- d -

• d() : core::chemical::Adduct , core::chemical::AtomICoor
• d1() : core::scoring::FACTSRsdTypeInfo
• d2() : core::scoring::FACTSRsdTypeInfo
• D2H_SA_Energy() : core::scoring::methods::D2H_SA_Energy
• d_aa_set() : core::io::NomenclatureManager
• d_phi() : protocols::frag_picker::PhiPsiTalosIO
• d_psi() : protocols::frag_picker::PhiPsiTalosIO
• daemon_set() : protocols::pack_daemon::MultistateFitnessFunction
• daemons() : protocols::pack_daemon::DaemonSet
• DaemonSet() : protocols::pack_daemon::DaemonSet
• damp_long_range() : core::scoring::etable::Etable
• DarcParticleSwarmMinimizer() : protocols::pockets::DarcParticleSwarmMinimizer
• DarcPSO_elsts_score_() : protocols::pockets::DarcParticleSwarmMinimizer
• DarcPSO_fp_compare_() : protocols::pockets::DarcParticleSwarmMinimizer
• data() : core::conformation::RotamerSetBase , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pose::Pose , core::scoring::Energies , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• data_annotations() : core::io::rna::RDAT
• data_int() : protocols::denovo_design::components::StructureData
• data_integrity_check() : core::sequence::SequenceAlignment
• data_ptr() : core::conformation::Residue
• data_real() : protocols::denovo_design::components::StructureData
• data_str() : protocols::denovo_design::components::StructureData
• data_struct() : core::scoring::data_struct
• database_dir() : protocols::farna::libraries::BasePairStepLibrary
• database_directory() : core::chemical::ResidueTypeSet
• database_fname() : protocols::toolbox::task_operations::DatabaseThread
• database_table() : protocols::toolbox::task_operations::ReadResfileFromDB
• DatabaseEntryWorkUnit() : protocols::wum::DatabaseEntryWorkUnit
• DatabaseFilter() : protocols::features::DatabaseFilter
• DatabaseJobInputter() : protocols::features::DatabaseJobInputter
• DatabaseJobOutputter() : protocols::features::DatabaseJobOutputter
• DatabaseOccSolEne() : core::scoring::geometric_solvation::DatabaseOccSolEne
• DatabaseThread() : protocols::toolbox::task_operations::DatabaseThread
• DataBuffer() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• DataLoader() : protocols::jd2::parser::DataLoader
• DataLoaderCreator() : protocols::jd2::parser::DataLoaderCreator
• DataLoaderFactory() : protocols::jd2::parser::DataLoaderFactory
• DataLoaderRegistrator() : protocols::jd2::parser::DataLoaderRegistrator< T >
• DataPoint() : protocols::cluster::DataPoint
• datatype() : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• dB_dBdnmtr() : core::scoring::FACTSResidueInfo
• dB_dBnmtr() : core::scoring::FACTSResidueInfo
• db_session() : protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB
• dBR() : core::pack::annealer::FASTERAnnealer
• dBR_dG() : core::scoring::FACTSResidueInfo
• DbTrajectoryReader() : protocols::trajectory::DbTrajectoryReader
• DbTrajectoryRecorder() : protocols::canonical_sampling::DbTrajectoryRecorder
• DbTrajectoryWriter() : protocols::trajectory::DbTrajectoryWriter
• DC() : core::scoring::DC
• dc_from_pose() : core::scoring::methods::DipolarCouplingEnergy
• dCCdB_fastRes() : core::scoring::electron_density::ElectronDensity
• dCCdBs() : core::scoring::electron_density::ElectronDensity
• dCCdx_aacen() : core::scoring::electron_density::ElectronDensity
• dCCdx_cen() : core::scoring::electron_density::ElectronDensity
• dCCdx_fastRes() : core::scoring::electron_density::ElectronDensity
• dCCdx_PointFast() : core::scoring::electron_density::ElectronDensity
• dCCdx_res() : core::scoring::electron_density::ElectronDensity
• DCcomputed() : core::scoring::DC
• dcenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• DCerr() : core::scoring::DC
• dchi4E_dchi4() : core::scoring::methods::ProClosureEnergy
• dchidevpen_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchidevpen_dchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_domg() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_domg() : core::pack::dunbrack::RotamerLibraryScratchSpace
• Dconst() : core::scoring::DC , core::scoring::RDC
• DCval() : core::scoring::DC
• ddG() : protocols::ddg::ddGMover
• ddg() : protocols::seeded_abinitio::GrowPeptides
• ddG() : protocols::simple_moves::ddG
• ddg_based() : protocols::seeded_abinitio::SeedFoldTree
• ddG_for_single_residue() : protocols::simple_filters::AlaScan , protocols::simple_filters::DdGScan
• ddG_mover() : protocols::simple_filters::DdGScan
• ddG_threshold() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::simple_filters::RotamerBoltzmannWeight
• DDGBindOptEData() : protocols::optimize_weights::DDGBindOptEData
• ddGData() : protocols::ddG::ddGData
• DdGFeatures() : protocols::features::DdGFeatures
• DdGFeaturesCreator() : protocols::features::DdGFeaturesCreator
• DdgFilter() : protocols::simple_filters::DdgFilter
• ddGMover() : protocols::ddg::ddGMover
• DDGMutationOptEData() : protocols::optimize_weights::DDGMutationOptEData
• DdGScan() : protocols::simple_filters::DdGScan
• ddomain_pot() : protocols::hybridization::DDomainParse
• DDomainParse() : protocols::hybridization::DDomainParse
• DDPlookup() : core::scoring::interface_::DDPlookup
• DDPscore() : core::scoring::interface_::DDPscore
• dE_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_perchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_rot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• deallocate_array() : core::graph::ArrayPool< T >
• deallocate_arraypoolelement() : core::scoring::EnergyGraph
• deallocate_arrays() : protocols::sparta::Sparta::SpartaLib
• deallocate_buffers() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering
• debug() : protocols::antibody::SnugDock , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::checkpoint::CheckPointer , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::toolbox::task_operations::SeqprofConsensusOperation
• debug_dump_icoor() : core::chemical::ResidueType
• debug_five() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_four() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_note_accepted_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_projected_deltaE_of_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_rejected_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_one() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_output() : protocols::ddg::ddGMover
• debug_pause() : core::conformation::Conformation
• debug_print() : protocols::antibody::AntibodyNumberingParser
• debug_print_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_hierarchy() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_size_per_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_residue_torsions() : core::conformation::Conformation
• debug_three() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_two() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_zero() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debugging_output() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• DebuggingAnnealer() : core::pack::annealer::DebuggingAnnealer
• DebugOut_MpiFileBuffer() : protocols::jd2::DebugOut_MpiFileBuffer
• decide_cuts() : protocols::hybridization::HybridizeFoldtreeDynamic
• decide_if_sequence_recovery_improved() : protocols::optimize_weights::IterativeOptEDriver
• decide_is_d_aa() : core::io::NomenclatureManager
• decide_is_known_achiral() : core::io::NomenclatureManager
• decide_is_l_aa() : core::io::NomenclatureManager
• decide_procrastinate_hpatch_computations() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• decide_procrastinate_surface_computations() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• decide_read_from_binary() : core::pack::dunbrack::RotamerLibrary
• decide_read_from_binary_02() : core::pack::dunbrack::RotamerLibrary
• decide_read_from_binary_10() : core::pack::dunbrack::RotamerLibrary
• decide_to_keep_pose() : protocols::stepwise::monte_carlo::mover::DeleteMover
• decide_write_binary() : core::pack::dunbrack::RotamerLibrary
• decide_write_binary_02() : core::pack::dunbrack::RotamerLibrary
• decide_write_binary_10() : core::pack::dunbrack::RotamerLibrary
• declare_all_existing_rotwells_encountered() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• declare_all_rotamers_initialized() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• declare_atom_neighbor_1sided() : core::scoring::NeighborList
• declare_atoms_neighbors() : core::scoring::NeighborList
• declare_chemical_bond() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , protocols::environment::ProtectedConformation
• declare_covalent_bond() : protocols::denovo_design::components::StructureData
• declare_covalent_bond_in_pose() : protocols::denovo_design::components::StructureData
• declare_edge_energies_final() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• declare_energies_final() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• declare_energies_final_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• declare_minimization_over() : protocols::optimize_weights::OptEMultifunc
• declare_polymer_bond() : protocols::denovo_design::components::StructureData
• declare_remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• DeclareBond() : protocols::cyclic_peptide::DeclareBond
• decompose_bb_hb_into_pair_energies() : core::scoring::hbonds::HBondOptions
• decompose_structure() : protocols::medal::MedalMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate
• DecomposeAndReweightEnergiesCalculator() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• decoy_compatibility() : protocols::noesy_assign::PeakAssignment
• decoy_count() : protocols::boinc::Boinc
• decoy_tag() : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• DecoyFileData() : core::io::raw_data::DecoyFileData
• decoys() : protocols::jd2::archive::ArchiveBase , protocols::wum::WorkUnit_SilentStructStore
• decoys_returned() : protocols::jd2::archive::Batch
• DecoySetEvaluation() : protocols::toolbox::DecoySetEvaluation
• DecoyStruct() : core::io::raw_data::DecoyStruct
• decrease_double_lazy_ig_memlimit() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• decrease_linmem_ig_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• decreasing() : protocols::loops::Loop , protocols::nonlocal::Region
• decrement_from_cached() : core::pack::interaction_graph::RotamerDots
• decrement_reference_pose_mapping_after_seqpos() : core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet
• dEddofs_to_dEdvars() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• deep_clone() : core::scoring::constraints::Constraints
• deep_copy() : core::scoring::constraints::ConstraintSet
• deep_copy_from() : core::scoring::constraints::Constraints
• default_allow_bondangles() : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_set() : protocols::helical_bundle::MakeBundle
• default_build_hits_at_all_positions() : protocols::match::downstream::DownstreamAlgorithm
• default_commands() : core::pack::task::ResfileContents
• default_crick_params_file() : protocols::helical_bundle::MakeBundle
• default_crick_params_file_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_omega0_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega1() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_all() : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_set() : protocols::helical_bundle::MakeBundle
• default_delta_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_t_set() : protocols::helical_bundle::MakeBundle
• default_filename() : core::pack::task::operation::ReadResfile
• default_helix_length() : protocols::helical_bundle::MakeBundle
• default_helix_length_set() : protocols::helical_bundle::MakeBundle
• default_invert() : protocols::helical_bundle::MakeBundle
• default_invert_set() : protocols::helical_bundle::MakeBundle
• default_master() : protocols::match::output::WriteUpstreamHitKinemage
• default_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_set() : protocols::helical_bundle::MakeBundle
• default_omega1() : protocols::helical_bundle::MakeBundle
• default_omega1_set() : protocols::helical_bundle::MakeBundle
• default_options() : core::chemical::ResidueLoader , core::conformation::symmetry::SymmDataLoader , core::import_pose::PoseFromPDBLoader , core::io::silent::SilentFileLoader , core::scoring::electron_density::ElectronDensityLoader , core::scoring::fiber_diffraction::FiberDiffractionLoader , protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::surface_docking::SurfaceVectorLoader
• default_position_from_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• default_r0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_set() : protocols::helical_bundle::MakeBundle
• default_rama_table_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• default_repeating_unit_offset() : protocols::helical_bundle::MakeBundle
• default_repeating_unit_offset_set() : protocols::helical_bundle::MakeBundle
• default_residue_name() : protocols::helical_bundle::MakeBundle
• default_residue_name_set() : protocols::helical_bundle::MakeBundle
• default_value() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::helical_bundle::PerturbBundleOptions
• default_z0_offset() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z0_offset_set() : protocols::helical_bundle::MakeBundle
• default_z1() : protocols::helical_bundle::MakeBundle
• default_z1_offset() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z1_offset_set() : protocols::helical_bundle::MakeBundle
• default_z1_set() : protocols::helical_bundle::MakeBundle
• define_active_site_from_gridlig_file() : protocols::match::MatcherTask
• define_active_site_from_residue_radii_list() : protocols::match::MatcherTask
• define_bins() : protocols::magnesium::SampleGrid
• define_loops() : protocols::docking::DockingHighResLegacy
• define_match_by_single_downstream_positioning() : protocols::match::MatcherTask
• define_moving_res() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• define_residue_selector_xml_schema() : core::select::residue_selector::ResidueSelectorFactory
• define_start_window() : protocols::simple_moves::ClassicFragmentMover
• defined() : protocols::jumping::MembraneJump
• defined_adducts() : core::chemical::ResidueType
• defined_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• DefineMovableLoops() : protocols::seeded_abinitio::DefineMovableLoops
• defines_dof_derivatives() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::YHHPlanarityEnergy
• defines_high_order_terms() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::EnergyMethod
• defines_intrares_dof_derivatives() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::RNA_SuiteEnergy
• defines_intrares_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy , protocols::scoring::methods::InterchainPairEnergy
• defines_intrares_energy_for_residue() : core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• defines_residue_pair_energy() : core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::sym_e::symEnergy
• defines_score_for_residue() : core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OneBodyEnergy
• defines_score_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::StackElecEnergy
• defines_score_for_rsd() : core::scoring::methods::YHHPlanarityEnergy
• defs2BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• defs2BuildPositions_findts() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• degree() : protocols::sasa_scores::Poly
• delete_act_coord_atom() : core::chemical::ResidueType
• delete_atom() : core::chemical::ResidueType , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• delete_atom_alias() : core::chemical::ResidueType
• delete_chain_ending() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• delete_child_proton() : core::chemical::ResidueType
• delete_content_only() : protocols::simple_filters::FileRemoveFilter
• delete_db() : protocols::loophash::LoopHashLibrary
• delete_diagonal_peaks() : protocols::noesy_assign::CrossPeakList
• delete_edge() : core::graph::Graph , core::graph::UEEdge< V, E > , core::kinematics::FoldTree , core::pack::interaction_graph::SimpleInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::sewing::MonteCarloAssemblyMover , protocols::sewing::SewGraph
• delete_everything() : core::graph::Graph
• delete_extra_vertices() : core::kinematics::FoldTree
• delete_graph_edges_using_domain_map() : core::scoring::Energies
• delete_in_progress_files() : protocols::jd2::FileSystemJobDistributor
• delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• delete_jump_and_intervening_cutpoint() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData
• delete_jump_seqpos() : core::kinematics::FoldTree
• delete_leading_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• delete_loop() : protocols::loops::Loops
• delete_metalbinding_atom() : core::chemical::ResidueType
• delete_polymer_residue() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_pose() : protocols::features::ProteinSilentReport
• delete_pose_from_tag() : protocols::features::ProteinSilentReport
• delete_position() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• delete_property() : core::chemical::ResidueType
• delete_record() : protocols::features::FeaturesReporter , protocols::features::JobDataFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::RotamerFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures
• delete_records_from_table() : protocols::features::FeaturesReporter
• delete_res() : core::pose::PDBInfo
• delete_residue() : protocols::frags::FragLib , protocols::frags::TorsionFragmentLibrary
• delete_residue_range_slow() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_residue_slow() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_residues() : protocols::denovo_design::components::Segment
• delete_residues_in_pose() : protocols::denovo_design::components::StructureData
• delete_segment() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData
• delete_segment_nopose() : protocols::denovo_design::components::StructureData
• delete_segments() : protocols::sewing::Assembly
• delete_self_edges() : core::kinematics::FoldTree
• delete_seqpos() : core::kinematics::AtomTree , core::kinematics::FoldTree
• delete_seqpos_simple() : core::kinematics::FoldTree
• delete_source_residue() : core::id::SequenceMapping
• delete_submotif_info() : core::pose::full_model_info::FullModelInfo
• delete_target_residue() : core::id::SequenceMapping
• delete_terminal_chi() : core::chemical::ResidueType
• delete_trailing_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• delete_unordered_edge() : core::kinematics::FoldTree
• DeleteActCoordAtom() : core::chemical::DeleteActCoordAtom
• DeleteAtom() : core::chemical::DeleteAtom
• DeleteChainMover() : protocols::simple_moves::DeleteChainMover
• DeleteChainsMover() : protocols::simple_moves::DeleteChainsMover
• DeleteChildProton() : core::chemical::DeleteChildProton
• deleted() : core::graph::UEEdge< V, E >
• DeleteMetalbindingAtom() : core::chemical::DeleteMetalbindingAtom
• DeleteMover() : protocols::stepwise::monte_carlo::mover::DeleteMover
• DeleteProperty() : core::chemical::DeleteProperty
• DeleteRegionMover() : protocols::grafting::simple_movers::DeleteRegionMover
• deletes_any_property() : core::chemical::ResidueTypeFinder
• deletes_any_variant() : core::chemical::ResidueTypeFinder
• deletes_atom() : core::chemical::DeleteAtom , core::chemical::PatchOperation
• deletes_atoms() : core::chemical::Patch , core::chemical::PatchCase
• deletes_properties() : core::chemical::Patch , core::chemical::PatchCase
• deletes_property() : core::chemical::DeleteProperty , core::chemical::PatchOperation
• deletes_variant() : core::chemical::DeleteVariantType , core::chemical::PatchOperation
• deletes_variants() : core::chemical::Patch , core::chemical::PatchCase
• DeleteTerminalChi() : core::chemical::DeleteTerminalChi
• DeleteVariantType() : core::chemical::DeleteVariantType
• delta() : core::pose::Pose , protocols::dna::DNABase , protocols::helical_bundle::PerturbBundleOptions , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::simple_moves::ContingentAcceptMover
• delta_atr_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_chi_zz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_components() : core::scoring::dna::DNATorsionPotential
• delta_cutoff() : core::chemical::rna::RNA_FittedTorsionInfo , core::scoring::dna::DNATorsionPotential
• delta_filter_thresholds() : protocols::protein_interface_design::filters::FilterScanFilter
• delta_filters() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::protein_interface_design::filters::FilterScanFilter
• delta_north() : core::chemical::rna::RNA_FittedTorsionInfo
• delta_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_all() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_omega1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_south() : core::chemical::rna::RNA_FittedTorsionInfo
• delta_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_X_xx() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_X_yy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_X_zz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_z1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_z1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• deltaE_best() : protocols::enzdes::EnzdesFlexibleRegion
• DeltaFilter() : protocols::simple_filters::DeltaFilter
• deltaG_bind() : protocols::optimize_weights::DGBindOptEData
• dens_grad() : core::scoring::electron_density::ElectronDensity
• DenseEnergyContainer() : core::scoring::DenseEnergyContainer
• DenseIGRepacker() : protocols::pack_daemon::DenseIGRepacker
• DenseNeighborConstIterator() : core::scoring::DenseNeighborConstIterator
• DenseNeighborIterator() : core::scoring::DenseNeighborIterator
• DensePDEdge() : core::pack::interaction_graph::DensePDEdge
• DensePDInteractionGraph() : core::pack::interaction_graph::DensePDInteractionGraph
• DensePDNode() : core::pack::interaction_graph::DensePDNode
• density() : protocols::hybridization::FragmentBiasAssigner
• density_change_trigger() : core::scoring::electron_density::ElectronDensity
• density_grid_search() : protocols::electron_density::DockIntoDensityMover
• density_nbr() : protocols::hybridization::FragmentBiasAssigner
• DensityScoringClaimer() : protocols::topology_broker::DensityScoringClaimer
• dentropy_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dependencies() : protocols::forge::build::BuildInstruction
• dependencies_exist() : protocols::forge::build::BuildManager
• dependencies_satisfied() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• dependent() : core::optimization::DOF_Node
• dependent_atoms() : core::conformation::symmetry::SymmetryInfo
• dependent_begin() : core::optimization::symmetry::SymMinimizerMap
• dependent_dofs() : core::conformation::symmetry::SymmetryInfo
• dependent_end() : core::optimization::symmetry::SymMinimizerMap
• dependent_on() : protocols::forge::build::BuildInstruction
• dependent_torsions() : core::conformation::symmetry::SymmetryInfo
• depends_on_polymer_lower() : core::chemical::AtomICoor
• depends_on_polymer_upper() : core::chemical::AtomICoor
• depends_on_residue_connection() : core::chemical::AtomICoor
• depermute() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• depermute_disulfide_list() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• deposition_date() : core::io::HeaderInformation
• deprecated_eval_atom_derivative() : core::scoring::constraints::ConstraintSet
• deprecated_eval_atom_derivative_for_residue_pairs() : core::scoring::constraints::ConstraintSet
• depth() : core::optimization::DOF_Node , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , protocols::frag_picker::VallResidue
• depth_first_connected_component_counting() : core::pack::interaction_graph::NodeBase
• deriv_check() : core::optimization::MinimizerOptions , protocols::farna::options::RNA_MinimizerOptions , protocols::simple_moves::MinMover
• deriv_check_local() : protocols::normalmode::NormalModeMinimizer
• deriv_check_result() : core::optimization::AtomTreeMinimizer , core::optimization::CartesianMinimizer , core::optimization::NumericalDerivCheckResult , protocols::normalmode::NormalModeMinimizer
• deriv_check_to_stdout() : core::optimization::MinimizerOptions
• deriv_check_verbose() : core::optimization::MinimizerOptions
• deriv_multiply() : core::conformation::symmetry::SymmetryInfo
• deriv_score() : core::scoring::mm::MMLJEnergyTable , core::scoring::mm::MMLJScore
• deriv_type_from_name() : core::scoring::hbonds::HBondTypeManager
• derivative_atom() : core::scoring::disulfides::DisulfideAtomIndices
• derivative_graph() : core::scoring::symmetry::SymmetricEnergies
• derivatives() : core::scoring::lkball::WaterBuilder
• DerivCheckDataPoint() : core::optimization::DerivCheckDataPoint
• derive_from_src_lib() : protocols::frags::TorsionFragmentLibrary
• derive_LW_orientation() : core::pose::rna::BasePair
• derive_peptide() : protocols::analysis::PeptideDeriverFilter
• derive_staple_constraints_() : protocols::simple_moves::PeptideStapleMover
• derived_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• derived_prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• DerivedSequenceMapping() : core::sequence::DerivedSequenceMapping
• derivs() : core::scoring::hbonds::HBond
• DerivVectorPair() : core::scoring::DerivVectorPair
• DescentDirectionAlgorithm() : core::optimization::DescentDirectionAlgorithm
• describe_fragments() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::PValuedFragmentScoreManager
• describe_score() : protocols::frag_picker::scores::BFactor , protocols::frag_picker::scores::DisulfideIdentity , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• deserialize() : core::grid::CartGrid< T > , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeAtom , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnitBase
• design() : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::docking::DockingHighResLegacy , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::simple_moves::DesignRepackMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• design_all_aas() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_antigen() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_any() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• design_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_framework() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_layer() : protocols::flxbb::LayerDesignOperation
• design_loop() : protocols::toolbox::task_operations::RestrictToLoops
• design_mover() : protocols::simple_moves::MSDMover
• design_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• design_only_target_residues() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_proline() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_protocol_enum_to_string() : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_is_present() : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_string_to_enum() : protocols::antibody::design::AntibodyDesignEnumManager
• design_refine() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_refine_cart_relax() : protocols::forge::remodel::RemodelMover
• design_refine_seq_relax() : protocols::forge::remodel::RemodelMover
• design_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• design_shell() : protocols::toolbox::task_operations::DesignAroundOperation
• design_strategy() : protocols::antibody::design::CDRSeqDesignOptions
• design_targets() : protocols::enzdes::EnzdesBaseProtocol
• design_targets_score() : protocols::enzdes::EnzdesBaseProtocol
• designable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_only() : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter
• DesignableResiduesFilter() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• DesignAroundOperation() : protocols::toolbox::task_operations::DesignAroundOperation
• DesignContrast() : core::io::sequence_comparation::DesignContrast
• designed_residue() : protocols::dna::PDBOutput
• designing_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• DesignMinimizeHbonds() : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• DesignProteinBackboneAroundDNA() : protocols::dna::DesignProteinBackboneAroundDNA
• DesignRepackMover() : protocols::simple_moves::DesignRepackMover
• DesignTask() : protocols::flxbb::DesignTask
• DesignTask_Layer() : protocols::flxbb::DesignTask_Layer
• DesignTask_Normal() : protocols::flxbb::DesignTask_Normal
• DesignVsNativeComparison() : protocols::enzdes::DesignVsNativeComparison
• desired_entity_history_size() : protocols::pack_daemon::TopEntitySet
• desired_loops() : protocols::LoopRebuild
• desired_remodelres_in_vicinity() : protocols::forge::remodel::ResidueVicinityInfo
• desired_result() : core::chemical::ResidueTypeSelectorSingle
• destroy() : boost::unordered_object_pool< T, UserAllocator >
• DestructionEvent() : core::pose::signals::DestructionEvent
• desymmeterize() : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_upstream_restype_for_constraint() : protocols::match::Matcher
• detach() : core::pose::datacache::ObserverCache , protocols::moves::PyMolObserver
• detach_after_modify() : protocols::forge::build::BuildInstruction
• detach_conformation_obs() : core::pose::Pose
• detach_connection_obs() : core::conformation::Conformation
• detach_destruction_obs() : core::pose::Pose
• detach_energy_obs() : core::pose::Pose
• detach_from() : core::pose::datacache::CacheableObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• detach_from_conformation() : core::scoring::constraints::ConstraintSet
• detach_general_obs() : core::conformation::Conformation , core::pose::Pose
• detach_identity_obs() : core::conformation::Conformation
• detach_impl() : core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::moves::PyMolObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• detach_length_obs() : core::conformation::Conformation
• detach_topological_observer() : core::kinematics::AtomTree
• detach_xyz_obs() : core::conformation::Conformation
• detached_clone() : core::scoring::constraints::ConstraintSet , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• detached_copy() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose , core::scoring::constraints::ConstraintSet , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• detailed_balance() : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_search() : protocols::hybridization::TMalign
• detect_and_set_camelid_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type_new_rule() : protocols::antibody::AntibodyInfo
• detect_any_overlap_with_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• detect_background_residue_and_first_class_residue_neighbors() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• detect_background_residue_and_first_class_residue_overlap() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• detect_bonds() : core::conformation::Conformation , protocols::simple_moves::DeleteChainsMover
• detect_camelid_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_connecting_subunits() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover
• detect_disulfides() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , protocols::denovo_design::components::StructureData
• detect_fullatom() : core::io::silent::SilentStruct
• detect_neighborship() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• detect_neighborship_with_node() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• detect_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• detect_pseudobonds() : core::conformation::Conformation , protocols::simple_moves::DeleteChainsMover
• detect_regular_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• DetectProteinLigandInterface() : protocols::enzdes::DetectProteinLigandInterface
• DetectSymmetry() : protocols::simple_moves::symmetry::DetectSymmetry
• determine_all_match_relevant_downstream_atoms() : protocols::match::MatcherTask
• determine_atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• determine_best_constraint() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• determine_carbohydrate_polymer_info() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_check_Ctermini_for_this_chain() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_check_Ntermini_for_this_chain() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_correct_length() : protocols::features::LoopAnchorFeatures
• determine_crossover_behavior() : core::scoring::etable::BaseEtableEnergy< Derived >
• determine_cyclization_viability() : protocols::simple_moves::DisulfideInsertionMover
• determine_dna_interface() : protocols::dna::DnaInterfaceFinder
• determine_flexible_regions() : protocols::enzdes::EnzdesFlexBBProtocol
• determine_found_residues_compatibility() : protocols::enzdes::SecondaryMatchProtocol
• determine_if_designing() : core::pack::task::ResidueLevelTask_
• determine_if_repacking() : core::pack::task::ResidueLevelTask_
• determine_interface() : protocols::dna::DnaInterfaceFinder
• determine_IUPAC_names() : core::chemical::carbohydrates::CarbohydrateInfo
• determine_job_ids_to_run() : protocols::jd2::MPIWorkPartitionJobDistributor
• determine_job_list() : protocols::jd3::JobQueen
• determine_jobs_for_next_round() : protocols::jd3::JobDistributor
• determine_largest_nbr_atom_distance() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• determine_loop() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• determine_loops_to_model() : protocols::forge::remodel::RemodelLoopMover
• determine_mg_orbital_frame() : protocols::magnesium::MgOrbitalFrameFinder
• determine_nonstandard_polymer_status() : core::conformation::Residue
• determine_overlap() : protocols::simple_moves::MergePDBMover , protocols::simple_moves::RepeatPropagationMover
• determine_polarization_groups() : core::scoring::MultipoleElecPotential
• determine_polymer_connections() : core::chemical::carbohydrates::CarbohydrateInfo
• determine_protein_interface() : protocols::dna::DnaInterfaceFinder
• determine_ramachandran_hash() : protocols::features::BetaTurnDetection
• determine_ramachandran_hash_for_residue_with_dihedrals() : protocols::features::BetaTurnDetection
• determine_redundant_conformer_groups() : protocols::match::downstream::LigandConformerBuilder
• determine_redundant_upstream_matchres() : protocols::match::output::OutputWriter
• determine_res_cb_deviation() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• determine_res_to_recompute() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• determine_residue_connection() : core::scoring::etable::count_pair::CountPairFactory
• determine_rotcounts_for_restype() : core::pack::rotamer_set::ContinuousRotamerSet
• determine_same_chain_next() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_same_chain_prev() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_score_variations() : protocols::jd2::archive::NormalizedEvaluatedArchive
• determine_separate_chemical_entity() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• determine_upstream_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• deviation() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• DFIRE_Energy() : core::scoring::methods::dfire::DFIRE_Energy
• DFIRE_Potential() : core::scoring::methods::dfire::DFIRE_Potential
• dfpmin() : core::optimization::Minimizer
• dfpmin_armijo() : core::optimization::Minimizer
• DFPMinConvergedAbsolute() : core::optimization::DFPMinConvergedAbsolute
• DFPMinConvergedFractional() : core::optimization::DFPMinConvergedFractional
• dfs() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• dfs_cycle_finder() : protocols::sewing::RepeatAssemblyMover
• dfunc() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::func_1d , core::optimization::Multifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::scoring::CenHBPotential , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::methods::LK_SigmoidalFunc , core::scoring::SmoothScoreTermCoeffs , protocols::electron_density::BfactorMultifunc , protocols::electron_density::VoxelSpacingMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::jumping::ChainbreakDistFunc , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• dfunc_component() : core::scoring::func::MixtureFunc
• dfunc_exact() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• dfunc_numeric() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• dG_dCi() : core::scoring::FACTSResidueInfo
• DGBindOptEData() : protocols::optimize_weights::DGBindOptEData
• Di() : core::scoring::FACTSResidueInfo
• die() : core::scoring::etable::coulomb::Coulomb
• DiffAtomSasaFilter() : protocols::enzdes::DiffAtomSasaFilter
• difference_from() : core::chemical::gasteiger::GasteigerAtomTypeData
• different_resgroup() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• different_restype() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• differentiate() : protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::Mean , protocols::pack_daemon::PowExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy
• diffuse_ring() : protocols::qsar::scoring_grid::SingleGrid
• dihedral() : core::chemical::ResidueType , core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• dihedral_between_bonded_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• dihedral_constraint_energy() : core::scoring::constraints::ConstraintEdge
• dihedral_rmsd() : protocols::frag_picker::DiversifyDihedralsSelector
• DihedralConstraint() : core::scoring::constraints::DihedralConstraint
• DihedralConstraintCreator() : core::scoring::constraints::DihedralConstraintCreator
• DihedralConstraintsScore() : protocols::frag_picker::scores::DihedralConstraintsScore
• DihedralPairConstraint() : core::scoring::constraints::DihedralPairConstraint
• DihedralPairConstraintCreator() : core::scoring::constraints::DihedralPairConstraintCreator
• dihedrals_for_atom() : core::chemical::ResidueType
• dijkstras() : protocols::toolbox::ResidueNetwork
• dim() : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dimension() : protocols::noesy_assign::CrossPeak
• dimension_etable_arrays() : core::scoring::etable::Etable
• dimension_memb_etable_arrays() : core::scoring::etable::MembEtable
• dimer1() : core::scoring::DimerPairing
• dimer2() : core::scoring::DimerPairing
• DimerPairing() : core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• dimsizes() : protocols::match::Bool3DGrid
• DipolarCoupling() : core::scoring::DipolarCoupling
• DipolarCouplingEnergy() : core::scoring::methods::DipolarCouplingEnergy
• dipole() : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• dir() : protocols::jd2::archive::Batch
• directory() : core::chemical::AtomTypeSet
• DirectReadoutEnergy() : core::scoring::methods::DirectReadoutEnergy
• DirectReadoutPotential() : core::scoring::dna::DirectReadoutPotential
• dis() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• dis_U1D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• disable() : protocols::ligand_docking::ResidueTorsionRestraints
• disable_auto_update() : core::scoring::NeighborList
• disable_autotemp() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• disable_build_stage() : protocols::loop_modeling::LoopModeler
• disable_centroid_stage() : protocols::loop_modeling::LoopModeler
• disable_constraint_scoreterms() : protocols::enzdes::EnzdesBaseProtocol
• disable_design_for_non_designing_cdrs() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_fullatom_stage() : protocols::loop_modeling::LoopModeler
• disable_ignorefinished() : protocols::jobdist::BaseJobDistributor
• disable_inprogress() : protocols::jobdist::BaseJobDistributor
• disable_output() : protocols::jobdist::BaseJobDistributor
• disable_proline_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_sampling_of_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• DisableAntibodyRegionOperation() : protocols::antibody::task_operations::DisableAntibodyRegionOperation
• DisableCDRsOperation() : protocols::antibody::task_operations::DisableCDRsOperation
• disallow_aas() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• disallow_bps_at_extra_min_res() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• disallow_carboxyl_conjugation_at_glu_asp() : core::chemical::ResidueTypeFinder
• disallow_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• disallow_movement_of_input_res() : protocols::toolbox::AtomLevelDomainMap
• disallow_noncanonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• disallow_pair() : protocols::denovo_design::connection::Connection
• disallow_properties() : core::chemical::ResidueTypeFinder
• disallow_quench() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• disallow_realign() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallow_resid() : core::pack::task::operation::OptH
• disallow_variants() : core::chemical::ResidueTypeFinder
• DisallowIfNonnative() : core::pack::task::operation::DisallowIfNonnative
• DisallowIfNonnativeRLT() : core::pack::task::operation::DisallowIfNonnativeRLT
• discard_conformation_domain_map() : core::scoring::Energies
• disconnect_segments() : protocols::denovo_design::components::StructureData
• disconnected_segments() : protocols::sewing::Assembly
• DisembodiedAssembly() : protocols::sewing::DisembodiedAssembly
• disjoint_set_sizes() : core::graph::DisjointSets
• DisjointSets() : core::graph::DisjointSets
• display_constraint_residues() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler
• display_func() : protocols::viewer::ConformationViewer
• display_if_necessary() : protocols::viewer::ConformationViewer
• display_progress() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• dist() : core::kinematics::ShortestPathInFoldTree , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::frag_picker::Contact , protocols::frag_picker::PhiPsiTalosIO , protocols::hybridization::TMalign , protocols::simple_filters::AlaScan , protocols::toolbox::ClusterBase
• dist2() : core::scoring::motif::ResPairMotif
• dist2_cut() : protocols::normalmode::NormalMode
• dist_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• dist_cutoff() : protocols::toolbox::CalcInterNeighborGroup , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_exponent() : core::select::util::SelectResiduesByLayer
• dist_midpoint() : core::select::util::SelectResiduesByLayer
• dist_pair() : core::scoring::SecondaryStructurePotential
• dist_square() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::toolbox::KClusterData
• dist_squared() : protocols::frag_picker::Contact , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• dist_track() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• distance() : core::chemical::Bond , core::chemical::orbitals::ICoorOrbitalData , core::chemical::orbitals::OrbitalType , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::vall::scores::VallFragmentScore , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::scoring::saxs::DistanceHistogram , protocols::antibody::clusters::CDRCluster , protocols::hybridization::DDomainParse , protocols::noesy_assign::CovalentCompliance , protocols::noesy_assign::FragsToAtomDist , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::toolbox::task_operations::RestrictToInterface
• distance_4d() : core::pose::rna::RNA_SuiteName
• distance_7d() : core::pose::rna::RNA_SuiteName
• distance_bound() : protocols::noesy_assign::CrossPeak
• distance_cutoff() : core::select::residue_selector::NumNeighborsSelector , protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter
• distance_matrix() : protocols::toolbox::ClusterBase
• distance_pair() : protocols::simple_moves::symmetry::SetupNCSMover
• distance_record() : protocols::noesy_assign::FragsToAtomDist
• distance_squared() : core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , protocols::frag_picker::VallResidue
• distance_squared_cb() : protocols::frag_picker::VallResidue
• distance_squared_cen() : protocols::frag_picker::VallResidue
• distance_threshold() : protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::ResidueBurialFilter
• distance_to_closest_magnesium() : protocols::magnesium::MgScanner
• DistanceChainbreakEnergy() : core::scoring::methods::DistanceChainbreakEnergy
• DistanceFunc() : core::scoring::custom_pair_distance::DistanceFunc
• DistanceHistogram() : core::scoring::saxs::DistanceHistogram
• DistancePairConstraint() : core::scoring::constraints::DistancePairConstraint
• DistancePointToLine() : core::scoring::sc::MolecularSurfaceCalculator
• DistanceRecord() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• DistanceScoreMover() : protocols::noesy_assign::DistanceScoreMover
• distbin() : core::scoring::methods::GoapEnergy
• distbin_map() : core::scoring::methods::GoapEnergy
• distinguish_backbone_and_sidechain() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• distinguish_backbone_and_sidechain_for_node() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• distinguish_pucker() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distribute_jobs_to_remote_daemons() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• distribute_pseudo_base_atom_derivatives() : core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy
• DistributionMap() : protocols::ligand_docking::DistributionMap
• disulf_atom_index() : core::scoring::disulfides::DisulfideAtomIndices
• disulfide_atom_indices() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_bonded() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_list() : protocols::protein_interface_design::movers::DisulfideMover
• disulfide_params() : core::scoring::disulfides::CentroidDisulfidePotential
• disulfide_RT() : core::scoring::disulfides::DisulfideMatchingPotential
• DisulfideAtomIndices() : core::scoring::disulfides::DisulfideAtomIndices
• DisulfideDistance() : protocols::frag_picker::scores::DisulfideDistance
• DisulfideEntropyFilter() : protocols::simple_filters::DisulfideEntropyFilter
• DisulfideFile() : core::io::raw_data::DisulfideFile
• DisulfideFilter() : protocols::protein_interface_design::filters::DisulfideFilter
• DisulfideIdentity() : protocols::frag_picker::scores::DisulfideIdentity
• DisulfideInsertionMover() : protocols::simple_moves::DisulfideInsertionMover
• DisulfideInsertionMoverCreator() : protocols::simple_moves::DisulfideInsertionMoverCreator
• DisulfideMatchingDatabase() : core::scoring::disulfides::DisulfideMatchingDatabase
• DisulfideMatchingEnergy() : core::scoring::disulfides::DisulfideMatchingEnergy
• DisulfideMatchingEnergyComponents() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• DisulfideMatchingEnergyContainer() : core::scoring::disulfides::DisulfideMatchingEnergyContainer
• DisulfideMatchingNeighborConstIterator() : core::scoring::disulfides::DisulfideMatchingNeighborConstIterator
• DisulfideMatchingNeighborIterator() : core::scoring::disulfides::DisulfideMatchingNeighborIterator
• DisulfideMatchingPotential() : core::scoring::disulfides::DisulfideMatchingPotential
• DisulfideMover() : protocols::protein_interface_design::movers::DisulfideMover
• disulfides() : core::io::raw_data::DisulfideFile , protocols::simple_moves::ForceDisulfidesMover
• disulfides_changed() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• DisulfidizeMover() : protocols::denovo_design::DisulfidizeMover
• DisulfJumpClaimer() : protocols::topology_broker::DisulfJumpClaimer
• DisulfMinData() : core::scoring::disulfides::DisulfMinData
• DisulfPairing() : protocols::jumping::DisulfPairing
• DisulfPairingLibrary() : protocols::jumping::DisulfPairingLibrary
• DisulfResNeighbConstIterator() : core::scoring::disulfides::DisulfResNeighbConstIterator
• DisulfResNeighbIterator() : core::scoring::disulfides::DisulfResNeighbIterator
• DisulfTemplate() : protocols::jumping::DisulfTemplate
• diversify() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• diversify_all_confs() : protocols::enzdes::DiversifyStoredRBConfs
• diversify_backbone_only_rotamers() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• diversify_cst_conformers() : protocols::jumping::ResiduePairJump
• diversify_dof_conformers() : protocols::jumping::ResiduePairJump
• DiversifyCrmsdByClustering() : protocols::frag_picker::DiversifyCrmsdByClustering
• DiversifyCrmsdSelector() : protocols::frag_picker::DiversifyCrmsdSelector
• DiversifyDihedralsSelector() : protocols::frag_picker::DiversifyDihedralsSelector
• DiversifyStoredRBConfs() : protocols::enzdes::DiversifyStoredRBConfs
• divide_up_mutations() : protocols::pmut_scan::PointMutScanDriver
• divide_up_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• divides_backbone_and_sidechain_energetics() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy
• dk() : core::scoring::electron_density::OneGaussianScattering
• dK_dphi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dK_dpsi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dljatr() : core::scoring::etable::Etable
• dljrep() : core::scoring::etable::Etable
• dm() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• DME_FilterMover() : protocols::simple_moves::DME_FilterMover
• DMS_values() : core::scoring::rna::data::RNA_DMS_Potential
• dmu_dphi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dmu_dpsi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• DNA_BaseEnergy() : core::scoring::methods::DNA_BaseEnergy
• DNA_BasePotential() : core::scoring::dna::DNA_BasePotential
• dna_chains() : protocols::dna::RestrictDesignToProteinDNAInterface
• DNA_DihedralEnergy() : core::scoring::methods::DNA_DihedralEnergy
• DNA_DihedralPotential() : core::scoring::dna::DNA_DihedralPotential
• DNA_EnvPairEnergy() : core::scoring::methods::DNA_EnvPairEnergy
• DNA_EnvPairPotential() : core::scoring::dna::DNA_EnvPairPotential
• dna_neighbors() : protocols::dna::DnaInterfaceFinder
• dna_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DNA_ReferenceEnergy() : core::scoring::methods::DNA_ReferenceEnergy
• dna_seq_tag() : protocols::dna::DnaInterfacePacker
• DNABase() : protocols::dna::DNABase
• DNABasepair() : protocols::dna::DNABasepair
• DNABasestep() : protocols::dna::DNABasestep
• DNABFormPotential() : core::scoring::dna::DNABFormPotential
• DnaChains() : protocols::dna::DnaChains
• DNAChiEnergy() : core::scoring::dna::DNAChiEnergy
• DnaDesignDef() : protocols::dna::DnaDesignDef
• DnaInterfaceFinder() : protocols::dna::DnaInterfaceFinder
• DnaInterfaceMinMover() : protocols::dna::DnaInterfaceMinMover
• DnaInterfaceMultiStateDesign() : protocols::dna::DnaInterfaceMultiStateDesign
• DnaInterfacePacker() : protocols::dna::DnaInterfacePacker
• DnaNeighbor() : protocols::dna::DnaNeighbor
• DNAParameters() : protocols::dna::DNAParameters
• DnaPosition() : protocols::dna::DnaPosition
• DNATorsionEnergy() : core::scoring::dna::DNATorsionEnergy
• DNATorsionPotential() : core::scoring::dna::DNATorsionPotential
• dneglnrotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dnmtr() : core::scoring::FACTSResidueInfo
• do_append() : protocols::stepwise::monte_carlo::mover::AddMover
• do_apply() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::loop_modeling::utilities::LoopFilter , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForFullatom
• do_caching() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• do_caching_simple() : protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• do_calibration() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• do_chain_closure_modeler() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_checks() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_checks_and_apply_protonated_H1_adenosine_variant() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• do_classic_intrares() : core::scoring::etable::BaseEtableEnergy< Derived >
• do_clustering() : protocols::cluster::ClusterPhilStyle , protocols::stepwise::modeler::StepWiseMinimizer , protocols::toolbox::ClusterPhilStyle
• do_compute_jump_rmsd() : protocols::nonlocal::StarTreeBuilder
• do_correct_NH() : core::scoring::ResidualDipolarCoupling
• do_cyclic_permutation() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• do_distributed_rerun() : protocols::abinitio::AbrelaxApplication
• do_dynamic_patching() : protocols::abinitio::IterativeBase
• do_fa_stack_scorefunction_checks() : core::scoring::methods::FreeDOF_Energy
• do_filter() : protocols::electron_density::DockIntoDensityMover
• do_final_repack() : protocols::relax::CentroidRelax
• do_frag_cycles() : protocols::loops::loop_closure::ccd::LoopClosure
• do_full_minimizing() : protocols::stepwise::modeler::StepWiseMinimizer
• do_init() : protocols::rpc::BasicCmdLineInit , protocols::rpc::BasicInit
• do_initialize() : protocols::md::CartesianMD
• do_intrastage_docking() : protocols::hybridization::HybridizeProtocol
• do_loop_closure() : protocols::medal::MedalMover
• do_main_loop() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• do_matching() : protocols::enzdes::SecondaryMatchProtocol
• do_MD() : protocols::md::CartesianMD
• do_md() : protocols::relax::FastRelax
• do_minimize() : protocols::md::CartesianMD , protocols::relax::FastRelax , protocols::stepwise::modeler::StepWiseMinimizer
• do_minimizing() : protocols::stepwise::modeler::StepWiseModeler
• do_not_sample_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• do_packing() : protocols::stepwise::modeler::packer::StepWisePacker
• do_prepack() : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• do_prepacking() : protocols::stepwise::modeler::StepWiseModeler
• do_prepend() : protocols::stepwise::monte_carlo::mover::AddMover
• do_random_fragment_insertions() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• do_random_moves() : protocols::farna::RNA_FragmentMonteCarlo
• do_redistribution() : protocols::cluster::ClusterPhilStyle
• do_refinement() : protocols::electron_density::DockIntoDensityMover
• do_remodel() : protocols::denovo_design::connection::Connection
• do_rerun() : protocols::abinitio::AbrelaxApplication
• do_restrict_absent_canonical_aas() : core::pack::task::ResidueLevelTask_
• do_rotation() : protocols::hybridization::TMalign
• do_same_strand() : protocols::jumping::SameStrand
• do_sampling() : protocols::stepwise::modeler::StepWiseModeler
• do_score() : protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::PNatLigPoseOptEData
• do_score_dev() : core::scoring::methods::LinearChainbreakEnergy
• do_score_ovp() : core::scoring::methods::LinearChainbreakEnergy
• do_screen() : protocols::stepwise::screener::AlignRMSD_Screener
• do_some_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• do_some_filtering() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• do_stage1_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage2_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3b_cycles() : protocols::abinitio::MembraneAbinitio
• do_stage4_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage5_cycles() : protocols::abinitio::ClassicAbinitio
• do_step() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• do_stepwise_lores() : protocols::stepwise::modeler::StepWiseModeler
• do_strand_sum() : protocols::jumping::SameStrand
• do_sugar_sampling() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• do_superimposition() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_test_move() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• do_the_modeler() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• do_the_move() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• doAngleDerivatives() : protocols::cartesian::MolecularDynamics
• doBondDerivatives() : protocols::cartesian::MolecularDynamics
• dock_domain_map() : core::pose::full_model_info::FullModelInfo
• dock_high_res() : protocols::antibody::design::GeneralAntibodyModeler
• dock_low_res() : protocols::antibody::design::GeneralAntibodyModeler
• dock_mcm_on_surface() : protocols::surface_docking::FullatomRelaxMover
• DockAndRetrieveSidechains() : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• DockDesignFilterFactory() : protocols::protein_interface_design::DockDesignFilterFactory
• docking() : protocols::antibody::SnugDockProtocol
• docking_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• docking_highres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_highres_mover() : protocols::docking::DockingProtocol
• docking_jump() : protocols::topology_broker::AsymFoldandDockClaimer
• docking_lowres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_lowres_mover() : protocols::docking::DockingProtocol
• DockingEnsemble() : protocols::docking::DockingEnsemble
• DockingEnsemblePrepackProtocol() : protocols::docking::DockingEnsemblePrepackProtocol
• DockingHighRes() : protocols::docking::DockingHighRes
• DockingHighResFilter() : protocols::docking::DockingHighResFilter
• DockingHighResLegacy() : protocols::docking::DockingHighResLegacy
• DockingInitialPerturbation() : protocols::docking::DockingInitialPerturbation
• DockingLowRes() : protocols::docking::DockingLowRes
• DockingLowResEnsemble() : protocols::docking::DockingLowResEnsemble
• DockingLowResFilter() : protocols::docking::DockingLowResFilter
• DockingNoRepack1() : protocols::toolbox::task_operations::DockingNoRepack1
• DockingNoRepack2() : protocols::toolbox::task_operations::DockingNoRepack2
• DockingPrepackProtocol() : protocols::docking::DockingPrepackProtocol
• DockingProtocol() : protocols::docking::DockingProtocol
• DockingScoreFunction() : core::scoring::DockingScoreFunction
• DockingSlideIntoContact() : protocols::docking::DockingSlideIntoContact
• DockIntoDensityMover() : protocols::electron_density::DockIntoDensityMover
• DockLatticeMover() : protocols::cryst::DockLatticeMover
• DockMCMCycle() : protocols::docking::DockMCMCycle
• DockMCMProtocol() : protocols::docking::DockMCMProtocol
• DockMinMover() : protocols::docking::DockMinMover
• DockSetupMover() : protocols::docking::DockSetupMover
• DockTaskFactory() : protocols::docking::DockTaskFactory
• DockWithHotspotMover() : protocols::protein_interface_design::movers::DockWithHotspotMover
• doDihedralDerivatives() : protocols::cartesian::MolecularDynamics
• does_final_fold_tree_exist() : protocols::topology_broker::TopologyBroker
• does_overlap() : core::scoring::packstat::Circle
• dof() : core::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose , protocols::rigid::RigidBodyDofPerturbMover
• dof_access() : core::environment::DofPassport
• DOF_Constraint() : core::scoring::constraints::DOF_Constraint
• DOF_DataPoint() : core::optimization::DOF_DataPoint
• dof_deriv_1benmeths_begin() : core::scoring::MinimizationNode
• dof_deriv_1benmeths_end() : core::scoring::MinimizationNode
• dof_deriv_2benmeths_begin() : core::scoring::MinimizationNode
• dof_deriv_2benmeths_end() : core::scoring::MinimizationNode
• DoF_helix_index() : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_ID() : core::id::DOF_ID
• dof_id() : core::id::DOF_ID_Range , core::optimization::DOF_DataPoint , core::optimization::DOF_Node , core::scoring::constraints::DOF_Constraint
• dof_id_begin() : core::kinematics::MoveMap
• dof_id_end() : core::kinematics::MoveMap
• dof_id_from_torsion_id() : core::conformation::Conformation
• DOF_ID_Map() : core::id::DOF_ID_Map< T >
• DOF_ID_Range() : core::id::DOF_ID_Range
• dof_id_ranges() : protocols::backrub::BackrubMover , protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• dof_is_independent() : core::conformation::symmetry::SymmetryInfo
• DoF_name() : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_Node() : core::optimization::DOF_Node
• dof_node() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• dof_node_for_chi() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• dof_node_from_id() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• dof_nodes() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• dof_refold_index() : core::kinematics::tree::Atom_
• DoF_sample_value() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_step_data() : core::optimization::NumDerivCheckData
• DoF_type() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_type_begin() : core::kinematics::MoveMap
• dof_type_end() : core::kinematics::MoveMap
• dof_val() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• DofClaim() : protocols::topology_broker::claims::DofClaim
• DOFElement() : protocols::environment::claims::DOFElement
• DOFHistogramRecorder() : protocols::simple_moves::DOFHistogramRecorder
• dofmover_compresses() : protocols::simple_moves::symmetry::SymmetrySlider
• DofPassport() : core::environment::DofPassport
• dofs() : protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::simple_moves::DOFHistogramRecorder
• dofs_for_pose0() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• dofs_info() : core::pose::copydofs::CopyDofsInfo
• dofs_to_vars() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• DofUnlock() : protocols::environment::DofUnlock
• doKIC() : protocols::generalized_kinematic_closure::GeneralizedKIC
• domain_map() : core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::Energies , core::scoring::NeighborList
• domain_map_during_minimization() : core::scoring::Energies
• domain_parse_templates() : protocols::hybridization::HybridizeProtocol
• DomainAssembly() : protocols::abinitio::DomainAssembly , protocols::hybridization::DomainAssembly
• DomainInterfaceFilter() : protocols::simple_filters::DomainInterfaceFilter
• doMD() : protocols::cartesian::MolecularDynamics
• dominant() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• doMinimising() : protocols::cartesian::MolecularDynamics
• don_bbg_in_bb_bb_hbond() : core::scoring::hbonds::HBondSet
• don_chem_type_from_name() : core::scoring::hbonds::HBondTypeManager
• don_dist_cutoff() : protocols::features::WaterFeatures
• don_hatm() : core::scoring::hbonds::HBond
• don_hatm_is_backbone() : core::scoring::hbonds::HBond
• don_hatm_is_protein_backbone() : core::scoring::hbonds::HBond
• don_res() : core::scoring::hbonds::HBond
• don_res_is_dna() : core::scoring::hbonds::HBond
• don_res_is_protein() : core::scoring::hbonds::HBond
• don_strength() : core::scoring::hbonds::HBondDatabase
• don_type() : core::scoring::hbonds::HBEvalTuple
• donorRes_occludingRes_geometric_sol_intra() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• dont_be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dont_check_overlap() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dont_check_rama() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dot() : core::scoring::EMapVector , core::scoring::EnergyEdge
• dot_coord() : core::pack::interaction_graph::RotamerDots
• dot_exposed() : core::pack::interaction_graph::InvRotamerDots
• DotSphere() : core::pack::interaction_graph::DotSphere
• double_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• double_lazy_ig_memlimit() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• DoubleDenseIGRepacker() : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleDensePDEdge() : core::pack::interaction_graph::DoubleDensePDEdge
• DoubleDensePDInteractionGraph() : core::pack::interaction_graph::DoubleDensePDInteractionGraph
• DoubleDensePDNode() : core::pack::interaction_graph::DoubleDensePDNode
• DoubleLayerKinematicAbinitio() : protocols::abinitio::DoubleLayerKinematicAbinitio
• DoubleLazyEdge() : core::pack::interaction_graph::DoubleLazyEdge
• DoubleLazyInteractionGraph() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• DoubleLazyNode() : core::pack::interaction_graph::DoubleLazyNode
• downcast_cstedge() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator
• DownJumpSRFD() : core::fragment::DownJumpSRFD
• downsample_pfront_poses() : protocols::design_opt::GreedyOptMutationMover
• downstream() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• downstream_algorithms() : protocols::match::Matcher
• downstream_atom() : core::kinematics::Edge , core::kinematics::FoldTree
• downstream_atoms_required_inside_active_site() : protocols::match::MatcherTask
• downstream_builder() : protocols::match::Matcher
• downstream_builders() : protocols::match::Matcher
• downstream_combine() : core::id::SequenceMapping
• downstream_conf_id() : protocols::match::downstream_hit , protocols::match::Hit
• downstream_hit() : protocols::match::downstream_hit
• downstream_jump_residue() : core::kinematics::FoldTree
• downstream_jump_stub() : core::conformation::Conformation
• downstream_orientation_atoms() : protocols::match::MatcherTask
• downstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose_from_hit() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• downstream_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• downstream_res_nr() : protocols::jumping::JumpSample
• DownstreamAlgorithm() : protocols::match::downstream::DownstreamAlgorithm
• DownstreamBuilder() : protocols::match::downstream::DownstreamBuilder
• DownstreamCoordinateKinemageWriter() : protocols::match::output::DownstreamCoordinateKinemageWriter
• DownstreamRMSEvaluator() : protocols::match::output::DownstreamRMSEvaluator
• dp() : protocols::fldsgn::topology::DimerPairing
• DP_iter() : protocols::hybridization::TMalign
• DP_Matrix() : core::sequence::DP_Matrix
• DPScoringScheme() : core::sequence::DPScoringScheme
• dr_cycles() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• draw_random_phi_psi_from_cdf() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• draw_random_phi_psi_from_extra_cdf() : core::scoring::Ramachandran
• drawn_out_heavyatom_hydrogenatom_energy() : core::scoring::hbonds::HBondEnergy
• drift() : protocols::simple_moves::GenericMonteCarloMover
• drop_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• drop_all_edges() : core::graph::Graph , core::graph::Node , core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E > , core::pack::interaction_graph::NodeBase
• drop_all_edges_for_node() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• drop_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• drop_edge() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase
• drop_inter_group_edges() : protocols::simple_moves::GreenPacker
• drop_intra_group_edges() : protocols::simple_moves::GreenPacker
• drop_random_rate() : protocols::topology_broker::ConstraintClaimer
• drop_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_rotamers() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_rotamers_by_index() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_small_submatrices_where_possible() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::PDEdge
• drop_strand_pairs() : protocols::fldsgn::topology::StrandPairingSet
• drop_unsatisfied_voxels() : protocols::match::OccupiedSpaceHash
• drop_zero_submatrices_where_possible() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::PDEdge
• drotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dry_run() : protocols::relax::RelaxProtocolBase
• ds_atom_present() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• ds_find() : core::graph::DisjointSets
• ds_hitset_end_its() : protocols::match::output::CloudPDBWriter
• ds_hitset_its() : protocols::match::output::CloudPDBWriter
• ds_make_set() : core::graph::DisjointSets
• ds_union() : core::graph::DisjointSets
• dSA_dDi() : core::scoring::FACTSResidueInfo
• dsbuilders() : protocols::match::output::PDBWriter
• dscore() : core::scoring::mm::MMBondAngleScore , core::scoring::mm::MMBondLengthScore , core::scoring::mm::MMTorsionScore
• dslf_ca_dih() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cbs_ds() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cs_ang() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_fa13() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dih() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dst() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslfc_ang() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_bb_dih() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dih() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dst() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cen_dst() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_rot() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_RT() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_trans() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dsolv() : core::scoring::etable::Etable
• dsolv1() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• dsolv2() : core::scoring::etable::MembEtable
• dsolv_dBR() : core::scoring::FACTSResidueInfo
• dspos1_mode() : protocols::match::output::BestMatchesCollection
• dsq() : core::conformation::PointGraphEdgeData
• Dssp() : core::scoring::dssp::Dssp
• dssp() : core::scoring::dssp::Dssp
• dssp1() : core::scoring::motif::ResPairMotif
• dssp2() : core::scoring::motif::ResPairMotif
• dssp_featurizer() : core::scoring::dssp::Dssp
• dssp_phi() : protocols::frag_picker::VallResidue
• dssp_psi() : protocols::frag_picker::VallResidue
• dssp_reduced() : core::scoring::dssp::Dssp
• dssp_reduced_IG_as_L() : core::scoring::dssp::Dssp
• dssp_reduced_IG_as_L_if_adjcent_H() : core::scoring::dssp::Dssp
• dssp_state() : core::scoring::dssp::StrandPairingSet
• DsspDesignOperation() : protocols::toolbox::task_operations::DsspDesignOperation
• DsspMover() : protocols::moves::DsspMover
• dt() : protocols::md::MDBase
• dtest_cutoff() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DualMonteCarlo() : protocols::moves::DualMonteCarlo
• dualspace() : protocols::relax::FastRelax
• dummy_modify() : protocols::forge::build::BuildManager
• DummyClass() : protocols::toolbox::DummyClass
• dump() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::func_1d , core::optimization::Multifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::checkpoint::FileBuffer , protocols::electron_density::BfactorMultifunc , protocols::electron_density::VoxelSpacingMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• dump_aligned_motif() : core::scoring::motif::ResPairMotif
• dump_ASU() : protocols::simple_moves::PeriodicBoxMover
• dump_BRIX() : protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• dump_cif() : core::pose::Pose
• dump_conformer() : protocols::ligand_docking::Transform
• dump_debug_pdb() : protocols::scoring::ImplicitFastClashCheck
• dump_decoy_or_score() : protocols::canonical_sampling::CanonicalSamplingMover
• dump_eggshell() : protocols::pockets::EggshellGrid
• dump_file() : core::pose::Pose , protocols::simple_filters::EvaluatedTrialMover
• dump_initial_results() : protocols::indel::IndelOptimizationMover
• dump_invrots_tree_as_multimodel_pdbs() : protocols::toolbox::match_enzdes_util::InvrotTree
• dump_jump_log() : protocols::abinitio::KinematicAbinitio
• dump_linkers() : protocols::sic_dock::LinkerScore
• dump_matching_motifs() : protocols::sic_dock::scores::MotifHashRigidScore
• dump_minimal_pdb() : protocols::sic_dock::Rose
• dump_motif() : protocols::sewing::scoring::MotifScorer
• dump_motif_hit() : protocols::motifs::MotifHit
• dump_motifs_pdb() : core::scoring::motif::MotifHits
• dump_oriented_pose_and_fp_to_pdb() : protocols::pockets::PlaidFingerprint
• dump_packertask() : protocols::flxbb::DesignTask
• dump_PCS_info() : protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• dump_pdb() : core::pack::rotamer_set::RotamerSets , core::pose::Pose , core::scoring::motif::ResPairMotif , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::farna::options::RNA_BasicOptions , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::sic_dock::Rose
• dump_pdb_name() : protocols::protein_interface_design::filters::FilterScanFilter
• dump_pdb_to_file() : protocols::helix_capper::HelixNCapperMover , protocols::vip::VIP_Mover
• dump_pdb_when_fail() : protocols::fldsgn::BluePrintBDR
• dump_pdbs() : protocols::ddg::ddGMover , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• dump_pose() : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• dump_pose_and_map() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor
• dump_pose_fname() : protocols::simple_filters::RelativePoseFilter
• dump_poses() : protocols::md::CartesianMD
• dump_pymol() : protocols::jumping::JumpSample
• dump_resfile() : core::scoring::motif::MotifHits
• dump_scored_pdb() : core::pose::Pose
• dump_scores() : protocols::jobdist::PlainPdbJobDistributor
• dump_scoring_table() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_silent() : protocols::jobdist::PlainSilentFileJobDistributor
• dump_structures() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• dump_table() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_trisbpy() : protocols::sic_dock::scores::TrisBpyScore
• dump_vd_info() : core::chemical::ResidueType
• dump_weights() : protocols::noesy_assign::PeakAssignment
• dump_xtc_format_decoy() : protocols::canonical_sampling::CanonicalSamplingMover
• dumpExemplarToFile() : protocols::pockets::PocketGrid
• dumpGridToFile() : protocols::pockets::PocketGrid
• DumpPdb() : protocols::simple_moves::DumpPdb
• dumpTargetPocketsToFile() : protocols::pockets::PocketGrid
• dumpTargetPocketsToPDB() : protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• dun02() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• dunbrack_accept() : protocols::simple_moves::sidechain_moves::SidechainMover
• DunbrackConstraint() : core::pack::dunbrack::DunbrackConstraint
• DunbrackConstraintCreator() : core::pack::dunbrack::DunbrackConstraintCreator
• DunbrackEnergy() : core::pack::dunbrack::DunbrackEnergy
• DunbrackRotamer() : core::pack::dunbrack::DunbrackRotamer< S, N, P >
• DunbrackRotamerLibrarySpecification() : core::chemical::rotamers::DunbrackRotamerLibrarySpecification
• DunbrackRotamerMeanSD() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• DunbrackRotamerSampleData() : core::pack::dunbrack::DunbrackRotamerSampleData
• DunbrackSCSampler() : protocols::match::upstream::DunbrackSCSampler
• duplicate_residues_by_type() : protocols::simple_moves::RepeatPropagationMover
• dw_dr() : core::scoring::elec::FAElecContextData
• dweight() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• dynamic_grid_refinement() : protocols::match::MatcherTask
• DynamicAggregateFunction() : protocols::pack_daemon::DynamicAggregateFunction