- e -

• E_elec() : core::scoring::FACTSResidueInfo
• E_solv() : core::scoring::FACTSResidueInfo
• E_solv_pair() : core::scoring::FACTSResidueInfo
• E_solv_self() : core::scoring::FACTSResidueInfo
• eat_until_delimiter() : core::chemical::sdf::SDFParser
• Edge() : core::graph::Edge
• edge() : core::graph::EdgeListElement
• Edge() : core::kinematics::Edge
• edge() : core::scoring::rna::data::RNA_Datum
• edge_exists() : core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E >
• edge_label() : core::kinematics::FoldTree
• edge_list_begin() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::NodeBase
• edge_list_element_pool() : core::graph::Graph
• edge_list_end() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::NodeBase
• edge_list_iterator_at_end() : core::pack::interaction_graph::InteractionGraphBase
• edge_weight() : core::pack::interaction_graph::EdgeBase
• EdgeBase() : core::pack::interaction_graph::EdgeBase
• EdgeList() : core::graph::EdgeList
• edgeList() : core::sequence::SequenceCoupling
• EdgeListConstIterator() : core::graph::EdgeListConstIterator
• EdgeListElement() : core::graph::EdgeListElement
• EdgeListIterator() : core::graph::EdgeListIterator
• edgePotBetween() : core::sequence::SequenceCoupling
• edgePots() : core::sequence::SequenceCoupling
• edges_match() : core::chemical::AutomorphismIterator
• effective_sequence_separation() : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint
• Ei() : core::scoring::FACTSResidueInfo
• EItem() : core::optimization::EItem
• elec_die() : core::scoring::methods::EnergyMethodOptions
• elec_group_file() : core::scoring::methods::EnergyMethodOptions
• elec_max_dis() : core::scoring::methods::EnergyMethodOptions
• elec_min_dis() : core::scoring::methods::EnergyMethodOptions
• elec_no_dis_dep_die() : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_die() : core::scoring::methods::EnergyMethodOptions
• elec_sigmoidal_die_params() : core::scoring::methods::EnergyMethodOptions
• elec_weight() : core::scoring::elec::FA_ElecEnergy
• ElecAtom() : core::scoring::elec::ElecAtom
• ElecDensAllAtomCenEnergy() : core::scoring::electron_density::ElecDensAllAtomCenEnergy
• ElecDensAtomwiseEnergy() : core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• ElecDensCenEnergy() : core::scoring::electron_density::ElecDensCenEnergy
• ElecDensEnergy() : core::scoring::electron_density::ElecDensEnergy
• elecF2() : core::scoring::FACTSResidueInfo
• ElectronConfiguration() : core::chemical::ElectronConfiguration
• ElectronDensity() : core::scoring::electron_density::ElectronDensity
• ElectronDensityAtomwise() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• ElectronDensityLoader() : core::scoring::electron_density::ElectronDensityLoader
• ElectronDensityLoaderCreator() : core::scoring::electron_density::ElectronDensityLoaderCreator
• ElectronDensityOptions() : core::scoring::electron_density::ElectronDensityOptions
• ElectronDensityOptionsCreator() : core::scoring::electron_density::ElectronDensityOptionsCreator
• element() : core::chemical::AtomType
• Element() : core::chemical::Element
• element() : core::chemical::Element , core::chemical::ElementSet , core::chemical::sdf::MolFileIOAtom
• element_index() : core::chemical::ElementSet
• element_set() : core::chemical::ChemicalManager , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::ResidueType , core::chemical::ResidueTypeSet
• element_set_tag() : core::chemical::ResidueLoaderOptions
• element_type() : core::chemical::Atom
• ElementSet() : core::chemical::ElementSet
• emap() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• EMapVector() : core::scoring::EMapVector
• empty() : core::conformation::Conformation , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet , core::graph::ArrayPool< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::ResidueCoordinateChangeList , core::pose::Pose , core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• empty_clone() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::MultiConstraint
• empty_record() : core::pose::PDBInfo
• enable_custom_variant_types() : core::chemical::ResidueProperties , core::chemical::ResidueType
• encode_aa_string() : core::scoring::methods::NMerSVMEnergy
• encode_nmer() : core::scoring::methods::NMerSVMEnergy
• encode_wtd_avg_aa_string() : core::scoring::methods::NMerSVMEnergy
• end() : core::conformation::membrane::Span , core::environment::DofPassport , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::Frame , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::EdgeList , core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets , core::pack::task::TaskFactory , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , core::scoring::packstat::trace
• end1() : core::scoring::dssp::StrandPairing
• end_const() : core::io::raw_data::RawFileData
• energies() : core::io::silent::SilentStruct , core::pose::Pose
• Energies() : core::scoring::Energies
• energies_from_pose() : core::io::silent::SilentStruct
• energies_into_pose() : core::io::silent::SilentStruct
• energies_not_yet_computed() : core::scoring::EnergyEdge
• energies_updated() : core::scoring::Energies
• energy() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::scmin::SidechainStateAssignment , core::scoring::constraints::Constraints , core::scoring::hbonds::HBond
• energy_computed() : core::scoring::constraints::ConstraintEdge , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• energy_cut() : core::import_pose::pose_stream::SilentFilePoseInputStream
• energy_graph() : core::scoring::Energies
• energy_graph_no_state_check() : core::scoring::Energies
• energy_method() : core::scoring::ScoringManager
• energy_method_options() : core::scoring::ScoreFunction
• energy_names() : core::io::silent::EnergyNames , core::io::silent::SilentStruct
• EnergyDependentCalculator() : core::pose::metrics::EnergyDependentCalculator
• EnergyEdge() : core::scoring::EnergyEdge
• EnergyEval() : core::fragment::picking_old::vall::eval::EnergyEval
• EnergyEvent() : core::pose::signals::EnergyEvent
• EnergyGraph() : core::scoring::EnergyGraph
• EnergyMethod() : core::scoring::methods::EnergyMethod
• EnergyMethodOptions() : core::scoring::methods::EnergyMethodOptions
• EnergyMethodRegistrator() : core::scoring::methods::EnergyMethodRegistrator< T >
• EnergyNames() : core::io::silent::EnergyNames
• EnergyNode() : core::scoring::EnergyNode
• ensure_lrenergy_container_is_up_to_date() : core::scoring::disulfides::FullatomDisulfideEnergy
• ensure_size() : core::optimization::Particle
• entropy() : core::pack::dunbrack::RotamerLibraryScratchSpace
• entropy_feature() : core::scoring::methods::ProQ_Energy
• enum2name_() : core::pose::datacache::CacheableDataType
• enumerate_chi_sets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• enumeration_shell() : core::scoring::FACTSResidueInfo
• env_id() : core::environment::DofPassport
• EnvCore() : core::environment::EnvCore
• EnvEnergy() : core::scoring::methods::EnvEnergy
• EnvPairPotential() : core::scoring::EnvPairPotential
• envsmooth_zero_negatives() : core::scoring::methods::EnergyMethodOptions
• EnvSmoothEnergy() : core::scoring::methods::EnvSmoothEnergy
• epsilon() : core::pose::Pose
• epsilon_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• epsilon_components() : core::scoring::dna::DNATorsionPotential
• epsilon_north() : core::chemical::rna::RNA_FittedTorsionInfo
• epsilon_south() : core::chemical::rna::RNA_FittedTorsionInfo
• equalBase() : core::grid::CartGrid< T >
• equalDimensions() : core::grid::CartGrid< T >
• erase() : core::graph::EdgeList , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints
• erase_comment() : core::io::silent::SilentStruct
• esolvE() : core::scoring::FACTSResidueInfo
• estimate_dfunc() : core::scoring::func::Func
• etable() : core::scoring::etable::BaseEtableEnergy< Derived >
• Etable() : core::scoring::etable::Etable
• etable() : core::scoring::ScoringManager
• etable_options() : core::scoring::methods::EnergyMethodOptions
• etable_type() : core::scoring::methods::EnergyMethodOptions
• EtableAtom() : core::scoring::etable::etrie::EtableAtom
• EtableEvaluator() : core::scoring::etable::EtableEvaluator
• EtableFunc() : core::scoring::func::EtableFunc
• EtableOptions() : core::scoring::etable::EtableOptions
• EtableParamsOnePair() : core::scoring::etable::EtableParamsOnePair
• eval_atom_atom_fa_elecE() : core::scoring::etable::coulomb::Coulomb
• eval_atom_derivative() : core::scoring::constraints::ConstraintsEnergy , core::scoring::cryst::XtalMLEnergy , 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::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::GenBornPotential , core::scoring::hackaro::HackAroEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , 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_SugarCloseEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::vdwaals::VDW_Energy
• eval_atom_derivative_aro_aro() : core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::hackaro::HackAroEnergy
• eval_atom_derivative_base_base() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_intra_RNA() : core::scoring::methods::LK_PolarNonPolarEnergy
• eval_atom_derivative_RNA() : core::scoring::elec::RNA_FA_ElecEnergy
• eval_atom_derivative_rna_backbone_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_rna_base_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_derivative_rna_repulsive() : core::scoring::rna::RNA_LowResolutionPotential
• eval_atom_energy() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• eval_atom_nonpolar_derivative() : core::scoring::FACTSPotential
• eval_atom_polar_derivative() : core::scoring::FACTSPotential
• eval_base_pair_derivative() : core::scoring::dna::DNA_BasePotential
• eval_base_pair_Z_scores() : core::scoring::dna::DNA_BasePotential
• eval_base_step_derivative() : core::scoring::dna::DNA_BasePotential
• eval_base_step_Z_scores() : core::scoring::dna::DNA_BasePotential
• eval_cd_1b() : core::scoring::ScoreFunction
• eval_cd_2b() : core::scoring::ScoreFunction
• eval_cd_2b_bb_bb() : core::scoring::ScoreFunction
• eval_cd_2b_bb_sc() : core::scoring::ScoreFunction
• eval_cd_2b_sc_sc() : core::scoring::ScoreFunction
• eval_cd_intrares_energy() : core::scoring::ScoreFunction
• eval_ci_1b() : core::scoring::ScoreFunction
• eval_ci_2b() : core::scoring::ScoreFunction
• eval_ci_2b_bb_bb() : core::scoring::ScoreFunction
• eval_ci_2b_bb_sc() : core::scoring::ScoreFunction
• eval_ci_2b_sc_sc() : core::scoring::ScoreFunction
• eval_ci_intrares_energy() : core::scoring::ScoreFunction
• eval_context_derivatives() : core::scoring::elec::FA_GrpElecEnergy
• eval_csa() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• eval_cubic_polynomial() : core::scoring::etable::Etable
• eval_d_lk_fraction_dr_over_r() : core::scoring::methods::LK_BallEnergy
• eval_dc() : core::scoring::methods::DipolarCouplingEnergy
• eval_dE_dR_over_r() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
• eval_dE_dR_over_r_() : core::scoring::etable::BaseEtableEnergy< Derived >
• eval_dE_dR_over_r_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• eval_desolvation_derivs_no_count_pair() : core::scoring::methods::LK_BallEnergy
• eval_dfa_elecE_dr_over_r() : core::scoring::etable::coulomb::Coulomb
• eval_dfire_pair_energy() : core::scoring::methods::dfire::DFIRE_Potential
• eval_dipolar() : core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• eval_dna_bform_bb_torsion_score_residue() : core::scoring::dna::DNABFormPotential
• eval_dna_bform_chi_torsion_score_residue() : core::scoring::dna::DNABFormPotential
• eval_dof_derivative() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::pHEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_fa_mbenv() : core::scoring::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy
• eval_grp_trunc() : core::scoring::elec::GroupElec
• eval_impl() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• eval_improper_torsion_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_improper_torsions() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_derivs_two_from_rsd1() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_derivs_two_from_rsd2() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_energies_two_from_rsd1() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_angle_energies_two_from_rsd2() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_bond_energy() : core::scoring::methods::CartesianBondedEnergy
• eval_interresidue_bond_length_derivs() : core::scoring::methods::CartesianBondedEnergy
• eval_intrares_atom_derivative() : core::scoring::constraints::Constraints
• eval_intrares_derivatives() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , 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::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• eval_intrares_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , 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::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , 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_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy
• eval_intrares_energy_ext() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• eval_intraresidue_dof_derivative() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::TwoBodyEnergy
• eval_likelihood_potential() : core::scoring::rna::RNA_SuitePotential
• eval_lj() : core::scoring::rna::RNA_LJ_BaseEnergy
• eval_lk() : core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_PolarNonPolarEnergy
• eval_lk_ball_fraction_deriv() : core::scoring::methods::LK_BallEnergy
• eval_lk_efficient() : core::scoring::methods::LK_PolarNonPolarEnergy
• eval_lk_fraction() : core::scoring::methods::LK_BallEnergy
• eval_long_range_twobody_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_multibody_atom_derivative() : core::scoring::constraints::ConstraintSet
• eval_n() : core::scoring::elec::FA_GrpElecEnergy
• eval_non_residue_pair_energy() : core::scoring::constraints::ConstraintSet
• eval_npd_atom_derivative() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_omega_score_all() : core::scoring::OmegaTether
• eval_omega_score_residue() : core::scoring::OmegaTether
• eval_onebody_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_p_aa_pp_score() : core::scoring::Rama2BOffset
• eval_PB_energy_residue() : core::scoring::PoissonBoltzmannPotential
• eval_r2bo_omega_score() : core::scoring::Rama2BOffset
• eval_r2bo_rama_score() : core::scoring::Rama2BOffset
• eval_rama_score_all() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• eval_rama_score_residue() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• eval_rama_score_residue_nonstandard_connection() : core::scoring::Ramachandran
• eval_res() : core::scoring::methods::GoapEnergy
• eval_residue_derivatives() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::SmoothEnvEnergy
• eval_residue_dof_derivative() : 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
• eval_residue_pair_derivatives() : core::scoring::carbon_hbonds::CarbonHBondEnergy , 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::electron_density::FastDensEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , 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::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_SuiteEnergy
• eval_residue_pair_derivatives_one_way() : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• eval_residue_pair_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_respair_atom_derivative() : core::scoring::constraints::Constraints
• eval_respair_group_coulomb() : core::scoring::elec::GroupElec
• eval_respair_group_derivatives() : core::scoring::elec::GroupElec
• eval_rna_base_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• eval_rna_base_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• eval_rotameric_energy_bb_dof_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• eval_rotameric_energy_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• eval_score() : core::scoring::methods::CartesianBondedEnergy , core::scoring::rna::RNA_SuitePotential
• eval_singleres_angle_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_angle_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_energy() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_improper_torsion_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_improper_torsions_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_length_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_length_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_torsion_derivatives() : core::scoring::methods::CartesianBondedEnergy
• eval_singleres_torsion_energies() : core::scoring::methods::CartesianBondedEnergy
• eval_standard_coulomb() : core::scoring::elec::GroupElec
• eval_suiteness_bonus() : core::scoring::rna::RNA_SuitePotential
• eval_tuple() : core::scoring::hbonds::HBond
• eval_twobody_neighbor_energies() : core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• eval_type() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge , core::scoring::hbonds::HBEvalTuple , core::scoring::hbonds::HBond
• eval_ws_atom_derivative() : core::scoring::constraints::Constraints
• evaluate() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential , core::scoring::rna::data::RNA_DMS_Potential , core::scoring::saxs::SinXOverX
• evaluate_cbeta() : core::scoring::MembranePotential
• evaluate_cen_rot_env_and_cbeta_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_env_and_cbeta_score() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_orientation_deriv() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_orientation_score() : core::scoring::CenRotEnvPairPotential
• evaluate_cen_rot_pair_score() : core::scoring::CenRotEnvPairPotential
• evaluate_context_change_for_packing() : core::scoring::FACTSPotential
• evaluate_env() : core::scoring::MembranePotential
• evaluate_env_and_cbeta_deriv() : core::scoring::SmoothEnvPairPotential
• evaluate_env_and_cbeta_scores() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• evaluate_extent() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• evaluate_nonpolar_energy() : core::scoring::FACTSPotential
• evaluate_pair() : core::scoring::MembranePotential
• evaluate_pair_and_cenpack_deriv() : core::scoring::SmoothEnvPairPotential
• evaluate_pair_and_cenpack_score() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• evaluate_polar_energy() : core::scoring::FACTSPotential
• evaluate_polar_otf_energy() : core::scoring::FACTSPotential
• evaluate_rotamer_background_energies() : 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::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_background_energy_maps() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy
• evaluate_rotamer_intrares_energies() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_intrares_energy_maps() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::ScoreFunction
• evaluate_rotamer_pair_energies() : 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::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::PairEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::ScoreFunction , core::scoring::vdwaals::VDW_Energy
• evaluator() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• Event() : core::scoring::packstat::Event
• events() : core::pose::datacache::LengthEventCollector
• ex1() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex1_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_exposed() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_exposed_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex1aro_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex2_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_exposed() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_exposed_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex2aro_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex3() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex3_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ex4() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::motif::Xfrag
• ex4_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ExactOccludedHbondSolEnergy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• examine_edge() : core::chemical::RigidDistanceVisitor
• examine_vertex() : core::chemical::RigidDistanceVisitor
• exclude_DNA_DNA() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• exclude_intra_res_protein() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• exclude_intra_res_RNA() : core::scoring::hbonds::HBondOptions
• exclude_monomer_fa_elec() : core::scoring::methods::EnergyMethodOptions
• exclude_protein_protein_fa_elec() : core::scoring::methods::EnergyMethodOptions
• exclude_self_hbonds() : core::scoring::hbonds::HBondOptions
• exclude_variants() : core::chemical::ResidueSelector
• ExcludedResPredicate() : core::scoring::ExcludedResPredicate
• EXCN_AtomNotFound() : core::id::EXCN_AtomNotFound
• EXCN_Env_Exception() : core::environment::EXCN_Env_Exception
• EXCN_FTSketchGraph() : core::environment::EXCN_FTSketchGraph
• EXCN_Illegal_Arguments() : core::conformation::membrane::EXCN_Illegal_Arguments
• EXCN_InvalidFoldTree() : core::kinematics::EXCN_InvalidFoldTree
• EXCN_Membrane() : core::conformation::membrane::EXCN_Membrane
• EXCN_Membrane_Bounds() : core::conformation::membrane::EXCN_Membrane_Bounds
• EXCN_MembraneFoldTree() : core::conformation::membrane::EXCN_MembraneFoldTree
• EXCN_NonMembrane() : core::conformation::membrane::EXCN_NonMembrane
• EXCN_Resource_Definition() : core::conformation::membrane::EXCN_Resource_Definition
• EXCN_VirtualRsd() : core::conformation::membrane::EXCN_VirtualRsd
• exdna_sample_level() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• exec() : core::scoring::APBSWrapper
• exit_if_missing_heavy_atoms() : core::io::pdb::FileDataOptions
• expand() : core::grid::CartGrid< T >
• expand_node_labels_partial_by_contig() : core::kinematics::TreeVizBuilder
• expandToUnitCell() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• experimental_technique_in_progress() : core::io::pdb::HeaderInformation
• experimental_technique_to_string() : core::io::pdb::HeaderInformation
• experimental_techniques() : core::io::pdb::HeaderInformation
• expid() : core::scoring::RDC
• exposed_hydrophobic_data() : core::pack::interaction_graph::exposed_hydrophobic_data
• extend() : core::fragment::SecondaryStructure , core::scoring::dssp::StrandPairing , core::scoring::TMscore
• extend_to() : core::scoring::dssp::StrandPairing
• ExtendedPoseInputStream() : core::import_pose::pose_stream::ExtendedPoseInputStream
• extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• extra_minimize_res() : core::pose::full_model_info::FullModelInfo
• extra_parameter() : core::chemical::AtomType
• extra_parameter_index() : core::chemical::AtomTypeSet
• extra_parameter_indices() : core::chemical::AtomTypeSet
• extrachi_cutoff() : core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• extrachi_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• ExtraChiCutoff() : core::pack::task::operation::ExtraChiCutoff
• extract_pose_balls() : core::pose::xyzStripeHashPose
• extract_writeable_cacheable_data() : core::io::silent::SilentStruct
• ExtraQuadraticRepulsion() : core::scoring::etable::ExtraQuadraticRepulsion
• ExtraRotamers() : core::pack::task::operation::ExtraRotamers
• ExtraRotamersGeneric() : core::pack::task::operation::ExtraRotamersGeneric