- 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
• damp_long_range() : core::scoring::etable::Etable
• data() : core::conformation::RotamerSetBase , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pose::Pose , core::scoring::electron_density::ElectronDensity , core::scoring::Energies
• data_annotations() : core::io::rna::RDAT
• data_integrity_check() : core::sequence::SequenceAlignment
• data_ptr() : core::conformation::Residue
• database_directory() : core::chemical::ResidueTypeSet
• DatabaseOccSolEne() : core::scoring::geometric_solvation::DatabaseOccSolEne
• dB_dBdnmtr() : core::scoring::FACTSResidueInfo
• dB_dBnmtr() : core::scoring::FACTSResidueInfo
• dBR() : core::pack::annealer::FASTERAnnealer
• dBR_dG() : core::scoring::FACTSResidueInfo
• 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_pat() : 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
• 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
• debug_dump_icoor() : core::chemical::ResidueType
• debug_pause() : core::conformation::Conformation
• debug_residue_torsions() : core::conformation::Conformation
• DebuggingAnnealer() : core::pack::annealer::DebuggingAnnealer
• 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_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::dunbrack::SingleResiduePeptoidLibrary
• declare_atom_neighbor_1sided() : core::scoring::NeighborList
• declare_atoms_neighbors() : core::scoring::NeighborList
• declare_chemical_bond() : core::conformation::Conformation
• 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
• 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
• decompose_bb_hb_into_pair_energies() : core::scoring::hbonds::HBondOptions
• decoy_tag() : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• DecoyFileData() : core::io::raw_data::DecoyFileData
• 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_
• decrement_from_cached() : core::pack::interaction_graph::RotamerDots
• default_commands() : core::pack::task::ResfileContents
• default_filename() : core::pack::task::operation::ReadResfile
• 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
• default_value() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• defined_adducts() : core::chemical::ResidueType
• defines_dof_derivatives() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , 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::Rama2BOffsetEnergy , 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::PattersonCorrEnergy , 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::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::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_BallEnergy , 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::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , 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_Mg_Energy , 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
• 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::PattersonCorrEnergy , 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::PoissonBoltzmannEnergy , core::scoring::methods::Rama2BOffsetEnergy , 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::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
• 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
• 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
• delete_everything() : core::graph::Graph
• delete_extra_vertices() : core::kinematics::FoldTree
• delete_graph_edges_using_domain_map() : core::scoring::Energies
• delete_jump_and_intervening_cutpoint() : core::kinematics::FoldTree
• delete_jump_seqpos() : core::kinematics::FoldTree
• delete_polymer_residue() : core::conformation::Conformation , core::pose::Pose
• delete_position() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• delete_property() : core::chemical::ResidueType
• delete_res() : core::pose::PDBInfo
• delete_residue_range_slow() : core::conformation::Conformation
• delete_residue_slow() : core::conformation::Conformation
• delete_segment() : core::kinematics::FoldTree
• 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_target_residue() : core::id::SequenceMapping
• delete_unordered_edge() : core::kinematics::FoldTree
• DeleteAtom() : core::chemical::DeleteAtom
• deleted() : core::graph::UEEdge< V, E >
• DeleteProperty() : core::chemical::DeleteProperty
• delta() : core::pose::Pose
• delta_components() : core::scoring::dna::DNATorsionPotential
• delta_cutoff() : core::chemical::rna::RNA_FittedTorsionInfo , core::scoring::dna::DNATorsionPotential
• delta_north() : core::chemical::rna::RNA_FittedTorsionInfo
• delta_south() : core::chemical::rna::RNA_FittedTorsionInfo
• dens_grad() : core::scoring::electron_density::ElectronDensity
• DenseEnergyContainer() : core::scoring::DenseEnergyContainer
• 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_change_trigger() : core::scoring::electron_density::ElectronDensity
• dentropy_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• 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_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
• deposition_date() : core::io::pdb::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
• depth_first_connected_component_counting() : core::pack::interaction_graph::NodeBase
• deriv_check() : core::optimization::MinimizerOptions
• deriv_check_result() : core::optimization::AtomTreeMinimizer , core::optimization::CartesianMinimizer , core::optimization::NumericalDerivCheckResult
• 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
• DerivCheckDataPoint() : core::optimization::DerivCheckDataPoint
• 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
• deserialize() : core::grid::CartGrid< T >
• design_any() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• design_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• DesignContrast() : core::io::sequence_comparation::DesignContrast
• designing_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• desired_result() : core::chemical::ResidueSelectorSingle
• DestructionEvent() : core::pose::signals::DestructionEvent
• detach() : core::pose::datacache::ObserverCache
• 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
• 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
• detach_length_obs() : core::conformation::Conformation
• detach_xyz_obs() : core::conformation::Conformation
• detatch_topological_observer() : core::kinematics::AtomTree
• 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
• detect_disulfides() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation
• 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
• determine_crossover_behavior() : core::scoring::etable::BaseEtableEnergy< Derived >
• determine_if_designing() : core::pack::task::ResidueLevelTask_
• determine_if_repacking() : core::pack::task::ResidueLevelTask_
• determine_IUPAC_names() : core::chemical::carbohydrates::CarbohydrateInfo
• determine_nonstandard_polymer_status() : core::conformation::Residue
• determine_polymer_connections() : core::chemical::carbohydrates::CarbohydrateInfo
• determine_residue_connection() : core::scoring::etable::count_pair::CountPairFactory
• determine_rotcounts_for_restype() : core::pack::rotamer_set::ContinuousRotamerSet
• 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
• 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::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
• dfunc_component() : core::scoring::func::MixtureFunc
• dG_dCi() : core::scoring::FACTSResidueInfo
• Di() : core::scoring::FACTSResidueInfo
• die() : core::scoring::etable::coulomb::Coulomb
• 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
• 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
• DihedralConstraint() : core::scoring::constraints::DihedralConstraint
• DihedralConstraintCreator() : core::scoring::constraints::DihedralConstraintCreator
• DihedralPairConstraint() : core::scoring::constraints::DihedralPairConstraint
• DihedralPairConstraintCreator() : core::scoring::constraints::DihedralPairConstraintCreator
• dihedrals_for_atom() : core::chemical::ResidueType
• dimension_etable_arrays() : core::scoring::etable::Etable
• dimer1() : core::scoring::DimerPairing
• dimer2() : core::scoring::DimerPairing
• DimerPairing() : core::scoring::DimerPairing
• DipolarCoupling() : core::scoring::DipolarCoupling
• DipolarCouplingEnergy() : core::scoring::methods::DipolarCouplingEnergy
• directory() : core::chemical::AtomTypeSet
• DirectReadoutEnergy() : core::scoring::methods::DirectReadoutEnergy
• DirectReadoutPotential() : core::scoring::dna::DirectReadoutPotential
• disable_auto_update() : core::scoring::NeighborList
• disallow_aas() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT
• disallow_noncanonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• disallow_quench() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• disallow_resid() : core::pack::task::operation::OptH
• DisallowIfNonnative() : core::pack::task::operation::DisallowIfNonnative
• DisallowIfNonnativeRLT() : core::pack::task::operation::DisallowIfNonnativeRLT
• discard_conformation_domain_map() : core::scoring::Energies
• disjoint_set_sizes() : core::graph::DisjointSets
• DisjointSets() : core::graph::DisjointSets
• 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
• dist2() : core::scoring::motif::ResPairMotif
• dist_pair() : core::scoring::SecondaryStructurePotential
• 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
• distance_4d() : core::pose::rna::RNA_SuiteName
• distance_7d() : core::pose::rna::RNA_SuiteName
• distance_cutoff() : core::pack::task::residue_selector::NumNeighborsSelector
• distance_squared() : core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• 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
• 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
• distribute_pseudo_base_atom_derivatives() : core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy
• 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_params() : core::scoring::disulfides::CentroidDisulfidePotential
• disulfide_RT() : core::scoring::disulfides::DisulfideMatchingPotential
• DisulfideAtomIndices() : core::scoring::disulfides::DisulfideAtomIndices
• DisulfideFile() : core::io::raw_data::DisulfideFile
• 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
• disulfides() : core::io::raw_data::DisulfideFile
• disulfides_changed() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• DisulfMinData() : core::scoring::disulfides::DisulfMinData
• DisulfResNeighbConstIterator() : core::scoring::disulfides::DisulfResNeighbConstIterator
• DisulfResNeighbIterator() : core::scoring::disulfides::DisulfResNeighbIterator
• 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
• 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
• DNABFormPotential() : core::scoring::dna::DNABFormPotential
• DNAChiEnergy() : core::scoring::dna::DNAChiEnergy
• DNATorsionEnergy() : core::scoring::dna::DNATorsionEnergy
• DNATorsionPotential() : core::scoring::dna::DNATorsionPotential
• dneglnrotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dnmtr() : core::scoring::FACTSResidueInfo
• do_classic_intrares() : core::scoring::etable::BaseEtableEnergy< Derived >
• do_fa_stack_scorefunction_checks() : core::scoring::methods::FreeDOF_Energy
• do_restrict_absent_canonical_aas() : core::pack::task::ResidueLevelTask_
• do_score_dev() : core::scoring::methods::LinearChainbreakEnergy
• do_score_ovp() : core::scoring::methods::LinearChainbreakEnergy
• dock_domain_map() : core::pose::full_model_info::FullModelInfo
• DockingScoreFunction() : core::scoring::DockingScoreFunction
• 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
• 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_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_is_independent() : core::conformation::symmetry::SymmetryInfo
• 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_step_data() : core::optimization::NumDerivCheckData
• dof_type_begin() : core::kinematics::MoveMap
• dof_type_end() : core::kinematics::MoveMap
• dof_val() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• DofPassport() : core::environment::DofPassport
• 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
• dominant() : core::conformation::ResidueKinWriter
• don_bbg_in_bb_bb_hbond() : core::scoring::hbonds::HBondSet
• don_chem_type_from_name() : core::scoring::hbonds::HBondTypeManager
• 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
• 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_
• DoubleDensePDEdge() : core::pack::interaction_graph::DoubleDensePDEdge
• DoubleDensePDInteractionGraph() : core::pack::interaction_graph::DoubleDensePDInteractionGraph
• DoubleDensePDNode() : core::pack::interaction_graph::DoubleDensePDNode
• 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
• downstream() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• downstream_atom() : core::kinematics::Edge , core::kinematics::FoldTree
• downstream_combine() : core::id::SequenceMapping
• downstream_jump_residue() : core::kinematics::FoldTree
• downstream_jump_stub() : core::conformation::Conformation
• DP_Matrix() : core::sequence::DP_Matrix
• DPScoringScheme() : core::sequence::DPScoringScheme
• draw_random_phi_psi_from_cdf() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• drawn_out_heavyatom_hydrogenatom_energy() : core::scoring::hbonds::HBondEnergy
• 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_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_zero_submatrices_where_possible() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::PDEdge
• drotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• ds_find() : core::graph::DisjointSets
• ds_make_set() : core::graph::DisjointSets
• ds_union() : core::graph::DisjointSets
• dSA_dDi() : core::scoring::FACTSResidueInfo
• 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
• 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_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
• 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
• dump_aligned_motif() : core::scoring::motif::ResPairMotif
• dump_motifs_pdb() : core::scoring::motif::MotifHits
• dump_pdb() : core::io::pdb::FileData , core::pack::rotamer_set::RotamerSets , core::pose::Pose , core::scoring::motif::ResPairMotif
• dump_resfile() : core::scoring::motif::MotifHits
• dump_scored_pdb() : core::pose::Pose
• dump_vd_info() : core::chemical::ResidueType
• dun02() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• DunbrackConstraint() : core::pack::dunbrack::DunbrackConstraint
• DunbrackConstraintCreator() : core::pack::dunbrack::DunbrackConstraintCreator
• DunbrackEnergy() : core::pack::dunbrack::DunbrackEnergy
• DunbrackRotamer() : core::pack::dunbrack::DunbrackRotamer< S, N, P >
• DunbrackRotamerMeanSD() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• DunbrackRotamerSampleData() : core::pack::dunbrack::DunbrackRotamerSampleData
• dw_dr() : core::scoring::elec::FAElecContextData
• dweight() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode