- e -

E_elec() : core::scoring::FACTSResidueInfo
E_solv() : core::scoring::FACTSResidueInfo
E_solv_pair() : core::scoring::FACTSResidueInfo
E_solv_self() : core::scoring::FACTSResidueInfo
Edge() : core::graph::Edge
edge() : core::graph::EdgeListElement
Edge() : core::kinematics::Edge
edge() : core::scoring::rna::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_max_dis() : core::scoring::methods::EnergyMethodOptions
elec_min_dis() : core::scoring::methods::EnergyMethodOptions
elec_no_dis_dep_die() : 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::ElementSet
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
elementToType() : core::chemical::sdf::elementToType
emap() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
EMapVector() : core::scoring::EMapVector
embed_for_FA() : core::membrane::geometry::EmbeddingFactory
embed_from_pdb() : core::membrane::geometry::EmbeddingFactory
embed_from_search_and_score() : core::membrane::geometry::EmbeddingFactory
embed_from_topology() : core::membrane::geometry::EmbeddingFactory
EmbedDefFallbackConfiguration() : core::membrane::io::EmbedDefFallbackConfiguration
EmbedDefIO() : core::membrane::io::EmbedDefIO
EmbedDefLoader() : core::membrane::io::EmbedDefLoader
EmbedDefOptions() : core::membrane::io::EmbedDefOptions
embedding_center() : core::conformation::membrane::MembraneInfo
embedding_depth() : core::conformation::membrane::MembraneInfo
embedding_normal() : core::conformation::membrane::MembraneInfo
EmbeddingFactory() : core::membrane::geometry::EmbeddingFactory
EmbedSearchParamsFallbackConfiguration() : core::membrane::io::EmbedSearchParamsFallbackConfiguration
EmbedSearchParamsIO() : core::membrane::io::EmbedSearchParamsIO
EmbedSearchParamsLoader() : core::membrane::io::EmbedSearchParamsLoader
EmbedSearchParamsOptions() : core::membrane::io::EmbedSearchParamsOptions
embres_map() : core::conformation::membrane::MembraneInfo
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::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
encode_aa_string() : core::scoring::methods::NMerSVMEnergy
encode_nmer() : core::scoring::methods::NMerSVMEnergy
encode_wtd_avg_aa_string() : core::scoring::methods::NMerSVMEnergy
end() : core::coarse::Rule , core::coarse::TranslatorSet , 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
enlarge_h_lj_wdepth() : core::chemical::AtomTypeSet
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
enumerate_chi_sets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
enumeration_shell() : core::scoring::FACTSResidueInfo
EnvCore() : core::environment::EnvCore
EnvEnergy() : core::scoring::methods::EnvEnergy
EnvPairPotential() : core::scoring::EnvPairPotential
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::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::BaseEtableEnergy< Derived > , core::scoring::GenBornPotential , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hackaro::HackAroEnergy , core::scoring::loop_graph::LoopCloseEnergy , 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::ResidualDipolarCouplingEnergyRigidSegments , 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::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , 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::geometric_solvation::GeometricSolEnergyEvaluator , 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_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() : core::coarse::CoarseEtable
eval_dE_dR_over_r() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
eval_dE_dR_over_r_() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::CoarseEtableEnergy
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 , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
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::CSD_TorsionEnergy , 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::PyContextIndependentTwoBodyEnergy , 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::methods::Fa_MbenvEnergy
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::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , 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::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::CoarseEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CSD_TorsionEnergy , 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::PyContextIndependentTwoBodyEnergy , 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::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , 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_lj() : core::scoring::rna::RNA_LJ_BaseEnergy
eval_lk() : 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_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_procheck_rama() : core::scoring::Ramachandran
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::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , 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
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_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 >
eval_score() : core::scoring::methods::CartesianBondedEnergy
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_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::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::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::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::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex1_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex1aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex1aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex1aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex1aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2aro() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2aro_exposed() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2aro_exposed_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex2aro_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex3() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex3_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex4() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ex4_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ExactOccludedHbondSolEnergy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
exclude_DNA_DNA() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
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::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
ExtendAlignerSW() : core::sequence::ExtendAlignerSW
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::ResidueLevelTask , core::pack::task::ResidueLevelTask_
extrachi_sample_level() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
ExtraChiCutoff() : core::pack::task::operation::ExtraChiCutoff
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