser
• DataLoaderCreatorCOP : protocols::jd2::parser
• DataLoaderCreatorOP : protocols::jd2::parser
• DataLoaderOP : protocols::jd2::parser
• DbTrajectoryReaderCOP : protocols::canonical_sampling , protocols::trajectory
• DbTrajectoryReaderOP : protocols::canonical_sampling , protocols::trajectory
• DbTrajectoryRecorderCOP : protocols::canonical_sampling
• DbTrajectoryRecorderOP : protocols::canonical_sampling
• DbTrajectoryWriterCOP : protocols::trajectory
• DbTrajectoryWriterOP : protocols::trajectory
• 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_main() : protocols
• ddG_mutation_correlation : protocols::optimize_weights
• ddG_mutation_correlation_with_unfolded_energy : protocols::optimize_weights
• DDGBindOptEDataOP : protocols::optimize_weights
• ddGCOP : protocols::simple_moves
• DdGFeaturesCOP : protocols::features
• DdGFeaturesOP : protocols::features
• DdgFilterCOP : protocols::simple_filters
• DdgFilterOP : protocols::simple_filters
• DDGMutationOptEDataOP : protocols::optimize_weights
• ddGOP : protocols::simple_moves
• ddGs : protocols::ddg
• DdGScanCOP : protocols::simple_filters
• DdGScanOP : protocols::simple_filters
• debug_dump_pose() : protocols::anchored_design
• decide_on_beta_jumping_from_frags() : protocols::abinitio
• decompose() : protocols::nonlocal
• DecomposeAndReweightEnergiesCalculatorCOP : protocols::toolbox::pose_metric_calculators
• DecomposeAndReweightEnergiesCalculatorOP : protocols::toolbox::pose_metric_calculators
• DecoySetEvaluationCOP : protocols::toolbox
• DecoySetEvaluationOP : protocols::toolbox
• DEFAULT_NCYCLES : protocols::hybridization
• DEFAULT_TEMP : protocols::abinitio::abscript
• define_chains() : protocols::stepwise::setup
• define_cut_point_stochasticly() : protocols::seeded_abinitio
• define_movemap_chains() : protocols::seeded_abinitio
• define_scorable_core_from_secondary_structure() : protocols::loops
• definite_terminal_root() : protocols::stepwise::modeler
• defs2allowedtypes() : protocols::motifs
• defs2map() : protocols::motifs
• defs2vector() : protocols::motifs
• DELETE : protocols::stepwise::monte_carlo
• delete_overhang_residues() : protocols::grafting
• delete_region() : protocols::grafting
• delete_this_struct_id() : protocols::features::strand_assembly
• delete_this_sw_can_by_sh_id_from_sw_by_comp() : protocols::features::strand_assembly
• delete_virtual_residues() : protocols::relax
• DeleteMoverOP : protocols::stepwise::monte_carlo::mover
• DeleteRegionMoverCOP : protocols::grafting
• DeleteRegionMoverOP : protocols::grafting
• DeltaFilterCOP : protocols::simple_filters
• DeltaFilterOP : protocols::simple_filters
• DenseIGRepackerCOP : protocols::pack_daemon
• DenseIGRepackerOP : protocols::pack_daemon
• DensityScoringClaimerAP : protocols::topology_broker
• DensityScoringClaimerCAP : protocols::topology_broker
• DensityScoringClaimerCOP : protocols::topology_broker
• DensityScoringClaimerOP : protocols::topology_broker
• DenyPdbIdFilterCOP : protocols::frag_picker
• DenyPdbIdFilterOP : protocols::frag_picker
• derive_sc_sc_restraints() : protocols::relax
• deserialize_db_listener_data() : protocols::features
• deserialize_xyz_coords() : protocols::features
• design_residues_list() : protocols::dna
• design_type_from_string() : protocols::antibody::design
• design_type_to_string() : protocols::antibody::design
• 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
• DesignTypeEnum : protocols::antibody::design
• DesignTypeEnum_total : protocols::antibody::design
• DesignVsNativeComparisonOP : protocols::enzdes
• detect_base_contacts() : protocols::stepwise::modeler::rna::bulge
• detect_phosphate_contacts() : protocols::stepwise::modeler::rna::phosphate
• detect_sugar_contacts() : protocols::stepwise::modeler::rna::sugar
• DetectProteinLigandInterfaceAP : protocols::enzdes
• DetectProteinLigandInterfaceCAP : protocols::enzdes
• DetectProteinLigandInterfaceCOP : protocols::enzdes
• DetectProteinLigandInterfaceOP : protocols::enzdes
• DetectSymmetryMoverCOP : protocols::simple_moves::symmetry
• DetectSymmetryMoverOP : protocols::simple_moves::symmetry
• determinant() : protocols::simple_filters
• determinant_sign() : protocols::simple_filters
• determine_core_heading_surface_heading_by_distance() : protocols::features::strand_assembly
• determine_frag_size() : protocols::abinitio::abscript
• determine_heading_direction_by_vector() : protocols::features::strand_assembly
• DFr : protocols::fldsgn::topology
• DFr_BAB : protocols::fldsgn::topology
• DFr_HPN : protocols::fldsgn::topology
• dG_binding_correlation : protocols::optimize_weights
• DGBindOptEDataCOP : protocols::optimize_weights
• DGBindOptEDataOP : protocols::optimize_weights
• DID_NOT_ADD_STRUCTURE : protocols::optimize_weights
• dihedral_distance() : protocols::idealize
• dihedralA : protocols::jumping
• dihedralAB : protocols::jumping
• dihedralB : protocols::jumping
• DihedralConstraintsScoreCOP : protocols::frag_picker::scores
• DihedralConstraintsScoreOP : protocols::frag_picker::scores
• DimerPairingCOP : protocols::fldsgn::topology
• DimerPairingOP : protocols::fldsgn::topology
• Direction : protocols::rigid
• 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
• discard_old_entity : protocols::pack_daemon
• discontinued_lower() : protocols::hybridization
• discontinued_upper() : protocols::hybridization
• dist_score() : protocols::sic_dock
• 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
• Distribution : protocols::ligand_docking
• DisulfideCyclizationViability : protocols::simple_moves
• DisulfideEntropyFilterCOP : protocols::simple_filters
• DisulfideEntropyFilterOP : protocols::simple_filters
• DisulfideInsertionMoverCOP : protocols::simple_moves
• DisulfideInsertionMoverOP : protocols::simple_moves
• DisulfJumpClaimerAP : protocols::topology_broker
• DisulfJumpClaimerCAP : protocols::topology_broker
• DisulfJumpClaimerCOP : protocols::topology_broker
• DisulfJumpClaimerOP : protocols::topology_broker
• DisulfPairingList : protocols::jumping
• DisulfPairingsList : protocols::jumping
• DiversifyStoredRBConfsCOP : protocols::enzdes
• DiversifyStoredRBConfsOP : protocols::enzdes
• dna_base_partner() : protocols::dna
• dna_comp_name_str() : protocols::dna
• dna_full_name3() : protocols::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
• do_I_skip() : protocols::scoring::methods::pcs2
• 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
• DockDesignFilterFactoryCOP : protocols::protein_interface_design
• DockDesignFilterFactoryOP : protocols::protein_interface_design
• docked_design : protocols::antibody::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
• DockingSetupMoverOP : protocols::docking
• DockingSlideIntoContactCOP : protocols::docking
• DockingSlideIntoContactOP : protocols::docking
• DOCKJUMP_TAG : protocols::rigid
• DockJumps : protocols::docking
• DockMCMCycleCOP : protocols::docking
• DockMCMCycleOP : protocols::docking
• DockMCMProtocolCOP : protocols::docking
• DockMCMProtocolOP : 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_id_to_string() : protocols::environment
• 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
• DoFType : protocols::helical_bundle
• dofType : protocols::jumping
• DofUnlockCOP : protocols::environment
• DofUnlockOP : protocols::environment
• DomainInterfaceFilterCOP : protocols::simple_filters
• DomainInterfaceFilterOP : protocols::simple_filters
• DoubleDenseIGRepackerCOP : protocols::pack_daemon
• DoubleDenseIGRepackerOP : protocols::pack_daemon
• DoubleLayerKinematicAbinitioCOP : protocols::abinitio
• DoubleLayerKinematicAbinitioOP : protocols::abinitio
• 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
• dssp() : protocols::simple_filters
• DsspDesignOperationOP : protocols::toolbox::task_operations
• DsspMoverOP : protocols::moves
• DualMonteCarloCOP : protocols::moves
• DualMonteCarloOP : protocols::moves
• dualspace : protocols::antibody::design
• DummyClassCOP : protocols::toolbox
• DummyClassOP : protocols::toolbox
• dump_as_pdb() : protocols::toolbox
• dump_atomtree_kinemage() : protocols::viewer
• dump_chis() : protocols::metal_interface
• dump_cutpoint_info() : protocols::anchored_design
• dump_foldtree_kinemage() : protocols::viewer
• dump_loophash_linkers() : protocols::sic_dock
• dump_matrix() : protocols::evaluation , protocols::toolbox
• dump_matrix_no() : protocols::evaluation , protocols::toolbox
• dump_movemap() : protocols::abinitio
• dump_points_pdb() : protocols::sic_dock
• dump_pose_kinemage() : protocols::viewer
• dump_residue_kinemage() : protocols::viewer
• dump_structure_kinemage() : protocols::viewer
• dump_tags_() : protocols::jumping
• dump_vall_fasta() : protocols::frags
• dumpcgo() : protocols::kinmatch
• dunbrack_print() : protocols::make_rot_lib
• DunbrackSCSamplerCOP : protocols::match::upstream
• DunbrackSCSamplerOP : protocols::match::upstream
• DynamicAggregateFunctionCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverCOP : protocols::pack_daemon
• DynamicAggregateFunctionDriverOP : protocols::pack_daemon
• DynamicAggregateFunctionOP : protocols::pack_daemon