- g -

• GA_Minimizer() : core::optimization::GA_Minimizer
• ga_mutation_probability() : core::optimization::MinimizerOptions
• gamma() : core::pose::CrystInfo , core::pose::Pose , core::scoring::CSA
• gamma_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• gamma_components() : core::scoring::dna::DNATorsionPotential
• gap_char() : core::sequence::Sequence
• gap_extend() : core::sequence::ScoringScheme
• gap_open() : core::sequence::ScoringScheme
• gapped_positions() : core::sequence::SequenceAlignment
• gasteiger_atom_type() : core::chemical::Atom , core::chemical::ResidueType
• gasteiger_atom_type_set() : core::chemical::ChemicalManager , core::chemical::gasteiger::PossibleAtomTypesForAtom
• GasteigerAtomTypeData() : core::chemical::gasteiger::GasteigerAtomTypeData
• GasteigerAtomTypeSet() : core::chemical::gasteiger::GasteigerAtomTypeSet
• gate_pssm_scores() : core::scoring::methods::NMerPSSMEnergy
• gate_svm_scores() : core::scoring::methods::NMerSVMEnergy
• gaussian() : core::scoring::SmoothScoreTermCoeffs
• gaussian_1d() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• gaussian_move() : core::kinematics::Jump
• gaussian_move_single_rb() : core::kinematics::Jump
• gaussian_parameter_set_alpha() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_beta() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_gamma() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_ap() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_minus() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_plus() : core::chemical::rna::RNA_FittedTorsionInfo
• GaussianChainDoubleFunc() : core::scoring::func::GaussianChainDoubleFunc
• GaussianChainFunc() : core::scoring::func::GaussianChainFunc
• GaussianChainQuadrupleFunc() : core::scoring::func::GaussianChainQuadrupleFunc
• GaussianChainSingleFunc() : core::scoring::func::GaussianChainSingleFunc
• GaussianChainTripleFunc() : core::scoring::func::GaussianChainTripleFunc
• GaussianFunc() : core::scoring::func::GaussianFunc
• GaussianOverlapEnergy() : core::scoring::methods::GaussianOverlapEnergy
• GaussianParameter() : core::chemical::rna::GaussianParameter
• gb_shell_intxn() : core::scoring::GenBornPotential
• gb_shell_intxn_deriv() : core::scoring::GenBornPotential
• GBPair_cut() : core::scoring::FACTSPotential
• GenBornEnergy() : core::scoring::methods::GenBornEnergy
• GenBornPoseInfo() : core::scoring::GenBornPoseInfo
• GenBornPotential() : core::scoring::GenBornPotential
• GenBornResidueInfo() : core::scoring::GenBornResidueInfo
• GenBornRotamerSetInfo() : core::scoring::GenBornRotamerSetInfo
• GeneralEvent() : core::conformation::signals::GeneralEvent , core::pose::signals::GeneralEvent
• generate_atom_indices() : core::chemical::ResidueType
• generate_from_sequence() : core::sequence::SequenceProfile
• generate_gaussian_1d() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• generate_id() : core::environment::EnvCore
• generate_insert_map() : core::fragment::FragSet
• generate_reversed() : core::scoring::dssp::Pairing
• generate_sub_fragment() : core::fragment::AnnotatedFragData , core::fragment::FragData
• generate_sub_frame() : core::fragment::Frame
• GenerateConcaveSurface() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateConvexSurface() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateMolecularSurfaces() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateResidues() : core::chemical::sdf::SDFParser
• GenerateToroidalSurface() : core::scoring::sc::MolecularSurfaceCalculator
• GenericResidueConnectionData() : core::scoring::etable::etrie::GenericResidueConnectionData
• GenericRule() : core::coarse::GenericRule
• geo_dim_type_from_name() : core::scoring::hbonds::HBondTypeManager
• geometric_dimension() : core::scoring::hbonds::Polynomial_1d
• geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• GeometricSolEnergy() : core::scoring::geometric_solvation::GeometricSolEnergy
• GeometricSolEnergyEvaluator() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get() : core::chemical::sdf::elementToType , core::id::AtomID_Map< T > , core::kinematics::MoveMap , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::PoseMetricContainer , core::pose::metrics::StructureDependentCalculator , core::scoring::EMapVector , core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::saxs::DistanceHistogram , core::scoring::saxs::FormFactor
• get_2D_histogram() : core::scoring::orbitals::OrbitalsStatistics
• get_2way_orientation() : core::scoring::sasa::LeGrandSasa
• get_aa_submatrix_energies() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_aa_submatrix_energies_for_edge() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• get_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• get_abego_string() : core::util::ABEGOManager
• get_acceptor_base_atm_xyz() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_adjacent_background_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_adjacent_dlazy_node() : core::pack::interaction_graph::DoubleLazyNode
• get_adjacent_dpd_node() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode
• get_adjacent_faster_node() : core::pack::interaction_graph::FASTERNode
• get_adjacent_first_class_node() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• get_adjacent_lazy_node() : core::pack::interaction_graph::LazyNode
• get_adjacent_linmem_node() : core::pack::interaction_graph::LinearMemNode
• get_adjacent_node() : core::pack::interaction_graph::NodeBase
• get_adjacent_otf_node() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_adjacent_symmin_node() : core::pack::interaction_graph::SymmMinimalistNode
• get_adjacent_symmlinmem_node() : core::pack::interaction_graph::SymmLinearMemNode
• get_AHDangle() : core::scoring::hbonds::HBond
• get_al_tensor_max_z() : core::scoring::ResidualDipolarCoupling
• get_al_tensor_trace() : core::scoring::ResidualDipolarCoupling
• get_ali_params() : core::scoring::TMscore
• get_aligner() : core::sequence::AlignerFactory
• get_all_atom_types_in_database() : core::chemical::AtomTypeDatabaseIO
• get_all_born_radii() : core::scoring::GenBornPotential
• get_all_comments() : core::io::silent::SilentStruct
• get_all_constraints() : core::scoring::constraints::ConstraintSet
• get_all_disulfides() : core::scoring::disulfides::DisulfideMatchingDatabase
• get_all_nondegenerate_conformers() : core::chemical::RingConformerSet
• get_all_poses() : core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream
• get_all_properties() : core::chemical::AtomType
• get_all_register_and_bulges() : core::scoring::dssp::StrandPairing
• get_all_residues_in_database() : core::chemical::ResidueDatabaseIO
• get_all_rotamer_samples() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_all_rotamer_samples_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_all_rotamer_samples_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_all_sasas() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_alt_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_alt_pd_energy_total() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_alt_score_() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl
• get_alt_state_atom_atom_overlaps() : core::pack::interaction_graph::HPatchEdge< V, E, G >
• get_alt_state_hASA_for_node_and_nbs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_alt_state_num_atoms() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_alt_state_rotamer_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_alternate() : core::pack::interaction_graph::SimpleNode
• get_alternate_sasa() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_alternate_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_alternate_state_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge
• get_alternate_state_energy_first_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_alternate_state_energy_second_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_alternate_state_sasa() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_anchor_residue() : core::conformation::symmetry::SymmData
• get_angle_score() : core::scoring::methods::GoapEnergy
• get_angles() : core::scoring::sasa::LeGrandSasa
• get_angular_momentum_quantum_number() : core::chemical::ElectronConfiguration
• get_antiparallel_weight() : core::scoring::SecondaryStructureWeights
• get_aro_axis_score_ANGLE() : core::scoring::hackaro::HackAroEnergy
• get_aro_axis_score_DIST() : core::scoring::hackaro::HackAroEnergy
• get_array_indices() : core::scoring::dna::DNA_BasePotential
• get_asymmetric_seqpos() : core::conformation::symmetry::SymmetryInfo
• get_atom() : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• get_atom_atom_carbon_hbond_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• get_atom_atom_coverage() : core::pack::interaction_graph::RotamerDots
• get_atom_atom_geometric_solvation_for_acceptor() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_atom_atom_geometric_solvation_for_donor() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_atom_atom_occ_solvation() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• get_atom_atom_overlaps_for_state() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• get_atom_atom_self_overlaps() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_atom_atom_self_overlaps_for_state() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_atom_coords_xyz() : core::pack::interaction_graph::RotamerDots
• get_atom_counts() : core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache
• get_atom_h2o_hbond_derivative() : core::scoring::methods::WaterAdductHBondEnergy
• get_atom_ids_by_torsion() : core::scoring::dna::DNATorsionPotential
• get_atom_index() : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::scoring::saxs::FormFactorManager
• get_atom_name_from_database_atom_index() : core::chemical::ResidueDatabaseIO
• get_atom_radius() : core::pack::interaction_graph::RotamerDots
• get_atom_sasa() : core::pack::interaction_graph::RotamerDots , core::scoring::sasa::SasaCalc
• get_atom_type_property() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_atom_type_set_name() : core::scoring::AtomVDW
• get_atom_weight() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• get_atomic_number() : core::chemical::Element
• get_atomname() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• get_atomnames_size() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• get_AtomVDW() : core::scoring::ScoringManager
• get_average_cation_pi_ip_to_neutral_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_cation_sigma_ip_to_neutral_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_ip_change_cation_to_neutral() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_ip_change_neutral_to_anion() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_neutral_pi_ip_to_anion_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_neutral_sigma_ip_to_anion_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_background_node() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_background_node_index() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_BAHangle() : core::scoring::hbonds::HBond
• get_base_centroid() : core::scoring::rna::RNA_CentroidInfo
• get_base_coordinate_system() : core::scoring::hackaro::HackAroEnergy , core::scoring::rna::RNA_CentroidInfo
• get_base_vector() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_BAtorsion() : core::scoring::hbonds::HBond
• get_bb() : core::kinematics::MoveMap
• get_bb_bbE() : core::pack::rotamer_set::RotamerSets
• get_bb_E() : core::pack::interaction_graph::SimpleEdge
• get_bb_index() : core::pack::interaction_graph::SimpleEdge
• get_bbdep_nrchi_bin() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_bbind_nrchi_bin() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_best_exp_to_calc_chem_shift_mapping() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_beta_pairs() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• get_bg_bg_atom_atom_overlaps() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_bg_edge_list_begin() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_bg_edge_list_end() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_bg_edge_vector_up_to_date_() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_bin_size() : core::scoring::func::SplineFunc
• get_binary_name() : core::pack::dunbrack::RotamerLibrary
• get_binary_name_02() : core::pack::dunbrack::RotamerLibrary
• get_binary_name_10() : core::pack::dunbrack::RotamerLibrary
• get_bins_per_A2() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• get_bond_count() : core::chemical::sdf::atomTyper
• get_bond_length() : core::chemical::IdealBondLengthSet
• get_bondelement_count() : core::chemical::sdf::atomTyper
• get_bondtype_count() : core::chemical::sdf::atomTyper
• get_CA_xyz() : core::import_pose::PDBSilentStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• get_calc_chem_shift_value() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_calc_rot_freq() : core::pack::annealer::SimAnnealerBase
• get_calculator() : core::pose::metrics::PoseMetricContainer
• get_CarbonHBondPotential() : core::scoring::ScoringManager
• get_cart_unitCell() : core::scoring::electron_density::ElectronDensity
• get_cartesian_bonded_linear() : core::scoring::methods::EnergyMethodOptions
• get_cartesian_bonded_parameters() : core::scoring::methods::EnergyMethodOptions
• get_CenHBPotential() : core::scoring::ScoringManager
• get_CenRotEnvPairPotential() : core::scoring::ScoringManager
• get_centroid() : core::scoring::hackaro::HackAroEnergy
• get_centroid_information() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• get_CentroidDisulfidePotential() : core::scoring::ScoringManager
• get_chains_connected() : core::scoring::methods::IntermolEnergy
• get_charged_residues_map() : core::scoring::methods::PBLifetimeCache
• get_chemical_name() : core::chemical::Element
• get_chemical_shift_energy() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_chemical_symbol() : core::chemical::Element
• get_chi() : core::kinematics::MoveMap
• get_closest_rotamer() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• get_comment() : core::io::silent::SilentStruct
• get_component_bounds() : core::conformation::symmetry::SymmetryInfo
• get_component_lower_bound() : core::conformation::symmetry::SymmetryInfo
• get_component_of_residue() : core::conformation::symmetry::SymmetryInfo
• get_component_upper_bound() : core::conformation::symmetry::SymmetryInfo
• get_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_coordinate_system() : core::scoring::disulfides::RT_helper
• get_cos_angle() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• get_cos_theta() : core::scoring::rna::RNA_Mg_Energy
• get_count_pair_data_for_residue() : core::scoring::trie::RotamerTrieBase
• get_count_pair_function() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• get_count_pair_function_trie() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDW_Energy
• get_creator() : core::io::silent::SilentStructFactory , core::scoring::constraints::ConstraintFactory , core::sequence::SequenceFactory
• get_CSA_data() : core::scoring::ChemicalShiftAnisotropy
• get_cst_factory() : core::scoring::constraints::ConstraintIO
• get_cst_names() : core::scoring::constraints::ConstraintFactory
• get_cube() : core::scoring::packstat::Octree2D
• get_curr_pd_energy_total() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_curr_state_energy_following_partial_state_assignment() : core::pack::interaction_graph::FASTEREdge
• get_curr_state_recent_state_id() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• get_curr_state_surface_energy() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_current() : core::pack::interaction_graph::SimpleNode
• get_current_energy() : core::pack::interaction_graph::SimpleEdge
• get_current_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_current_network_state() : core::pack::interaction_graph::FASTERInteractionGraph
• get_current_rotamer() : core::pack::interaction_graph::LinearMemNode
• get_current_sasa() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_current_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• get_current_state_atom_atom_overlaps() : core::pack::interaction_graph::HPatchEdge< V, E, G >
• get_current_state_for_node() : core::pack::interaction_graph::FASTERInteractionGraph
• get_current_state_num_atoms() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_state_rotamer_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_state_sasa() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , 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
• get_cutpoint_open_from_pdb_info() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• get_data() : core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• get_data_ref() : core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• get_data_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_database() : core::scoring::hbonds::HBondDatabase
• get_DatabaseOccSolEne() : core::scoring::ScoringManager
• get_DC_data() : core::scoring::DipolarCoupling
• get_DC_data_type() : core::scoring::DC
• get_DDPLookupTable() : core::scoring::ScoringManager
• get_debug_rmsd() : core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• get_default_parameter() : core::chemical::AtomTypeSet
• get_deltaE_for_neighbor_following_perturbation() : core::pack::interaction_graph::FASTEREdge
• get_deltaE_for_perturbation() : core::pack::interaction_graph::FASTEREdge
• get_deltaE_for_relaxed_state_following_perturbation() : core::pack::interaction_graph::FASTERNode
• get_deriv_count() : core::optimization::func_1d
• get_deriv_for_chemical_shift_data_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_descriptor() : core::chemical::ElectronConfiguration
• get_DirectReadoutPotential() : core::scoring::ScoringManager
• get_distance_score() : core::scoring::methods::GoapEnergy
• get_disulfide_derivatives() : core::scoring::disulfides::FullatomDisulfidePotential
• get_disulfide_derivatives_old() : core::scoring::disulfides::FullatomDisulfidePotential
• get_disulfide_params() : core::scoring::disulfides::FullatomDisulfidePotential
• get_DisulfideMatchingPotential() : core::scoring::ScoringManager
• get_dlazy_edge() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• get_dlazy_ig_owner() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyNode
• get_dlazy_node() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph
• get_DNA_BasePotential() : core::scoring::ScoringManager
• get_DNABFormPotential() : core::scoring::ScoringManager
• get_DNATorsionPotential() : core::scoring::ScoringManager
• get_dof_axis_and_end_pos() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• get_dof_derivative_weight() : core::conformation::symmetry::SymmetryInfo
• get_dof_id() : core::optimization::CartesianMinimizerMap
• get_dofs() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_dot_covered() : core::pack::interaction_graph::DotSphere
• get_dpd_edge() : core::pack::interaction_graph::DensePDInteractionGraph
• get_dpd_node() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph
• get_dpdig_owner() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDNode
• get_dssp_reduced_IG_as_L_secstruct() : core::scoring::dssp::Dssp
• get_dssp_secstruct() : core::scoring::dssp::Dssp
• get_E_haro_one_way() : core::scoring::orbitals::OrbitalsScore
• get_E_hpol_one_way() : core::scoring::orbitals::OrbitalsScore
• get_edge() : core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E > , core::pack::interaction_graph::InteractionGraphBase
• get_edge_exists() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• get_edge_list_begin() : core::pack::interaction_graph::InteractionGraphBase
• get_edge_list_end() : core::pack::interaction_graph::InteractionGraphBase
• get_edge_memory_usage() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_edge_reweight() : core::pack::task::IGEdgeReweighter
• get_edge_table_ptr() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_edge_to_bg_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_edge_to_hpatch_bg_node() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_edge_to_surface_bg_node() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_edge_vector_up_to_date() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_edge_weight() : core::pack::interaction_graph::InteractionGraphBase
• get_edges_position_in_nodes_edge_vector() : core::pack::interaction_graph::EdgeBase
• get_eID() : core::coarse::CoarseEtable
• get_electron_affinity() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_electron_configuration() : core::chemical::Element
• get_electronegativity() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_element() : core::chemical::sdf::atomTyper
• get_element_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_embed_params_from_file() : core::membrane::io::EmbedSearchParamsIO
• get_embedding_from_file() : core::membrane::io::EmbedDefIO
• get_embedfile_from_options() : core::membrane::io::EmbedDefFallbackConfiguration
• get_energy() : core::io::silent::SilentStruct
• get_energy_current_state_assignment() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_energy_following_partial_state_assignment() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_energy_following_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• get_energy_for_alt_state() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_energy_for_perturbed_state() : core::pack::interaction_graph::FASTEREdge
• get_energy_for_state_pair() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• get_energy_node() : core::scoring::EnergyGraph
• get_energy_owner() : core::scoring::EnergyEdge
• get_energy_PD_current_state_assignment() : core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_energy_state() : core::scoring::methods::PBLifetimeCache
• get_energy_sum_for_vertex_group() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_entries_per_torsion_bin() : core::scoring::Ramachandran
• get_entries_per_torsion_bin_left() : core::scoring::Ramachandran2B
• get_entries_per_torsion_bin_right() : core::scoring::Ramachandran2B
• get_EnvPairPotential() : core::scoring::ScoringManager
• get_equiv() : core::pack::rotamer_set::RotamerLinks
• get_eval_count() : core::optimization::func_1d
• get_ex_flags() : core::pack::task::ResidueLevelTask_
• get_exp_val() : core::scoring::func::SplineFunc
• get_f1_f2() : core::scoring::rna::RNA_TorsionPotential
• get_fa_stack_deriv() : core::scoring::rna::RNA_FullAtomStackingEnergy
• get_fa_stack_score() : core::scoring::rna::RNA_FullAtomStackingEnergy
• get_FACTSPotential() : core::scoring::ScoringManager
• get_faster_edge() : core::pack::interaction_graph::FASTERInteractionGraph
• get_faster_node() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph
• get_fasterig_owner() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode
• get_ff() : core::scoring::saxs::FormFactorManager
• get_filename() : core::scoring::func::SplineFunc
• get_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• get_first() : core::scoring::packstat::trace
• get_first_class_node() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_first_class_node_index() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_first_node_ind() : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• get_fixedbb_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_fixedbb_node() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_fmax() : core::scoring::hbonds::FadeInterval
• get_fmin() : core::scoring::hbonds::FadeInterval
• get_focus() : core::pack::task::residue_selector::NeighborhoodResidueSelector
• get_foldtree_seqsep() : core::scoring::SecondaryStructurePotential
• get_formal_charge() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_frag_atoms() : core::kinematics::AtomTree
• get_frag_descendant_local_xyz() : core::kinematics::AtomTree
• get_frag_factory() : core::fragment::FragmentIO
• get_frag_local_stub() : core::kinematics::AtomTree
• get_frag_local_xyz() : core::kinematics::AtomTree
• get_frag_parent_local_xyz() : core::kinematics::AtomTree
• get_frag_pseudo_stub_id() : core::kinematics::AtomTree
• get_ft_node_bounds() : core::kinematics::TreeVizBuilder
• get_ft_node_lower_bound() : core::kinematics::TreeVizBuilder
• get_ft_node_subroot() : core::kinematics::TreeVizBuilder
• get_full_id() : core::fragment::TorsionInfoSet
• get_FullatomDisulfidePotential() : core::scoring::ScoringManager
• get_func() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::DihedralConstraint
• get_func_factory() : core::scoring::constraints::ConstraintIO
• get_gaussian_potential_score() : core::scoring::rna::RNA_Mg_Energy
• get_gaussian_score() : core::scoring::rna::RNA_Mg_Energy
• get_GDTHA() : core::scoring::TMscore
• get_GDTTS() : core::scoring::TMscore
• get_GenBornPotential() : core::scoring::ScoringManager
• get_grid_spacing() : core::scoring::electron_density::ElectronDensityOptions
• get_HAdist() : core::scoring::hbonds::HBond
• get_half_width() : core::scoring::func::LinearPenaltyFunction
• get_handedness_score_flag() : core::scoring::SecondaryStructureWeights
• get_hASA_for_node_and_nbs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_hightemp() : core::pack::annealer::SimAnnealerBase
• get_histogram_vector() : core::scoring::orbitals::OrbitalsStatistics
• get_hpatch_bg_edge() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_hpatch_bg_node() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hpatch_node() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hpatch_owner() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_hpatch_score() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_hybrid_orbital_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_hydrogens() : core::scoring::orbitals::OrbitalsAssigned
• get_i() : core::scoring::packstat::Octree2D
• get_ideal_conformer_by_CP_parameters() : core::chemical::RingConformerSet
• get_ideal_conformer_by_name() : core::chemical::RingConformerSet
• get_ideal_conformer_from_nus() : core::chemical::RingConformerSet
• get_idx_for_other_pose() : core::pose::full_model_info::FullModelInfo
• get_idx_for_other_pose_with_residue() : core::pose::full_model_info::FullModelInfo
• get_incident_dlazy_edge() : core::pack::interaction_graph::DoubleLazyNode
• get_incident_dpd_edge() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode
• get_incident_edge() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_incident_faster_edge() : core::pack::interaction_graph::FASTERNode
• get_incident_hpatch_edge() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_incident_lazy_edge() : core::pack::interaction_graph::LazyNode
• get_incident_linmem_edge() : core::pack::interaction_graph::LinearMemNode
• get_incident_otf_edge() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_incident_pd_edge() : core::pack::interaction_graph::PDNode
• get_incident_surface_edge() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_incident_symmin_edge() : core::pack::interaction_graph::SymmMinimalistNode
• get_incident_symmlinmem_edge() : core::pack::interaction_graph::SymmLinearMemNode
• get_include_subunit() : core::conformation::symmetry::SymmData
• get_index() : core::grid::CartGrid< T >
• get_index_of_adjacent_background_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_index_of_adjacent_first_class_node() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• get_index_of_adjacent_node() : core::pack::interaction_graph::NodeBase
• get_inneriterations() : core::pack::annealer::SimAnnealerBase
• get_input_streams() : core::import_pose::pose_stream::MetaPoseInputStream
• get_input_stub() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_instance() : core::chemical::ChemicalManager , core::chemical::orbitals::OrbitalTypeMapper , core::fragment::picking_old::FragmentLibraryManager , core::io::silent::SilentStructFactory , core::pack::dunbrack::RotamerLibrary , core::pack::interaction_graph::RotamerDotsRadiusData , core::pack::interaction_graph::SurfacePotential , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::pack::task::residue_selector::ResidueSelectorFactory , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintIO , core::scoring::geometric_solvation::GridInfo , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::saxs::SinXOverX , core::scoring::ScoringManager , core::sequence::SequenceFactory , core::SVNVersion
• get_interfaces() : core::conformation::symmetry::SymmData
• get_intrares_countpair() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• get_ionization_potential() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_j() : core::scoring::packstat::Octree2D
• get_jump() : core::kinematics::MoveMap , core::kinematics::ShortestPathInFoldTree
• get_jump_atom_id() : core::kinematics::AtomTree
• get_jump_clones() : core::conformation::symmetry::SymmData
• get_jump_name() : core::conformation::symmetry::SymmetryInfo
• get_jump_name_to_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_jump_name_to_subunits() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_jump_num() : core::conformation::symmetry::SymmetryInfo
• get_jump_num_to_contig_of_resi() : core::kinematics::TreeVizBuilder
• get_jump_string_to_jump_num() : core::conformation::symmetry::SymmData
• get_jump_that_builds_residue() : core::kinematics::FoldTree
• get_KB_description() : core::scoring::func::SplineFunc
• get_known_atoms() : core::scoring::saxs::FormFactorManager
• get_l_equivalent() : core::scoring::methods::ReferenceEnergy , core::scoring::P_AA , core::scoring::Ramachandran
• get_lazy_edge() : core::pack::interaction_graph::LazyInteractionGraph
• get_lazy_ig_owner() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyNode
• get_lazy_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph
• get_least_common_ancertor_jump() : core::conformation::symmetry::SymmData
• get_least_common_ancertor_virtual() : core::conformation::symmetry::SymmData
• get_library_by_aa() : core::pack::dunbrack::RotamerLibrary
• get_library_name_02() : core::pack::dunbrack::RotamerLibrary
• get_linmem_ig_owner() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode
• get_linmem_node() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph
• get_lips_exp_from_lipofile() : core::membrane::io::LipoFileIO
• get_lips_filename_from_options() : core::membrane::io::LipoFileFallbackConfiguration
• get_lj_hbond_hdis() : core::scoring::etable::Etable
• get_lj_hbond_OH_donor_dis() : core::scoring::etable::Etable
• get_lk_fractional_contribution() : core::scoring::methods::LK_BallEnergy
• get_lk_fractional_contribution_for_single_water() : core::scoring::methods::LK_BallEnergy
• get_localstrandpair_penalty() : core::scoring::SecondaryStructureWeights
• get_locator_id() : core::membrane::io::EmbedDefFallbackConfiguration , core::membrane::io::EmbedSearchParamsFallbackConfiguration , core::membrane::io::LipoFileFallbackConfiguration , core::membrane::io::SpanFileFallbackConfiguration
• get_loop_atom() : core::scoring::loop_graph::LoopGraph
• get_loop_distance2() : core::scoring::loop_graph::LoopCloseEnergy
• get_loop_distance2_deriv() : core::scoring::loop_graph::LoopCloseEnergy
• get_lower_bound_dy() : core::scoring::func::SplineFunc
• get_lower_bound_x() : core::scoring::func::SplineFunc
• get_lower_bound_y() : core::scoring::func::SplineFunc
• get_lowest_energy_conformer() : core::chemical::RingConformerSet
• get_lowtemp() : core::pack::annealer::SimAnnealerBase
• get_lp_xyz() : core::scoring::orbitals::OrbitalsAssigned
• get_magnetic_anisotropy_deriv_for_src_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_magnetic_anisotropy_deriv_for_src_base() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_main_group() : core::chemical::Element
• get_manager() : core::scoring::saxs::FormFactorManager
• get_mapreso() : core::scoring::electron_density::ElectronDensityOptions
• get_masks() : core::scoring::sasa::LeGrandSasa
• get_matching_CS_data_entry() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_max0() : core::scoring::hbonds::FadeInterval
• get_max_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_max_surface_deltaE_guess() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• get_maxE_contribution_to_pi_system() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_Membrane_FAPotential() : core::scoring::ScoringManager
• get_MembranePotential() : core::scoring::ScoringManager
• get_message() : core::pack::task::ResfileReaderException
• get_metal_binding_atoms() : core::chemical::ResidueType , core::conformation::Residue
• get_mg_potential_costheta_gaussian_parameter() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• get_mg_potential_costheta_indirect_gaussian_parameter() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• get_mg_potential_gaussian_parameter() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• get_mg_potential_indirect_gaussian_parameter() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• get_min0() : core::scoring::hbonds::FadeInterval
• get_minimization_node() : core::scoring::MinimizationEdge , core::scoring::MinimizationGraph
• get_minimization_owner() : core::scoring::MinimizationEdge
• get_MMBondAngleLibrary() : core::scoring::ScoringManager
• get_MMBondLengthLibrary() : core::scoring::ScoringManager
• get_MMLJEnergyTable() : core::scoring::ScoringManager
• get_MMLJLibrary() : core::scoring::ScoringManager
• get_MMTorsionLibrary() : core::scoring::ScoringManager
• get_mol_data() : core::chemical::ResidueType , core::chemical::sdf::MolData
• get_mol_data_string_vector() : core::chemical::sdf::MolData
• get_n_alignments() : core::scoring::ResidualDipolarCoupling
• get_n_baserotamers_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• get_n_carbons() : core::chemical::carbohydrates::CarbohydrateInfo
• get_n_residue_groups() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_residue_types() : core::conformation::RotamerSetBase , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_rotamers_for_residue_group() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_rotamers_for_residue_type() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_sampling_rotamers_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• get_NACCESS_SASA_radii() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_NACCESS_SASA_radii_with_expanded_polars() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_name() : core::chemical::gasteiger::GasteigerAtomTypeData , core::grid::CartGrid< T > , core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::ChainSelector , core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector , core::pack::task::residue_selector::JumpDownstreamSelector , core::pack::task::residue_selector::JumpUpstreamSelector , core::pack::task::residue_selector::NeighborhoodResidueSelector , core::pack::task::residue_selector::NotResidueSelector , core::pack::task::residue_selector::NumNeighborsSelector , core::pack::task::residue_selector::OrResidueSelector , core::pack::task::residue_selector::ResidueIndexSelector , core::pack::task::residue_selector::ResidueSelector , core::pose::datacache::CacheableDataType , core::scoring::hbonds::FadeInterval , core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaMethod , core::scoring::ScoreFunction
• get_natoms() : core::scoring::PQR
• get_nblist() : core::scoring::symmetry::NBListCache
• get_ncaa_rotlib_n_bin_per_rot() : core::chemical::ResidueType
• get_ncaa_rotlib_path() : core::chemical::ResidueType
• get_NCAARotamerLibrary() : core::pack::dunbrack::RotamerLibrary
• get_ncac() : core::scoring::disulfides::RT_helper
• get_nearest_UC() : core::scoring::electron_density::ElectronDensity
• get_network_state() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_njumps_subunit() : core::conformation::symmetry::SymmetryInfo
• get_nNumber_hybrid_lone_pairs() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_node() : core::graph::Edge , core::graph::Graph , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase
• get_node_index() : core::graph::Edge , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase
• get_node_state_offset() : core::pack::interaction_graph::InteractionGraphBase
• get_nonjump_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_nonzero_weighted_scoretypes() : core::scoring::ScoreFunction
• get_nres_subunit() : core::conformation::symmetry::SymmetryInfo
• get_nu() : core::kinematics::MoveMap
• get_num_aa_types() : core::pack::interaction_graph::OnTheFlyNode
• get_num_aatypes() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_num_atoms() : core::pack::interaction_graph::RotamerDots
• get_num_background_nodes() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_num_bg_edges() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_num_chains_frozen() : core::scoring::methods::IntermolEnergy
• get_num_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_num_covered() : core::pack::interaction_graph::DotSphere
• get_num_covered_total() : core::pack::interaction_graph::RotamerDots
• get_num_edges() : core::pack::interaction_graph::InteractionGraphBase
• get_num_edges_to_background_nodes() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_num_edges_to_larger_indexed_nodes() : core::graph::Node , core::pack::interaction_graph::NodeBase
• get_num_edges_to_smaller_indexed_nodes() : core::graph::Node , core::pack::interaction_graph::NodeBase
• get_num_incident_edges() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_num_nodes() : core::pack::interaction_graph::InteractionGraphBase
• get_num_nodes_v() : core::pack::interaction_graph::InteractionGraphBase
• get_num_res_types() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_restype_groups() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_rpe_calculations_count() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_num_states() : core::pack::interaction_graph::NodeBase
• get_num_states_for_aa_type() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_num_states_for_aa_types() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_num_states_for_node() : core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase
• get_num_states_for_restype_group() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_total_states() : core::pack::interaction_graph::InteractionGraphBase
• get_num_uncovered() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots
• get_num_unrecognized_atoms() : core::pose::PDBInfo
• get_num_unrecognized_res() : core::pose::PDBInfo
• get_num_virtual() : core::conformation::symmetry::SymmData
• get_number_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_electrons_in_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_electrons_in_p_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_hybrid_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_hybrid_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_missing_residue_connections() : core::scoring::methods::MissingEnergy
• get_number_of_connected_subgraphs() : core::scoring::methods::IntermolEnergy
• get_number_of_histograms() : core::scoring::orbitals::OrbitalsStatistics
• get_number_pi_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_sigma_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_unhybridized_lone_pairs() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_unhybridized_sigma_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_numeric_property() : core::chemical::ResidueType
• get_NVLookupTable() : core::scoring::ScoringManager
• get_offset() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_offset_table_size_in_bytes() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_offsets_for_aatypes() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_OmegaTether() : core::scoring::ScoringManager
• get_on_the_fly_node() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_on_the_fly_owner() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_one_body_energy() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_one_body_energy_current_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• get_one_body_energy_for_node_state() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_one_body_energy_for_relaxed_state() : core::pack::interaction_graph::FASTERNode
• get_orb_H_distance_and_energy() : core::scoring::orbitals::OrbitalsScore
• get_orb_orb_E() : core::scoring::orbitals::OrbitalsScore
• get_orbital_E_neg_pos() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_orbital_enum() : core::chemical::orbitals::OrbitalTypeMapper
• get_OrbitalsLookupTable() : core::scoring::ScoringManager
• get_orientation() : core::scoring::sasa::LeGrandSasa
• get_origin() : core::conformation::symmetry::VirtualCoordinate , core::conformation::symmetry::VirtualCoordinates
• get_original_residue() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• get_original_residue_set() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• get_otf_node() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_otf_owner() : core::pack::interaction_graph::SymmOnTheFlyEdge
• get_other_ind() : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• get_other_node() : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• get_outeriterations() : core::pack::annealer::SimAnnealerBase
• get_outgoing_edges() : core::kinematics::FoldTree
• get_output_subunit() : core::conformation::symmetry::SymmData
• get_overlap() : core::scoring::sasa::LeGrandSasa
• get_overlap_cache() : core::pack::interaction_graph::RotamerDots
• get_owner() : core::graph::Edge , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase
• get_P_AA() : core::scoring::ScoringManager
• get_Paa_pp_deriv() : core::scoring::P_AA
• get_pair() : core::scoring::dssp::StrandPairing
• get_PairEPotential() : core::scoring::ScoringManager
• get_pairs() : core::scoring::dna::DirectReadoutPotential
• get_parallel_weight() : core::scoring::SecondaryStructureWeights
• get_parameter() : core::pose::full_model_info::FullModelParameters
• get_parent_jump() : core::conformation::symmetry::SymmData
• get_parent_remark() : core::io::silent::SilentStruct
• get_parent_remark_from_line() : core::io::silent::SilentStruct
• get_parent_residue() : core::kinematics::FoldTree
• get_parent_virtual() : core::conformation::symmetry::SymmData
• get_path_from_root() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_pbp() : core::scoring::methods::PBLifetimeCache
• get_pd_edge() : core::pack::interaction_graph::PDInteractionGraph
• get_pd_energy_delta() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_pd_node() : core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph
• get_pdb_lines() : core::import_pose::PDBSilentStruct
• get_pdig_owner() : core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDNode
• get_period() : core::chemical::Element
• get_phi_from_rsd() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_phipsi_bins() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• get_pi_electron_contribution_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_pleating() : core::scoring::dssp::StrandPairing
• get_PoissonBoltzmannPotential() : core::scoring::ScoringManager
• get_polymer_residue_direction() : core::kinematics::FoldTree
• get_pose() : core::scoring::methods::PBLifetimeCache
• get_pose_intensities() : core::scoring::saxs::SAXSEnergy
• get_pose_pack_data() : core::scoring::packstat::SimplePDB
• get_potential() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::PoissonBoltzmannPotential
• get_potential_RNA() : core::scoring::carbon_hbonds::CarbonHBondPotential
• get_potentials() : core::scoring::interface_::DDPlookup , core::scoring::nv::NVlookup
• get_pr_idx() : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• get_principal_quantum_number() : core::chemical::ElectronConfiguration
• get_probability_for_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_probability_for_rotamer_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_probability_for_rotamer_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_proline_correction() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_proline_correction_for_node() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_property() : core::chemical::Element
• get_property_name() : core::chemical::Element
• get_proposed_energy() : core::pack::interaction_graph::SimpleEdge
• get_ProQPotential() : core::scoring::ScoringManager
• get_pseudobonds_to_residue() : core::conformation::Residue
• get_psi_from_rsd() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_q() : core::scoring::saxs::SAXSEnergy
• get_R() : core::scoring::electron_density::ElectronDensity
• get_radii() : core::pack::interaction_graph::RotamerDots
• get_radius() : core::scoring::packstat::AtomRadiusMap
• get_Rama2BOffset() : core::scoring::ScoringManager
• get_Ramachandran() : core::scoring::ScoringManager
• get_Ramachandran2B() : core::scoring::ScoringManager
• get_random_conformer() : core::chemical::RingConformerSet
• get_random_local_min_conformer() : core::chemical::RingConformerSet
• get_random_neighbor() : core::pack::interaction_graph::FASTERNode
• get_random_neighbor_for_node() : core::pack::interaction_graph::FASTERInteractionGraph
• get_rb_center() : core::kinematics::Jump
• get_rb_delta() : core::kinematics::Jump
• get_RDC_data() : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl
• get_RDC_data_ref() : core::scoring::ResidualDipolarCoupling
• get_RDC_data_type() : core::scoring::RDC , core::scoring::ResidualDipolarCoupling_Rohl
• get_realatomdata_index() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_recent_history_size() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• get_recenter() : core::conformation::symmetry::SymmData
• get_ref_tags() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• get_reference_energy() : core::pack::dunbrack::SingleLigandRotamerLibrary
• get_reference_intensities() : core::scoring::saxs::SAXSEnergy
• get_register() : core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing
• get_rel_hphobic_sasa_by_charge() : core::scoring::sasa::SasaCalc
• get_relaxed_state() : core::pack::interaction_graph::FASTERNode
• get_res_centers() : core::scoring::packstat::SimplePDB
• get_res_list() : core::pose::full_model_info::FullModelParameters
• get_res_nodenames() : core::kinematics::TreeVizBuilder
• get_res_res_elecE() : core::scoring::GenBornPotential
• get_res_res_overlap() : core::pack::interaction_graph::RotamerDots
• get_residue() : core::fragment::FragData
• get_residue_edge() : core::kinematics::FoldTree
• get_residue_energy_by_svm() : core::scoring::methods::NMerSVMEnergy
• get_residue_energy_RNA_intra() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_residue_group_begin() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_group_index_for_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_hsasa() : core::scoring::sasa::SasaCalc
• get_residue_hsasa_bb() : core::scoring::sasa::SasaCalc
• get_residue_hsasa_sc() : core::scoring::sasa::SasaCalc
• get_residue_information() : core::io::pdb::FileData
• get_residue_mask() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation
• get_residue_pair_energy() : core::scoring::methods::Fa_MbsolvEnergy
• get_residue_pair_energy_one_way() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_residue_residue_h2o_hbonds_1way() : core::scoring::WaterAdductHBondPotential
• get_residue_sasa() : core::scoring::sasa::SasaCalc
• get_residue_sasa_bb() : core::scoring::sasa::SasaCalc
• get_residue_sasa_sc() : core::scoring::sasa::SasaCalc
• get_residue_type_begin() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_type_index_for_rotamer() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_type_with_variant_added() : core::chemical::ResidueTypeSet
• get_residue_type_with_variant_removed() : core::chemical::ResidueTypeSet
• get_residue_weight() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation
• get_reslabels() : core::pose::PDBInfo
• get_resource_loader() : core::membrane::io::EmbedDefFallbackConfiguration , core::membrane::io::EmbedSearchParamsFallbackConfiguration , core::membrane::io::LipoFileFallbackConfiguration , core::membrane::io::SpanFileFallbackConfiguration
• get_resource_options() : core::membrane::io::EmbedDefFallbackConfiguration , core::membrane::io::EmbedSearchParamsFallbackConfiguration , core::membrane::io::LipoFileFallbackConfiguration , core::membrane::io::SpanFileFallbackConfiguration
• get_ring_current_deriv_for_src_base() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_RNA_AtomVDW() : core::scoring::ScoringManager
• get_rna_axis_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_backbone_backbone_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_backbone_backbone_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_base_backbone_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_basepair_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_RNA_ChemicalShiftPotential() : core::scoring::ScoringManager
• get_RNA_CS_residue_parameters() : core::scoring::rna::chemical_shift::RNA_CS_parameters
• get_RNA_LowResolutionPotential() : core::scoring::ScoringManager
• get_rna_repulsive_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_stack_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_stagger_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_RNA_TorsionPotential() : core::scoring::ScoringManager
• get_root() : core::conformation::symmetry::SymmData
• get_ROSETTA_SASA_radii() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• get_rotamer_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_rotamer_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• get_rotamer_from_chi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_rotamer_from_chi_static() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• get_rotamer_samples() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• get_RotamerLibrary() : core::coarse::Translator
• get_RotamerLibraryName() : core::chemical::ResidueType
• get_rotamers() : core::pack::dunbrack::SingleLigandRotamerLibrary
• get_rotamers_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_rotation() : core::kinematics::Jump , core::kinematics::RT
• get_rotation_matrix() : core::conformation::symmetry::SymmData
• get_rotblock_index_for_sampling_rotamer() : core::pack::rotamer_set::ContinuousRotamerSet
• get_rsd_library() : core::pack::dunbrack::RotamerLibrary
• get_safe_max_dis2() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• get_sasa() : core::pack::interaction_graph::RotamerDots
• get_sasa_difference() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_sc_bbE() : core::pack::rotamer_set::RotamerSets
• get_score_multiply_subunit() : core::conformation::symmetry::SymmData
• get_score_subunit() : core::conformation::symmetry::SymmData
• get_scorefxn_info() : core::scoring::Energies
• get_scoring_scheme() : core::sequence::ScoringSchemeFactory
• get_scratch_atom_id() : core::pose::copydofs::CopyDofs
• get_second_node_ind() : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• get_second_node_num_states_per_aa() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_SecondaryStructurePotential() : core::scoring::ScoringManager
• get_self_terms() : core::scoring::FACTSPotential
• get_seq_names() : core::sequence::SequenceFactory
• get_seq_sep_scale() : core::scoring::SecondaryStructureWeights
• get_sequence() : core::sequence::SequenceFactory
• get_sequence_with_gaps_filled_with_n() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• get_shared_silent_data() : core::io::silent::SilentFileData
• get_silent_energies() : core::io::silent::SilentStruct
• get_silent_energy() : core::io::silent::SilentStruct
• get_silent_struct() : core::io::silent::SilentStructFactory
• get_silent_struct_in() : core::io::silent::SilentStructFactory
• get_silent_struct_out() : core::io::silent::SilentStructFactory
• get_silent_struct_type() : core::io::silent::SilentFileOptions
• get_simple_ig_owner() : core::pack::interaction_graph::SimpleEdge
• get_simple_node() : core::pack::interaction_graph::SimpleInteractionGraph
• get_single_rotamer_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_slide_info() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_slide_order() : core::conformation::symmetry::SymSlideInfo
• get_slide_type() : core::conformation::symmetry::SymSlideInfo
• get_SlideCriteriaType() : core::conformation::symmetry::SymSlideInfo
• get_SlideCriteriaVal() : core::conformation::symmetry::SymSlideInfo
• get_slope() : core::scoring::func::LinearPenaltyFunction
• get_smooth() : core::scoring::hbonds::FadeInterval
• get_SmoothEnvPairPotential() : core::scoring::ScoringManager
• get_span_filename_from_options() : core::membrane::io::EmbedSearchParamsFallbackConfiguration , core::membrane::io::SpanFileFallbackConfiguration
• get_sparse_aa_info() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_sparse_aa_info_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_sparse_aa_neighbor_info() : core::pack::interaction_graph::LinearMemEdge
• get_sparse_mat_info_for_curr_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_sparse_mat_info_for_state() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_spheres() : core::scoring::packstat::SimplePDB
• get_ss_cutoff() : core::scoring::SecondaryStructureWeights
• get_ss_lowstrand() : core::scoring::SecondaryStructureWeights
• get_ss_names() : core::io::silent::SilentStructFactory
• get_stability_metric() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_stack_elec_deriv() : core::scoring::rna::StackElecEnergy
• get_stack_elec_score() : core::scoring::rna::StackElecEnergy
• get_stacking_map() : core::pose::Pose
• get_start_with_current() : core::pack::annealer::SimAnnealerBase
• get_state_ind_for_this_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• get_state_offset_for_aatype() : core::pack::interaction_graph::OnTheFlyNode
• get_state_offset_for_restype_group() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_stretch_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_string_property() : core::chemical::ResidueType
• get_string_value() : core::io::silent::SilentStruct
• get_structure() : core::io::silent::SilentFileData
• get_stub() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_stub1() : core::chemical::orbitals::ICoorOrbitalData
• get_stub2() : core::chemical::orbitals::ICoorOrbitalData
• get_stub3() : core::chemical::orbitals::ICoorOrbitalData
• get_stub_transform() : core::conformation::Conformation , core::kinematics::AtomTree
• get_sub_score() : core::scoring::ScoreFunction
• get_sub_score_exclude_res() : core::scoring::ScoreFunction
• get_submatrix_index() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_subset() : core::conformation::membrane::SpanningTopology , core::scoring::MembraneTopology
• get_subunit_name_to_component() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_subunit_num_to_virt_id() : core::conformation::symmetry::SymmData
• get_subunits() : core::conformation::symmetry::SymmData
• get_sugar_env_score() : core::scoring::rna::RNA_DataBackboneEnergy
• get_sum_water_weight_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• get_surface_area() : core::scoring::packstat::LeeRichards
• get_surface_bg_edge() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• get_surface_bg_node() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_surface_deltaE_for_neighbor() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• get_surface_deltaE_for_neighbors_state_substitution() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• get_surface_node() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_surface_owner() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_surface_score() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• get_surface_score_difference() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_svm_nodes() : core::scoring::methods::NMerSVMEnergy
• get_symbols() : core::util::ABEGOManager
• get_symmetry_name() : core::conformation::symmetry::SymmData
• get_symmetry_type() : core::conformation::symmetry::SymmData
• get_symmin_ig_owner() : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistNode
• get_symmin_node() : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_symmlinmem_ig_owner() : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode
• get_symmlinmem_node() : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• get_symmMap() : core::scoring::electron_density::ElectronDensity
• get_table_size() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_tag_score_map() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• get_temperature() : core::pack::annealer::SimAnnealerBase
• get_template_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_TenANode() : core::scoring::TenANeighborEdge
• get_TMscore() : core::scoring::TMscore
• get_topology_from_spanfile() : core::membrane::io::SpanFileIO
• get_torsion_angle_atom_ids() : core::conformation::Conformation
• get_torsion_bin_index() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• get_TorsionID() : core::optimization::CartesianMinimizerMap
• get_total_base_axis_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_total_base_pair_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stack_axis_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stack_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stagger_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• get_total_dots() : core::pack::interaction_graph::DotSphere
• get_total_energy_in_curr_state_assignment_for_all_states() : core::pack::interaction_graph::FASTERNode
• get_total_exp_chemical_shift_data_points() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_total_hsasa() : core::scoring::sasa::SasaCalc
• get_total_hsasa_bb() : core::scoring::sasa::SasaCalc
• get_total_hsasa_sc() : core::scoring::sasa::SasaCalc
• get_total_rel_hsasa() : core::scoring::sasa::SasaCalc
• get_total_sasa() : core::scoring::sasa::SasaCalc
• get_total_sasa_bb() : core::scoring::sasa::SasaCalc
• get_total_sasa_sc() : core::scoring::sasa::SasaCalc
• get_totalE() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• get_transformation() : core::conformation::symmetry::SymmetricConformation
• get_translation() : core::kinematics::Jump , core::kinematics::RT
• get_translation_matrix() : core::conformation::symmetry::SymmData
• get_transrot_ref() : core::scoring::TMscore
• get_trie() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_two_body_energies_for_relaxed_states() : core::pack::interaction_graph::FASTEREdge
• get_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_two_body_energy_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_two_body_energy_smi() : core::pack::interaction_graph::DoubleLazyEdge
• get_two_body_table_size() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_type_difference_name() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_UnfoldedStatePotential() : core::scoring::ScoringManager
• get_unfoled_potential_file_weights() : core::scoring::UnfoldedStatePotential
• get_unrecognized_atoms() : core::pose::PDBInfo
• get_unrecognized_res_name() : core::pose::PDBInfo
• get_unrecognized_res_size() : core::pose::PDBInfo
• get_upper_bound_dy() : core::scoring::func::SplineFunc
• get_upper_bound_x() : core::scoring::func::SplineFunc
• get_upper_bound_y() : core::scoring::func::SplineFunc
• get_upstream_vrt() : core::conformation::symmetry::SymmetricConformation
• get_use_ncaa_rotlib() : core::chemical::ResidueType
• get_use_symmetry() : core::conformation::symmetry::SymmetryInfo
• get_valence_electrons_sp() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_Vall() : core::fragment::picking_old::FragmentLibraryManager
• get_vdw_atom_number() : core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_VDW_Energy
• get_version() : core::chemical::ResidueDatabaseIO
• get_vertex() : core::chemical::ResidueType , core::graph::UpperEdgeGraph< V, E >
• get_vertex_member_of_energy_sum_group() : core::pack::interaction_graph::InteractionGraphBase
• get_vertex_ptr() : core::graph::UpperEdgeGraph< V, E >
• get_virt_id_to_subunit_chain() : core::conformation::symmetry::SymmData
• get_virt_id_to_subunit_num() : core::conformation::symmetry::SymmData
• get_virt_id_to_subunit_residue() : core::conformation::symmetry::SymmData
• get_virtual_connects() : core::conformation::symmetry::SymmData
• get_virtual_coordinates() : core::conformation::symmetry::SymmData
• get_virtual_id_to_num() : core::conformation::symmetry::SymmData
• get_virtual_num_to_id() : core::conformation::symmetry::SymmData
• get_water_cos() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_water_weight_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• get_WaterAdductHBondPotential() : core::scoring::ScoringManager
• get_weight() : core::scoring::func::SplineFunc , core::scoring::ScoreFunction
• get_weighted_energy() : core::pack::interaction_graph::PDInteractionGraph
• get_weighted_energy_with_higher_indexed_nodes() : core::pack::interaction_graph::PDNode
• get_well_depth() : core::scoring::func::LinearPenaltyFunction
• get_x() : core::conformation::symmetry::VirtualCoordinate , core::conformation::symmetry::VirtualCoordinates
• get_x_middle() : core::scoring::func::LinearPenaltyFunction
• get_xy_bin() : core::scoring::dna::DirectReadoutPotential
• get_y() : core::conformation::symmetry::VirtualCoordinate , core::conformation::symmetry::VirtualCoordinates
• get_z_bin() : core::scoring::dna::DirectReadoutPotential
• get_zeta_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• getAANeighborOffsets() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• getAtomMask() : core::scoring::electron_density::ElectronDensity
• GetAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• getBase() : core::grid::CartGrid< T >
• getCachedScore() : core::scoring::electron_density::ElectronDensity
• getCoM() : core::scoring::electron_density::ElectronDensity
• GetDots() : core::scoring::sc::MolecularSurfaceCalculator
• getEffOrigin() : core::scoring::electron_density::ElectronDensity
• getFdrhoc() : core::scoring::electron_density::ElectronDensity
• getFSC() : core::scoring::electron_density::ElectronDensity
• getInfoLine() : core::scoring::cryst::PhenixInterface
• getIntensities() : core::scoring::electron_density::ElectronDensity
• getIntensitiesMasked() : core::scoring::electron_density::ElectronDensity
• getK() : core::scoring::constraints::KofNConstraint
• getListNames() : core::io::sequence_comparation::DesignContrast
• getMapMapError() : core::scoring::electron_density::ElectronDensity
• getMatrixPointer() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• getMax() : core::scoring::electron_density::ElectronDensity
• GetMaximumElectrons() : core::chemical::Bond
• getMaxValue() : core::grid::CartGrid< T >
• getMean() : core::scoring::electron_density::ElectronDensity
• getMemoryUsageInBytes() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• getMin() : core::scoring::electron_density::ElectronDensity
• GetMinimumElectrons() : core::chemical::Bond
• getMinValue() : core::grid::CartGrid< T >
• getModelMapError() : core::scoring::electron_density::ElectronDensity
• GetMoleculeComments() : core::chemical::sdf::MolFileParser
• GetMoleculeInfo() : core::chemical::sdf::MolFileParser
• GetMoleculeName() : core::chemical::sdf::MolFileParser
• GetMostStableType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• getNeighbors() : core::io::sequence_comparation::DesignContrast
• GetNumberOfElectrons() : core::chemical::Bond
• getNumberOfPoints() : core::grid::CartGrid< T >
• GetNumberOfResidues() : core::chemical::sdf::SDFParser
• GetNumberPossibleTypes() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• getNumBonds() : core::chemical::sdf::atomTyper
• getNumDerivH() : core::scoring::electron_density::ElectronDensity
• getOrigin() : core::scoring::electron_density::ElectronDensity
• getPdbCodes() : core::io::sequence_comparation::DesignContrast
• getPdbNames() : core::io::sequence_comparation::DesignContrast
• getPose() : core::pose::signals::GeneralEvent
• GetPropertyName() : core::chemical::gasteiger::GasteigerAtomTypeData
• getR() : core::scoring::cryst::PhenixInterface
• getRecordCollection() : core::io::pdb::Field
• GetResidueByName() : core::chemical::sdf::SDFParser
• GetResidueNameVector() : core::chemical::sdf::SDFParser
• GetResidueType() : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::MolFileParser
• GetResidueTypeOP() : core::chemical::sdf::MolFileParser
• getResolution() : core::scoring::electron_density::ElectronDensity
• getResolutionBins() : core::scoring::electron_density::ElectronDensity
• GetResults() : core::scoring::sc::MolecularSurfaceCalculator
• getRfree() : core::scoring::cryst::PhenixInterface
• getRSCC() : core::scoring::electron_density::ElectronDensity
• getScore() : core::scoring::cryst::PhenixInterface
• getScoreAndDerivs() : core::scoring::cryst::PhenixInterface
• getScoreWindowContext() : core::scoring::electron_density::ElectronDensity
• getSCscaling() : core::scoring::electron_density::ElectronDensity
• GetSDAltFileID() : core::chemical::Bond
• GetSDFileID() : core::chemical::Bond
• getSecStruct() : core::io::sequence_comparation::DesignContrast
• getStdev() : core::scoring::electron_density::ElectronDensity
• getsymmOps() : core::scoring::electron_density::ElectronDensity
• getTop() : core::grid::CartGrid< T >
• getTotalMemoryUsage() : core::graph::Graph , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase
• getTransform() : core::scoring::electron_density::ElectronDensity
• getType() : core::chemical::sdf::atomTyper
• getUseDensityInMinimizer() : core::scoring::electron_density::ElectronDensity
• getUseExactDerivatives() : core::scoring::electron_density::ElectronDensity
• getValue() : core::grid::CartGrid< T >
• getValueFrom() : core::io::pdb::Field
• getWindow() : core::scoring::electron_density::ElectronDensity
• global2local() : core::kinematics::Stub
• global_auto_rescale() : core::sequence::SequenceProfile
• global_offset() : core::fragment::FragSet
• gmax_cutoff_for_convergence() : core::optimization::MinimizerOptions
• GoapEnergy() : core::scoring::methods::GoapEnergy
• GoapRsdType() : core::scoring::methods::GoapRsdType
• graph() : core::chemical::ResidueType
• Graph() : core::graph::Graph
• GridInfo() : core::scoring::geometric_solvation::GridInfo
• gridpt() : core::grid::CartGrid< T >
• group() : core::conformation::ResidueKinWriter
• group1_resstring() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• group1_selector() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• group1_set() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• group2_resstring() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• group2_selector() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• group2_set() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• grsa_sc_feature() : core::scoring::methods::ProQ_Energy
• gss_sc_feature() : core::scoring::methods::ProQ_Energy