- r -

• r : core::optimization::EItem , core::scoring::packstat::Circle
• r0 : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• r0_ : core::scoring::ResidualDipolarCoupling
• r1 : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• r1_ : core::scoring::ResidualDipolarCoupling
• r2 : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• r2_ : core::scoring::ResidualDipolarCoupling
• r_ : core::scoring::packing::Ball
• R_ : core::scoring::ResidualDipolarCoupling
• r_cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_cell_dimensions : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_cell_volume : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• r_chi2 : core::scoring::saxs::FastSAXSEnergy
• r_ids_ : core::scoring::saxs::SAXSEnergy
• r_param : core::scoring::APBSConfig
• radii_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots , core::scoring::sc::MolecularSurfaceCalculator
• radii_set_ : core::scoring::sasa::SasaMethod
• radius : core::scoring::packstat::SimplePDB_Atom , core::scoring::packstat::Sphere , core::scoring::PQR , core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::Atom
• radius_ : core::chemical::SetNbrRadius , core::scoring::packstat::CavityBall
• radmax : core::scoring::sc::MolecularSurfaceCalculator
• ram_counts_ : core::scoring::Ramachandran
• ram_energ_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• ram_energ_left_ : core::scoring::Ramachandran2B
• ram_energ_right_ : core::scoring::Ramachandran2B
• ram_entropy_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• ram_entropy_left_ : core::scoring::Ramachandran2B
• ram_entropy_right_ : core::scoring::Ramachandran2B
• ram_probabil_ : core::scoring::Ramachandran
• rama2b_ : core::scoring::ScoringManager
• rama2bo_ : core::scoring::ScoringManager
• rama_ : core::scoring::Rama2BOffset , core::scoring::ScoringManager
• rama_energy_splines_ : core::scoring::Ramachandran
• rama_sampling_factor_ : core::scoring::Ramachandran
• rama_sampling_thold_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• rama_score_limit_ : core::scoring::Ramachandran2B
• ramp_width_A2_ : core::scoring::methods::LK_BallEnergy
• ran_annealing_since_pair_energy_table_cleared_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• randomize_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval
• randomize_missing_coords_ : core::io::pdb::FileDataOptions
• range2_is_bound_ : core::conformation::symmetry::SymDof
• range_pair_ : core::scoring::Hairpin
• rank : core::graph::DS_Node
• ratio_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• raw_parent_ : core::kinematics::tree::Atom_
• rb_center : core::kinematics::Jump
• rb_delta : core::kinematics::Jump
• rb_jump_ : core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface
• RCCO_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• RcellDimensions : core::scoring::electron_density::ElectronDensity
• rdc : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• rdcconst : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• rdcconst_ : core::scoring::ResidualDipolarCoupling
• rdcweight : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• rdcweight_ : core::scoring::ResidualDipolarCoupling
• reached_ : core::kinematics::AtomWithDOFChange
• reactivity_ : core::io::rna::RDAT
• reactivity_error_ : core::io::rna::RDAT
• read_fold_tree_ : core::import_pose::ImportPoseOptions
• read_link_records_ : core::io::pdb::PDB_DReaderOptions
• read_pdb_header_ : core::io::pdb::PDB_DReaderOptions
• realatomdata_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• realatomdata_index : core::scoring::rna::chemical_shift::ChemicalShiftData
• recent_history_hash_count_ : core::pack::annealer::FASTERAnnealer
• recent_history_hash_values_ : core::pack::annealer::FASTERAnnealer
• recent_history_head_ : core::pack::annealer::FASTERAnnealer
• recent_history_size_ : core::pack::annealer::FASTERAnnealer , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• recent_network_state_history_ : core::pack::annealer::FASTERAnnealer
• recenter_ : core::conformation::symmetry::SymmData
• record_annealer_trajectory_ : core::pack::annealer::FixbbSimAnnealer
• record_source_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• Reduced_Jdipolar_ : core::scoring::RDC , core::scoring::RDC_Rohl
• ref_atom_ : core::scoring::sc::CloserToAtom
• ref_energy_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleLigandRotamerLibrary
• ref_mini_pose_list_ : core::pose::rna::RNA_IdealCoord
• ref_pose_ : core::scoring::cryst::PhenixInterface
• ref_poses_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• ref_shift : core::scoring::rna::chemical_shift::ChemicalShiftData
• ref_tags_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• reference_coords_ : core::scoring::NeighborList
• reference_intensities_ : core::scoring::saxs::SAXSEnergy
• reference_shifts_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• region : core::util::Line
• regular_half_width : core::pose::rna::RNA_SuiteName
• REJECTED : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• rel_deriv_dev : core::optimization::symmetry::MinDebug
• rel_deriv_dev_ : core::optimization::SimpleDerivCheckResult
• rel_hydrophobic_sasa_by_charge_ : core::scoring::sasa::SasaCalc
• relative_tmh_ori_ : core::scoring::MembraneTopology
• relaxed1_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed2_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed_state_ : core::pack::interaction_graph::FASTERNode
• remap_pdb_atom_names_ : core::chemical::ResidueType
• remap_symm_ : core::scoring::electron_density::ElectronDensity
• remarks : core::io::pdb::FileData
• remarks_ : core::pose::PDBInfo
• remember_unrecognized_res_ : core::io::pdb::FileDataOptions
• remember_unrecognized_water_ : core::io::pdb::FileDataOptions
• renumber_decoys_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• rep_weight_ : core::scoring::etable::EtableEvaluator
• repacking_ : core::pack::task::ResidueLevelTask_
• replaces_residue_type_ : core::chemical::Patch
• report_this_as_effective_sequence_separation_ : core::scoring::constraints::MultiConstraint
• reps_for_nonzero_rank_ccs_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• repulsive : core::scoring::etable::AtomPairEnergy
• required_context_graphs_ : core::scoring::Energies
• res : core::scoring::packstat::SimplePDB_Atom
• res1 : core::pose::rna::BasePair , core::pose::rna::BaseStack
• res1_ : core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC
• res1_conn_dist_ : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• res1_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res1_cp_data_ : core::scoring::vdwaals::VDWTrieCountPair1B
• res1_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res1_dat_ : core::scoring::hbonds::HBondResPairMinData
• res1_data_ : core::scoring::methods::LKB_ResPairMinData
• res1_inds_ : core::scoring::disulfides::DisulfMinData
• res1_nb_ : core::scoring::hbonds::HBondEnergy
• res1_pbconn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2 : core::pose::rna::BasePair , core::pose::rna::BaseStack
• res2_ : core::scoring::CSA , core::scoring::DC , core::scoring::hbonds::HBondEnergy , core::scoring::RDC
• res2_conn_dist_ : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• res2_conn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2_cp_data_ : core::scoring::vdwaals::VDWTrieCountPair1B
• res2_cpdat_ : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairGeneric
• res2_dat_ : core::scoring::hbonds::HBondResPairMinData
• res2_data_ : core::scoring::methods::LKB_ResPairMinData
• res2_inds_ : core::scoring::disulfides::DisulfMinData
• res2_nb_ : core::scoring::hbonds::HBondEnergy
• res2_pbconn_point_path_dists_ : core::scoring::etable::count_pair::CountPairGeneric
• res2jumps_ : core::kinematics::ShortestPathInFoldTree
• res3_ : core::scoring::CSA
• res_ : core::scoring::constraints::BigBinConstraint , core::scoring::RDC_Rohl
• res_aa : core::scoring::rna::chemical_shift::ChemicalShiftData
• res_aa_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• res_collections_ : core::pack::scmin::AtomTreeCollection
• res_id_ : core::chemical::ResConnID
• res_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• res_interacts_with_asymmetric_unit_ : core::optimization::symmetry::SymMinimizerMap
• res_labels_ : core::scoring::packstat::SimplePDB
• res_list_ : core::pose::full_model_info::FullModelInfo , core::scoring::methods::ReferenceEnergyNoncanonical
• res_map_ : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T >
• res_min_data_ : core::scoring::MinimizationNode
• res_name_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• res_num_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_pair_min_data_ : core::scoring::MinimizationEdge
• res_size_ : core::scoring::packing::HolesParamsRes
• res_to_average_hASA_ : core::pack::interaction_graph::SurfacePotential
• res_type_linking_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• resA_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• resB_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• rescover : core::scoring::motif::MotifHits
• resfile_filename_ : core::pack::task::operation::ReadResfile
• resi1_ : core::scoring::motif::ResPairMotif
• resi2_ : core::scoring::motif::ResPairMotif
• resi_ : core::fragment::picking_old::vall::VallResidue
• resID1 : core::io::pdb::LinkInformation
• resID2 : core::io::pdb::LinkInformation
• resid_ : core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RotamerExplosion
• resid_2_bgenumeration_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• resid_2_connid_map_ : core::scoring::trie::RotamerTrieBase
• resid_2_disulfide_index_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• resid_2_moltenres_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• resid_2_moltenresid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• reside_type_param_map_ : core::scoring::mm::MMBondAngleResidueTypeParamSet
• residue : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::Atom
• residue1 : core::scoring::motif::MotifHit
• residue2 : core::scoring::motif::MotifHit
• residue_ : core::conformation::UltraLightResidue
• residue_change_id_ : core::kinematics::ResidueCoordinateChangeList
• residue_connection_data_ : core::scoring::etable::etrie::CountPairDataGeneric
• residue_connections_ : core::chemical::ResidueType
• residue_connid_for_entry_connid_ : core::scoring::trie::CPDataCorrespondence
• residue_coord_workspace_ : core::pack::scmin::CartSCMinMinimizerMap
• residue_coordinates_need_updating_ : core::conformation::Conformation
• residue_dEdN_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• residue_E_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_group_for_rotamers_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_group_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_hsasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_id_ : core::conformation::AtomGraphVertexData
• residue_indices_ : core::pack::task::operation::OperateOnCertainResidues
• residue_info_ : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• residue_list_ : core::conformation::parametric::Parameters
• residue_N_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_numbers_ : core::io::silent::SilentStruct
• residue_pair_constraints_ : core::scoring::constraints::ConstraintSet
• residue_rec_ : core::pose::PDBInfo
• residue_rel_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy
• residue_sasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_selection_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::PreventRepacking
• residue_selector_ : core::pack::task::operation::OperateOnResidueSubset
• residue_set_ : core::coarse::TranslatorSet
• residue_tasks_ : core::pack::task::PackerTask_
• residue_torsions_need_updating_ : core::conformation::Conformation
• residue_total_energies_ : core::scoring::Energies
• residue_total_energies_uptodate_ : core::scoring::Energies
• residue_total_energy_ : core::scoring::Energies
• residue_total_energy_uptodate_ : core::scoring::Energies
• residue_type_ : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::rna::RNA_ResidueType
• residue_type_for_rotamers_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_type_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_type_set_ : core::chemical::ResidueType , core::import_pose::ImportPoseOptions
• residue_type_set_tag_ : core::chemical::ResidueLoaderOptions
• residue_type_sets_ : core::chemical::ChemicalManager
• residue_types_ : core::chemical::ResidueTypeSet , core::scoring::BB_Pos
• residue_types_const_ : core::chemical::ResidueTypeSet
• residue_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• residues_ : core::conformation::Conformation , core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::scoring::packing::HolesParamsRes
• residues_for_atom_name_remapping_ : core::io::pdb::FileDataOptions
• residues_info_ : core::scoring::methods::LKB_ResiduesInfo
• residues_to_prevent_ : core::pack::task::operation::PreventRepacking
• residues_to_restrict_to_repacking_ : core::pack::task::operation::RestrictResidueToRepacking
• resl_params_ : core::scoring::packing::HolesEnergy
• resl_score : core::scoring::packing::HolesResult
• reslibraries_ : core::pack::dunbrack::RotamerLibrary
• resmap1_ : core::scoring::motif::MotifHits
• resmap2_ : core::scoring::motif::MotifHits
• resName : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation
• resName1 : core::io::pdb::LinkInformation
• resName2 : core::io::pdb::LinkInformation
• resnum : core::scoring::packstat::SimplePDB_Atom
• resnum_ : core::pack::task::operation::AppendResidueRotamerSet
• reso : core::scoring::electron_density::ElectronDensity
• resolve_ : core::coarse::CoarseEtable
• resSeq : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• resSeq1 : core::io::pdb::LinkInformation
• resSeq2 : core::io::pdb::LinkInformation
• restype2_ : core::chemical::AutomorphismIterator
• restype_ : core::chemical::AutomorphismIterator , core::chemical::orbitals::AssignOrbitals , core::chemical::RerootEdgeSorter , core::chemical::RerootRestypeVisitor , core::chemical::RigidDistanceVisitor
• restype_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• restype_group_for_rotamers_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• restype_index_ : core::pack::scmin::ResidueAtomTreeCollectionMomento
• restypegroup_adjacency_ : core::pack::interaction_graph::SymmOnTheFlyEdge
• restypeinfo_ : core::scoring::FACTSResidueInfo
• result : core::scoring::APBSWrapper
• results : core::scoring::sc::MolecularSurfaceCalculator
• return_val_ : core::scoring::func::ConstantFunc
• reverse_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• revision_id_ : core::scoring::constraints::ConstraintSet
• revision_id_current_ : core::scoring::constraints::ConstraintSet
• reweight_ : core::scoring::methods::D2H_SA_Energy
• reweight_symm_interactions_ : core::conformation::symmetry::SymmetryInfo
• rg : core::scoring::methods::RG_MinData
• rg_ : core::scoring::rna::RG_Energy_RNA
• rho_ : core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore
• rho_calc : core::scoring::electron_density::ElectronDensity
• rho_calc_as : core::scoring::electron_density::ElectronDensity
• rho_calc_atms : core::scoring::electron_density::ElectronDensity
• rho_calc_sum : core::scoring::electron_density::ElectronDensity
• rho_solv : core::scoring::electron_density::ElectronDensity
• rhq_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• rhs_ : core::scoring::ResidualDipolarCoupling
• right_ : core::pack::dunbrack::BBIndNRChiSample< P > , core::scoring::interface_::DDPlookup
• right_cdf_ : core::scoring::Ramachandran2B
• right_cdf_by_torsion_bin_ : core::scoring::Ramachandran2B
• right_ram_probabil_ : core::scoring::Ramachandran2B
• rinfo_ : core::io::pdb::GeometricRenameIsomorphismCallback
• ring_ : core::chemical::Bond
• ring_height_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_intensity_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_radius_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_size_ : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::RingConformerSet
• rings_and_their_edges_ : core::chemical::ResidueType
• rltoc_map_ : core::pack::task::operation::ResLvlTaskOperationFactory
• rmax_ : core::scoring::func::MixtureFunc
• rms : core::scoring::motif::MotifHit
• rms_target_ : core::scoring::methods::RMS_Energy
• rmsd_ : core::scoring::ResidualDipolarCoupling
• rna_ : core::import_pose::ImportPoseOptions
• rna_atom_vdw_ : core::scoring::rna::RNA_VDW_Energy , core::scoring::ScoringManager
• rna_axis_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_potential_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_weight_ : core::scoring::rna::RNA_LowResolutionPotential
• RNA_backbone_oxygen_atoms_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_backbone_xy_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_radius_cutoff2_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_radius_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_stagger_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_basepair_xy_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_bond_geometry_energy_ : core::scoring::constraints::ConstraintEdge
• rna_centroid_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_ch_o_bond_distance_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_chemical_shift_potential_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::ScoringManager
• rna_cos_theta_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_cos_theta_fade_zone_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_cs_params_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• rna_data_ : core::scoring::rna::data::RNA_DataInfo
• rna_data_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_data_info_with_conventional_numbering_ : core::io::rna::RNA_DataReader
• rna_dms_low_resolution_potential_ : core::scoring::ScoringManager
• rna_dms_potential_ : core::scoring::ScoringManager
• rna_filtered_base_base_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_fitted_torsion_info_ : core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionPotential
• rna_gaussian_variance_per_residue_ : core::scoring::loop_graph::LoopGraph
• rna_low_resolution_potential_ : core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::ScoringManager
• rna_mg_knowledge_based_potential_ : core::scoring::rna::RNA_Mg_Energy
• rna_options_ : core::scoring::methods::EnergyMethodOptions
• rna_raw_base_base_info_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_ScoringInfo
• rna_reactivities_ : core::scoring::rna::data::RNA_DataInfo
• rna_repulse_all_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_max_penalty_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_screen_scale_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_weight_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_residue_type_ : core::chemical::ResidueType
• rna_stagger_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_sugar_close_constraints_ : core::scoring::rna::RNA_SugarCloseEnergy
• rna_suite_name_ : core::scoring::rna::RNA_SuitePotential
• rna_suite_potential_ : core::scoring::rna::RNA_SuiteEnergy
• rna_suite_potential_for_suiteness_bonus_ : core::scoring::rna::RNA_SuiteEnergy
• rna_task_ : core::pack::task::ResidueLevelTask_
• rna_tight_torsions_ : core::chemical::rna::RNA_FittedTorsionInfo
• rna_torsion_potential_ : core::scoring::rna::RNA_TorsionEnergy
• rna_vdw_atom_ : core::scoring::rna::RNA_AtomVDW
• rna_vdw_parameter_ : core::scoring::rna::RNA_AtomVDW
• rna_verbose_ : core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_LowResolutionPotential
• root_ : core::chemical::RerootRestypeVisitor , core::conformation::symmetry::SymmData , core::kinematics::AtomTree
• root_atom_ : core::chemical::ResidueType , core::scoring::methods::GoapRsdType
• rosetta_atom_name_ : core::chemical::AddAtomAlias
• ROSETTA_SASA_radii_ : core::pack::interaction_graph::RotamerDotsRadiusData
• rot : core::pack::dunbrack::ChiSet
• rot_ : core::pack::dunbrack::CoarseRotamer
• rot_bin_ : core::pack::dunbrack::DunbrackConstraint
• rot_freq_ : core::pack::annealer::SimAnnealerBase
• rot_to_pack_ : core::pack::annealer::RotamerAssigningAnnealer
• rot_vec_pos_ : core::pack::dunbrack::DunbrackConstraint
• rot_well_ : core::pack::dunbrack::DunbrackRotamerSampleData
• ROT_X : core::kinematics::Jump
• ROT_Y : core::kinematics::Jump
• ROT_Z : core::kinematics::Jump
• rotamer_ : core::pack::dunbrack::RotamericData< T > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots
• rotamer_aa_ : core::chemical::ResidueType
• rotamer_couplings_ : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::task::operation::SetRotamerCouplings , core::pack::task::PackerTask_
• rotamer_energies_ : core::pack::interaction_graph::DoubleDensePDNode
• rotamer_id_ : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• rotamer_library_name_ : core::chemical::ResidueType
• rotamer_links_ : core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::task::operation::SetRotamerLinks , core::pack::task::PackerTask_
• rotamer_offsets_require_update_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• rotamer_operation_ : core::pack::task::operation::AppendRotamer
• rotamer_operations_ : core::pack::task::ResidueLevelTask_
• rotamer_probability_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotamer_representatives_ : core::pack::interaction_graph::SymmOnTheFlyNode
• rotamer_seq_sep_ : core::scoring::hbonds::HBondEnergy
• rotamer_set_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• rotamer_set_operation_ : core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamerSet
• rotamer_sets_ : core::pack::annealer::FASTERAnnealer , core::pack::annealer::RotamerAssigningAnnealer , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::rotamer_set::ContinuousRotamerSets
• rotamerid : core::pack::annealer::RotSub
• rotamers_ : core::pack::dunbrack::CoarseRotamerSet , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• rotamers_in_subtree_ : core::scoring::trie::TrieNode< AT, CPDATA >
• rotamers_vector_ : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• rotation : core::kinematics::RT
• rotation_matrices_ : core::conformation::symmetry::SymmData
• rotE_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophipsi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecopsi_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotlib_ : core::pack::dunbrack::RotamerConstraint
• rotno_2_packed_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• rots_for_nodes_ : core::pack::annealer::RotamerAssigningAnnealer
• rotsetops_ : core::pack::task::ResidueLevelTask_
• rotwell_ : core::pack::dunbrack::DunbrackRotamer< S, P > , core::pack::dunbrack::RotamerLibraryScratchSpace
• rotwell_exists_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rp : core::scoring::sc::MolecularSurfaceCalculator
• rsa_class_pred_ : core::scoring::methods::ProQ_Energy
• rsa_index_end_ : core::scoring::methods::D2H_SA_Energy
• rsa_index_start_ : core::scoring::methods::D2H_SA_Energy
• rsa_pred_ : core::scoring::methods::ProQ_Energy
• rsd1_ : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::scoring::func::ResiduePairXYZ
• rsd1_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd2_ : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator > , core::scoring::func::ResiduePairXYZ
• rsd2_type_name3_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• rsd_ : core::id::AtomID , core::id::NamedAtomID , core::id::TorsionID , core::scoring::AtomNeighbor , core::scoring::func::ResidueXYZ
• rsd_hsasa_ : core::scoring::sasa::SasaCalc
• rsd_hsasa_sc_ : core::scoring::sasa::SasaCalc
• rsd_id_ : core::optimization::SingleResidueMultifunc
• RSD_OMG_INDEX : core::pack::dunbrack::SingleResiduePeptoidLibrary
• RSD_PHI_INDEX : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• RSD_PSI_INDEX : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rsd_sasa_ : core::scoring::sasa::SasaCalc
• rsd_sasa_sc_ : core::scoring::sasa::SasaCalc
• rsd_type_ : core::conformation::Residue
• rsd_type_name3_ : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint
• rsd_type_name_ : core::pack::dunbrack::RotamerConstraint
• rsdgrps_ : core::scoring::elec::GroupElec
• rsdtype_ : core::io::pdb::GeometricRenameIsomorphismCallback , core::io::pdb::GeometricRenameVerticiesEquivalent
• rsdtypemap_ : core::scoring::methods::GoapEnergy
• rsigma_dot_ : core::scoring::SecondaryStructurePotential
• rswitch_ : core::scoring::constraints::BoundFunc
• RT : core::scoring::dna::DirectReadoutPotential
• rt6_ : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfrag
• rt_ : core::fragment::DownJumpSRFD , core::kinematics::Jump
• run_ : core::scoring::sc::MolecularSurfaceCalculator
• RV : core::scoring::electron_density::ElectronDensity