Here is a list of all class members with links to the classes they belong to:

- r -

• r : core::optimization::EItem , core::scoring::packing::Ball , core::scoring::packstat::Circle
• R() : core::scoring::ResidualDipolarCoupling
• 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
• R_PARAM() : core::scoring::APBSConfig::R_PARAM
• 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::packing::Ball , core::scoring::packstat::CavityBall , 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
• radius_for_attype() : core::pack::interaction_graph::RotamerDots
• 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
• Rama2BOffset() : core::scoring::Rama2BOffset
• Rama2BOffsetEnergy() : core::scoring::methods::Rama2BOffsetEnergy
• rama_ : core::scoring::Rama2BOffset , core::scoring::ScoringManager
• rama_bin_probability_left() : core::scoring::Ramachandran2B
• rama_bin_probability_right() : core::scoring::Ramachandran2B
• rama_energy_splines_ : core::scoring::Ramachandran
• rama_probability() : core::scoring::Ramachandran
• rama_sampling_factor_ : core::scoring::Ramachandran
• rama_sampling_thold_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• rama_score_limit_ : core::scoring::Ramachandran2B
• Ramachandran() : core::scoring::Ramachandran
• Ramachandran2B() : core::scoring::Ramachandran2B
• RamachandranEnergy() : core::scoring::methods::RamachandranEnergy
• RamachandranEnergy2B() : core::scoring::methods::RamachandranEnergy2B
• RamaE() : core::scoring::Ramachandran2B
• RamaE_Lower() : core::scoring::Ramachandran2B
• RamaE_Upper() : 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
• random_bin() : core::scoring::bin_transitions::BinTransitionCalculator
• random_bin_based_on_prev_and_next() : core::scoring::bin_transitions::BinTransitionCalculator
• random_bin_based_on_previous() : core::scoring::bin_transitions::BinTransitionCalculator
• random_bin_i() : core::scoring::bin_transitions::BinTransitionData
• random_bin_iplus1() : core::scoring::bin_transitions::BinTransitionData
• random_bin_iplus1_given_i() : core::scoring::bin_transitions::BinTransitionData
• random_mainchain_torsions_from_bin() : core::scoring::bin_transitions::BinTransitionCalculator
• random_mainchain_torsions_from_bins() : core::scoring::bin_transitions::BinTransitionCalculator
• random_mainchain_torsions_using_adjacent_bins() : core::scoring::bin_transitions::BinTransitionCalculator
• random_phipsi_from_rama() : core::scoring::Ramachandran
• random_phipsi_from_rama_by_torsion_bin() : core::scoring::Ramachandran
• random_phipsi_from_rama_by_torsion_bin_left() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_by_torsion_bin_right() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_left() : core::scoring::Ramachandran2B
• random_phipsi_from_rama_right() : core::scoring::Ramachandran2B
• random_tempname() : core::pack::dunbrack::RotamerLibrary
• random_trans() : core::kinematics::Jump
• random_tree_from_jump_points() : core::kinematics::FoldTree
• randomize() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::optimization::GA_Minimizer
• 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::FileData , core::io::pdb::FileDataOptions
• randomize_missing_coords_ : core::io::pdb::FileDataOptions
• range() : core::scoring::PairEPotential
• range1_lower() : core::conformation::symmetry::SymDof
• range1_upper() : core::conformation::symmetry::SymDof
• range2_is_bound() : core::conformation::symmetry::SymDof
• range2_is_bound_ : core::conformation::symmetry::SymDof
• range2_lower() : core::conformation::symmetry::SymDof
• range2_upper() : core::conformation::symmetry::SymDof
• range_check() : core::environment::FoldTreeSketch , core::scoring::dssp::StrandPairing
• range_pair_ : core::scoring::Hairpin
• RANGE_RESID : core::pack::task::ResfileContents
• rank : core::graph::DS_Node
• ratio() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• ratio_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• raw_array() : core::scoring::APBSConfig::I_PARAM , core::scoring::APBSConfig::R_PARAM
• raw_child_index() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_get_nonjump_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_input_stub_atom0() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_input_stub_atom1() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_input_stub_atom2() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_input_stub_atom3() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_parent() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_parent_ : core::kinematics::tree::Atom_
• raw_previous_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_previous_sibling() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• raw_stub_atom1() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• raw_stub_atom2() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• raw_stub_atom3() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• RawFileData() : core::io::raw_data::RawFileData
• rb_center : core::kinematics::Jump
• rb_delta : core::kinematics::Jump
• rb_index() : core::kinematics::Jump
• RB_JUMP : core::pose::datacache::CacheableDataType
• RCCO_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• RcellDimensions : core::scoring::electron_density::ElectronDensity
• RDAT() : core::io::rna::RDAT
• rdc : core::scoring::data_struct , core::scoring::data_structDa , core::scoring::data_structDaR , core::scoring::data_structR
• RDC() : core::scoring::RDC
• rdc_from_pose() : core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• RDC_lines : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl
• RDC_Rohl() : core::scoring::RDC_Rohl
• RDC_TYPE : core::scoring::RDC
• RDC_TYPE_CC : core::scoring::RDC
• RDC_TYPE_CH : core::scoring::RDC
• RDC_TYPE_CHN : core::scoring::RDC
• RDC_TYPE_NC : core::scoring::RDC
• RDC_TYPE_NCA : core::scoring::RDC
• RDC_TYPE_NH : core::scoring::RDC
• 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_ : core::io::rna::RDAT
• reactivity_error() : core::io::rna::RDAT
• reactivity_error_ : core::io::rna::RDAT
• read() : core::chemical::ElectronConfiguration , core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData , core::conformation::symmetry::SymDof , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::DownJumpSRFD , core::fragment::Frame , core::fragment::NonContinuousFrame , core::grid::CartGrid< T > , core::io::serialization::BUFFER
• read_aa_encoding_matrix() : core::scoring::methods::NMerSVMEnergy
• read_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• read_acc() : core::scoring::methods::ProQ_Energy
• read_all_files_() : core::import_pose::pose_stream::SilentFilePoseInputStream
• read_alternate_parameter_set() : core::scoring::etable::Etable
• read_and_set_properties() : core::chemical::carbohydrates::CarbohydrateInfo
• read_angle_database() : core::scoring::methods::IdealParametersDatabase
• read_angle_definitions() : core::scoring::methods::GoapEnergy
• read_angles() : core::scoring::sasa::LeGrandSasa
• read_atom_type_extra_parameters_table() : core::chemical::AtomTypeSet
• read_atom_type_properties_table() : core::chemical::AtomTypeSet
• read_average_res_hASA_database_file() : core::pack::interaction_graph::SurfacePotential
• read_backbone_info() : core::io::rna::RNA_DataReader
• read_bbdep_continuous_minimization_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• read_bbdep_table() : core::scoring::methods::IdealParametersDatabase
• read_bbind_continuous_minimization_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• read_binary() : core::scoring::motif::XformScore
• read_bond_file() : core::chemical::gasteiger::GasteigerAtomTypeSet
• read_constraint() : core::scoring::constraints::Constraint
• read_constraints() : core::scoring::constraints::ConstraintIO
• read_constraints_new() : core::scoring::constraints::ConstraintIO
• read_CSA_file() : core::scoring::ChemicalShiftAnisotropy
• read_cst_angles() : core::scoring::constraints::ConstraintIO
• read_cst_atom_pairs() : core::scoring::constraints::ConstraintIO
• read_cst_bindingsites() : core::scoring::constraints::ConstraintIO
• read_cst_coordinates() : core::scoring::constraints::ConstraintIO
• read_cst_file() : core::pose::full_model_info::FullModelParameters
• read_data() : core::fragment::BBTorsionSRFD , core::fragment::FragmentIO , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::scoring::constraints::BoundFunc , core::scoring::constraints::Constraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::sequence::MatrixScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment
• read_data_file() : core::scoring::packing::HolesParams , core::scoring::packing::HolesParamsRes
• read_data_from_file() : core::io::rna::RNA_DataReader
• read_data_from_rdat() : core::io::rna::RNA_DataReader
• read_data_info() : core::io::rna::RNA_DataReader
• read_database_file() : core::scoring::UnfoldedStatePotential
• read_datafile() : core::scoring::geometric_solvation::DatabaseOccSolEne
• read_DC_file() : core::scoring::DipolarCoupling
• read_def() : core::pack::dunbrack::DunbrackConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues
• read_disulfide_database() : core::scoring::disulfides::DisulfideMatchingDatabase
• read_disulfides() : core::pose::full_model_info::FullModelParameters
• read_DMS_low_resolution_stats_file() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• read_DMS_stats_file() : core::scoring::rna::data::RNA_DMS_Potential
• read_energy_weight_table() : core::scoring::methods::SequenceDependentRefEnergy
• read_file() : core::chemical::AtomTypeSet , core::chemical::ElementSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::IdealBondLengthSet , core::chemical::MMAtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , core::chemical::Patch , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::io::silent::SilentFileData
• read_files() : core::chemical::ResidueTypeSet
• read_fold_tree() : core::import_pose::ImportPoseOptions
• read_fold_tree_ : core::import_pose::ImportPoseOptions
• read_frag_data() : core::fragment::FragmentIO
• read_fragment_file() : core::fragment::ConstantLengthFragSet
• read_fragment_stream() : core::fragment::ConstantLengthFragSet
• read_from_binary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• read_from_binary_chk() : core::sequence::SequenceProfile
• read_from_checkpoint() : core::sequence::SequenceProfile
• read_from_database() : core::sequence::MatrixScoringScheme
• read_from_file() : core::fragment::SecondaryStructure , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::sequence::ChemicalShiftSequence , core::sequence::CompositeScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , core::sequence::SimpleScoringScheme
• read_from_files() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• read_full_model_parameters_from_remark() : core::io::silent::SilentFileData
• read_Goap_parameters() : core::scoring::methods::GoapEnergy
• read_hASA_score_database_file() : core::pack::interaction_graph::SurfacePotential
• read_hpatch_score_database_file() : core::pack::interaction_graph::SurfacePotential
• read_in_and_set_disulfides() : core::io::raw_data::DisulfideFile
• read_in_spanfile() : core::scoring::MembraneTopology
• read_individual_constraint_new() : core::scoring::constraints::ConstraintIO
• read_intensities() : core::scoring::saxs::SAXSEnergy
• read_length_database() : core::scoring::methods::IdealParametersDatabase
• read_link_records() : core::io::pdb::PDB_DReaderOptions
• read_link_records_ : core::io::pdb::PDB_DReaderOptions
• read_list_of_residues() : core::chemical::ResidueTypeSet
• read_masks() : core::scoring::sasa::LeGrandSasa
• read_mpSA() : core::scoring::methods::ProQ_Energy
• read_next_frames() : core::fragment::FragmentIO
• read_nmer_pssm() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_pssm_list() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_pssms_from_options() : core::scoring::methods::NMerPSSMEnergy
• read_nmer_svm() : core::scoring::methods::NMerSVMEnergy
• read_nmer_svm_list() : core::scoring::methods::NMerSVMEnergy
• read_nmer_svms_from_options() : core::scoring::methods::NMerSVMEnergy
• read_nmer_table() : core::scoring::methods::NMerRefEnergy
• read_nmer_table_list() : core::scoring::methods::NMerRefEnergy
• read_nmer_tables_from_options() : core::scoring::methods::NMerRefEnergy
• read_omega_tables() : core::scoring::OmegaTether
• read_options() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• read_P_AA() : core::scoring::P_AA
• read_P_AA_n() : core::scoring::P_AA
• read_P_AA_pp() : core::scoring::P_AA
• read_paapp_table_from_stream() : core::scoring::Rama2BOffset
• read_paapp_tables() : core::scoring::Rama2BOffset
• read_pdb_header() : core::io::pdb::PDB_DReaderOptions
• read_pdb_header_ : core::io::pdb::PDB_DReaderOptions
• read_pose() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• read_potential() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::methods::dfire::DFIRE_Potential
• read_potential_values() : core::scoring::methods::GoapEnergy
• read_profiles_and_entropy() : core::scoring::methods::ProQ_Energy
• read_psipred_ss2() : core::fragment::SecondaryStructure
• read_r2bo_tables() : core::scoring::Rama2BOffset
• read_rama() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• read_rama_map_file() : core::scoring::Ramachandran
• read_rama_map_file_shapovalov() : core::scoring::Ramachandran
• read_rdat_file() : core::io::rna::RDAT
• read_RDC_file() : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl
• read_reactivity_info() : core::io::rna::RNA_DataReader
• read_residue_type() : core::chemical::ResidueDatabaseIO
• read_residue_type_atom() : core::chemical::ResidueDatabaseIO
• read_residue_type_bond() : core::chemical::ResidueDatabaseIO
• read_residue_type_chi() : core::chemical::ResidueDatabaseIO
• read_residue_type_chi_rotamer() : core::chemical::ResidueDatabaseIO
• read_residue_type_cut_bond() : core::chemical::ResidueDatabaseIO
• read_residue_type_icoor() : core::chemical::ResidueDatabaseIO
• read_residue_type_properties() : core::chemical::ResidueDatabaseIO
• read_residue_type_proton_chi() : core::chemical::ResidueDatabaseIO
• read_residue_type_variant() : core::chemical::ResidueDatabaseIO
• read_residuetype_from_database() : core::chemical::ResidueDatabaseIO
• read_rotamer_definitions() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• read_rotameric_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• read_score_headers() : core::io::silent::SilentStruct
• read_sequence() : core::io::silent::SilentStruct
• read_silent_struct() : core::conformation::symmetry::SymmetryInfo
• read_silent_struct_type_from_remark() : core::io::silent::SilentFileData
• read_spectrum() : core::scoring::saxs::SAXSEnergy
• read_ss2() : core::scoring::methods::ProQ_Energy
• read_stream() : core::io::silent::SilentFileData
• read_symmetry_data_from_file() : core::conformation::symmetry::SymmData
• read_symmetry_data_from_stream() : core::conformation::symmetry::SymmData
• read_table_from_stream() : core::scoring::OmegaTether , core::scoring::Rama2BOffset
• read_tags_fast() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• read_talos_ss() : core::fragment::SecondaryStructure
• read_torsion_database() : core::scoring::methods::IdealParametersDatabase
• read_zpred() : core::scoring::methods::ProQ_Energy
• readMRCandResize() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• ReadResfile() : core::pack::task::operation::ReadResfile
• ReadResfileAndObeyLengthEvents() : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• ReadScRadii() : core::scoring::sc::MolecularSurfaceCalculator
• ready_for_nonideal_scoring() : core::scoring::ScoreFunction
• Real : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallResidue , core::pose::PDBInfo , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::sequence::ABEGO , core::sequence::ABEGOManager
• real_groups : core::indexed_structure_store::FragmentStore
• realatomdata_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• realatomdata_index : core::scoring::rna::chemical_shift::ChemicalShiftData
• RealFilter() : core::chemical::RealFilter
• reassign_atoms_for_intra_residue_stubs() : core::kinematics::FoldTree
• rebuild_pdb2pose() : core::pose::PDBInfo
• rebuild_polymer_bond_dependent_atoms() : core::conformation::Conformation
• rebuild_polymer_bond_dependent_atoms_this_residue_only() : core::conformation::Conformation
• rebuild_residue_connection_dependent_atoms() : core::conformation::Conformation
• recalculate_transforms() : core::conformation::symmetry::SymmetricConformation
• receive_observers_from() : core::conformation::Conformation
• 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
• reciprocalSpaceFilter() : core::scoring::electron_density::ElectronDensity
• recompute() : core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::metrics::StructureDependentCalculator
• recompute_parameters() : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc
• record_annealer_trajectory() : core::pack::annealer::FixbbSimAnnealer
• record_annealer_trajectory_ : core::pack::annealer::FixbbSimAnnealer
• record_source_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• redefine_chi() : core::chemical::ResidueType
• RedefineChi() : core::chemical::RedefineChi
• rederive_chain_endings() : core::conformation::Conformation
• rederive_chain_ids() : core::conformation::Conformation
• Reduced_Jdipolar() : core::scoring::RDC , core::scoring::RDC_Rohl
• 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_pose_for() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• 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 : core::id::AtomID_Map< T >
• reference : core::id::AtomID_Map< T >
• Reference : core::id::DOF_ID_Map< T >
• reference : core::id::DOF_ID_Map< T >
• Reference : core::id::NamedAtomID_Map< T >
• reference : core::id::NamedAtomID_Map< T > , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• reference_conformation() : core::environment::DofPassport
• reference_coords_ : core::scoring::NeighborList
• reference_intensities_ : core::scoring::saxs::SAXSEnergy
• reference_shifts_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• ReferenceEnergy() : core::scoring::methods::ReferenceEnergy
• ReferenceEnergyNoncanonical() : core::scoring::methods::ReferenceEnergyNoncanonical
• refresh_energy_cache() : core::scoring::FACTSResidueInfo
• refresh_ex1_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex2_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex3_sample_levels() : core::pack::task::ResidueLevelTask_
• refresh_ex4_sample_levels() : core::pack::task::ResidueLevelTask_
• region() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet , core::sequence::Line
• region_all() : core::fragment::FragSet
• region_simple() : core::fragment::FragSet
• register_bg_node_affected_by_rotsub() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_calculator() : core::pose::metrics::CalculatorFactory
• register_fc_node_affected_by_rotsub() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_fc_node_in_state0() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• register_ff() : core::scoring::saxs::FormFactorManager
• register_frag_id() : core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T >
• regular_half_width : core::pose::rna::RNA_SuiteName
• regularize_torsions() : core::scoring::rna::RNA_SuitePotential
• rehash_form_factors() : core::scoring::saxs::SAXSEnergy
• reindex_residues() : core::fragment::picking_old::vall::VallSection
• reindex_sections() : core::fragment::picking_old::vall::VallLibrary
• reinitialize_active_energy_methods() : core::scoring::MinimizationEdge
• reinitialize_minnode_for_residue() : core::scoring::ScoreFunction
• reject_change() : core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode
• reject_perturbation() : core::pack::interaction_graph::FASTERInteractionGraph
• REJECTED : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• rel_deriv_dev() : core::optimization::SimpleDerivCheckResult , 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
• relative_tmh_ori_ : core::scoring::MembraneTopology
• relax() : core::pack::interaction_graph::FASTERNode
• relax_after_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• relax_in_current_context() : core::pack::interaction_graph::FASTERInteractionGraph
• relax_neighbors() : core::pack::interaction_graph::FASTERNode
• relaxed1_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed2_ : core::pack::interaction_graph::FASTERInteractionGraph
• relaxed_state_ : core::pack::interaction_graph::FASTERNode
• release_buffers() : core::scoring::ResidualDipolarCoupling
• remap_pdb_atom_names() : core::chemical::ResidueType
• remap_pdb_atom_names_ : core::chemical::ResidueType
• remap_resid() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint
• remap_residue_level_tasks() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• remap_residue_positions() : core::scoring::constraints::ConstraintSet
• remap_symm_ : core::scoring::electron_density::ElectronDensity
• remap_value() : core::fragment::BaseCacheUnit , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T >
• remapped_clone() : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint
• RemarkInfo() : core::pose::RemarkInfo
• remarks : core::io::pdb::FileData , core::pose::PDBInfo
• Remarks : core::pose::PDBInfo
• remarks_ : core::pose::PDBInfo
• rematchResToPatterson() : core::scoring::electron_density::ElectronDensity
• remember_unrecognized_res() : core::io::pdb::FileDataOptions
• remember_unrecognized_res_ : core::io::pdb::FileDataOptions
• remember_unrecognized_water() : core::io::pdb::FileDataOptions
• remember_unrecognized_water_ : core::io::pdb::FileDataOptions
• remove_calculator() : core::pose::metrics::CalculatorFactory
• remove_constraint() : core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet
• remove_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet
• remove_cycles() : core::environment::FoldTreeSketch
• remove_gapped_positions() : core::sequence::SequenceAlignment
• remove_irrelevant_waters() : core::scoring::methods::LKB_ResidueInfo
• remove_method() : core::scoring::ScoreFunction
• remove_other_pose_at_idx() : core::pose::full_model_info::FullModelInfo
• remove_residue_pair_constraint() : core::scoring::constraints::ConstraintSet
• remove_residue_type() : core::chemical::ResidueTypeSet
• remove_residue_type_from_maps() : core::chemical::ResidueTypeSet
• remove_surface_waters() : core::scoring::packstat::SimplePDB
• remove_tag() : core::io::rna::RDAT
• remove_variant_type() : core::chemical::ResidueType
• RemoveHybridization() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• rename_energies() : core::io::silent::SilentStruct
• render() : core::environment::FoldTreeSketch
• render_movemap() : core::environment::DofPassport
• renormalize_weights() : core::scoring::func::SOGFunc_Impl
• renumber_all_decoys() : core::io::silent::SilentFileData
• renumber_decoys() : core::import_pose::pose_stream::SilentFilePoseInputStream
• renumber_decoys_ : core::import_pose::pose_stream::SilentFilePoseInputStream
• renumber_jumps() : core::kinematics::FoldTree
• reorder() : core::kinematics::FoldTree
• reorder_spans() : core::conformation::membrane::SpanningTopology
• rep_scoretype() : core::scoring::etable::BaseEtableEnergy< Derived >
• rep_weight() : core::scoring::etable::EtableEvaluator
• rep_weight_ : core::scoring::etable::EtableEvaluator
• repacking_ : core::pack::task::ResidueLevelTask_
• repacking_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• replace_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• replace_creator() : core::scoring::constraints::ConstraintFactory
• replace_res() : core::pose::PDBInfo
• replace_res_remap_bfactors() : core::pose::PDBInfo
• replace_residue() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose
• replace_residue_subtree() : core::kinematics::AtomTree
• replace_stub1() : core::chemical::orbitals::ICoorOrbitalData
• replace_stub2() : core::chemical::orbitals::ICoorOrbitalData
• replace_stub3() : core::chemical::orbitals::ICoorOrbitalData
• replace_tree() : core::kinematics::AtomTree
• replaces() : core::chemical::Patch
• replaces_residue_type_ : core::chemical::Patch
• ReplicateTask() : core::pack::task::operation::ReplicateTask
• report_adducts() : core::chemical::ResidueType
• report_parameter_features() : core::scoring::hbonds::HBondDatabase
• report_parameter_features_schema_to_db() : core::scoring::hbonds::HBondDatabase
• report_residue_type() : core::chemical::ResidueDatabaseIO
• report_residue_type_atom() : core::chemical::ResidueDatabaseIO
• report_residue_type_bond() : core::chemical::ResidueDatabaseIO
• report_residue_type_chi() : core::chemical::ResidueDatabaseIO
• report_residue_type_chi_rotamer() : core::chemical::ResidueDatabaseIO
• report_residue_type_cut_bond() : core::chemical::ResidueDatabaseIO
• report_residue_type_icoor() : core::chemical::ResidueDatabaseIO
• report_residue_type_properties() : core::chemical::ResidueDatabaseIO
• report_residue_type_proton_chi() : core::chemical::ResidueDatabaseIO
• report_residue_type_variant() : core::chemical::ResidueDatabaseIO
• report_this_as_effective_sequence_separation_ : core::scoring::constraints::MultiConstraint
• representative_atom_name() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• reps_for_nonzero_rank_ccs_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• repulsive : core::scoring::etable::AtomPairEnergy
• request_symmetrize_by_intersection() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• request_symmetrize_by_union() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• require_context_graph() : core::scoring::Energies
• require_context_graph_() : core::scoring::Energies , core::scoring::symmetry::SymmetricEnergies
• require_final() : core::chemical::ResidueType
• require_scoring() : core::scoring::Energies
• required_context_graphs() : core::scoring::Energies
• required_context_graphs_ : core::scoring::Energies
• requires_a_setup_for_derivatives_for_residue_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::LK_BallEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore
• requires_a_setup_for_derivatives_for_residue_pair_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::TwoBodyEnergy
• requires_a_setup_for_scoring_for_residue_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::LK_BallEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::orbitals::OrbitalsScore
• requires_a_setup_for_scoring_for_residue_pair_opportunity() : core::scoring::constraints::ConstraintsEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• requires_actcoord() : core::chemical::ResidueType , core::conformation::Residue
• requires_context_graph() : core::scoring::ScoreFunctionInfo
• RerootEdgeSorter() : core::chemical::RerootEdgeSorter
• RerootRestypeVisitor() : core::chemical::RerootRestypeVisitor
• res() : core::scoring::constraints::BigBinConstraint , core::scoring::packstat::SimplePDB_Atom , core::scoring::RDC_Rohl
• res1 : core::pose::rna::BasePair , core::pose::rna::BaseStack , core::scoring::CSA , core::scoring::DC , core::scoring::RDC
• 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::hbonds::HBondResPairMinData , core::scoring::methods::LKB_ResPairMinData
• 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 , core::scoring::CSA , core::scoring::DC , core::scoring::RDC
• 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::hbonds::HBondResPairMinData , core::scoring::methods::LKB_ResPairMinData
• 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
• res3_ : core::scoring::CSA
• res6() : core::scoring::methods::ProQ_Energy
• 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_changed_history_ : core::scoring::methods::VallLookbackData
• res_collections_ : core::pack::scmin::AtomTreeCollection
• res_cutoff_high : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions
• res_cutoff_low : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions
• res_feature() : core::scoring::methods::ProQ_Energy
• res_for_rotamer() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• res_haslabel() : core::pose::PDBInfo
• res_id_ : core::chemical::ResConnID
• res_identities_i_ : core::scoring::bin_transitions::BinTransitionData
• res_identities_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• res_index() : core::scoring::methods::dfire::DFIRE_Potential
• res_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• res_inds() : core::scoring::disulfides::DisulfMinData
• res_interacts_with_asymmetric_unit_ : core::optimization::symmetry::SymMinimizerMap
• res_labels() : core::scoring::packstat::SimplePDB
• res_labels_ : core::scoring::packstat::SimplePDB
• res_list() : core::pose::full_model_info::FullModelInfo
• 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_min_data_ : core::scoring::MinimizationNode
• res_moved() : core::scoring::Energies
• res_name() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• res_name3_str_ : core::pack::task::residue_selector::ResidueNameSelector
• res_name_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• res_name_str_ : core::pack::task::residue_selector::ResidueNameSelector
• res_num() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_num_ : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_pair_min_data() : core::scoring::MinimizationEdge
• res_pair_min_data_ : core::scoring::MinimizationEdge
• res_res_burial() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• res_res_burial_for_scoring() : core::scoring::FACTSPotential
• res_res_carbon_hbond_derivs_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• res_res_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• res_res_geometric_sol_one_way() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• res_res_occ_sol_one_way() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• res_res_weight() : core::pack::task::IGEdgeReweightContainer
• res_size_ : core::scoring::packing::HolesParamsRes
• res_to_average_hASA_ : core::pack::interaction_graph::SurfacePotential
• res_type_linking_constraint_energy() : core::scoring::constraints::ConstraintEdge
• res_type_linking_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• resA_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• ResAtomIndex : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions
• ResAtomIndexFuncMap : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions
• ResAtomIndexTuple : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions
• resB_atom_index_ : core::scoring::custom_pair_distance::atoms_and_func_struct
• rescale() : core::sequence::SequenceProfile
• rescale_fastscoring_temp_bins() : core::scoring::electron_density::ElectronDensity
• ResConnID() : core::chemical::ResConnID , core::conformation::PseudoBond
• rescover : core::scoring::motif::MotifHits
• reserve() : core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection
• reserve_buffers() : core::scoring::ResidualDipolarCoupling
• reserve_edge_space() : core::graph::UEVertex< V, E >
• reset() : core::import_pose::pose_stream::ExtendedPoseInputStream , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::MetaPoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::kinematics::Jump , core::kinematics::RT , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::pack::rotamer_set::BumpSelector , core::scoring::motif::ResPairMotif , core::scoring::packstat::AreaAccumulator
• Reset() : core::scoring::sc::MolecularSurfaceCalculator
• reset() : core::scoring::ScoreFunction
• reset_allowed_scoring() : core::scoring::MembraneTopology
• reset_alt_state_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• reset_alt_state_total_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• reset_arrays_danger_expert_only() : core::scoring::methods::LKB_ResidueInfo
• reset_boundaries() : core::grid::CartGrid< T >
• reset_chain_endings() : core::conformation::Conformation
• reset_dof_nodes() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• reset_edge_list_iterator_for_node() : core::pack::interaction_graph::InteractionGraphBase
• reset_energy_methods() : core::scoring::ScoreFunction
• reset_eval_count() : core::optimization::func_1d
• reset_from_previous_deltaHpatch_comp() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• reset_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• reset_jump_rb_deltas() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• reset_move_data() : core::conformation::Conformation
• reset_nblist() : core::scoring::Energies
• reset_recent_network_state_history() : core::pack::annealer::FASTERAnnealer
• reset_relaxed() : core::pack::interaction_graph::FASTERNode
• reset_relaxed_for_neighbors() : core::pack::interaction_graph::FASTERNode
• reset_res_moved() : core::scoring::Energies
• reset_residue_list() : core::conformation::parametric::Parameters
• reset_rpe_calculations_count() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• reset_state_energies() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge
• reset_structure_moved() : core::conformation::Conformation
• reset_surf() : core::scoring::packing::PoseBalls
• reset_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• reset_surface_residue_information() : core::scoring::solid_surface::SurfaceEnergies
• reset_tmh_insert() : core::scoring::MembraneTopology
• resetInstance() : core::scoring::func::USOGFunc
• resfile_commands() : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• resfile_filename_ : core::pack::task::operation::ReadResfile
• ResfileContents() : core::pack::task::ResfileContents
• ResfileReaderException() : core::pack::task::ResfileReaderException
• ResFilterComposition() : core::pack::task::operation::ResFilterComposition
• ResFilterCreatorMap : core::pack::task::operation::ResFilterFactory
• ResFilterFactory() : core::pack::task::operation::ResFilterFactory
• ResFilterRegistrator() : core::pack::task::operation::ResFilterRegistrator< T >
• resi() : core::fragment::picking_old::vall::VallResidue
• resi1() : core::scoring::motif::ResPairMotif
• resi1_ : core::scoring::motif::ResPairMotif
• resi2() : core::scoring::motif::ResPairMotif
• resi2_ : core::scoring::motif::ResPairMotif
• resi_ : core::fragment::picking_old::vall::VallResidue
• resid() : core::chemical::ResConnID , core::conformation::RotamerSetBase , core::io::pdb::ResidueInformation , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::task::operation::RotamerExplosion , core::scoring::constraints::AmbiguousNMRDistanceConstraint
• 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::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• resid_2_moltenres_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• resid_2_moltenres_vector() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• resid_2_moltenresid() : core::pack::rotamer_set::ContinuousRotamerSets
• resid_2_moltenresid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• resid_for_entry() : core::scoring::trie::CPDataCorrespondence
• reside_type_param_map_ : core::scoring::mm::MMBondAngleResidueTypeParamSet
• RESIDUAL_DIPOLAR_COUPLING_DATA : core::pose::datacache::CacheableDataType
• RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL : core::pose::datacache::CacheableDataType
• RESIDUAL_DIPOLAR_COUPLING_SEGMENTS_DATA : core::pose::datacache::CacheableDataType
• ResidualDipolarCoupling : core::scoring::RDC , core::scoring::ResidualDipolarCoupling
• ResidualDipolarCoupling_Rohl() : core::scoring::ResidualDipolarCoupling_Rohl
• ResidualDipolarCouplingEnergy() : core::scoring::methods::ResidualDipolarCouplingEnergy
• ResidualDipolarCouplingEnergy_Rohl() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• Residue : core::chemical::ICoorAtomID
• residue() : core::conformation::Conformation , core::conformation::parametric::Parameters
• Residue() : core::conformation::Residue
• RESIDUE : core::conformation::signals::IdentityEvent
• residue : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::conformation::UltraLightResidue
• Residue : core::pack::dunbrack::RotamerLibrary
• residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• Residue : core::pose::Pose
• residue() : core::pose::Pose
• Residue : core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::dna::DNA_BasePotential , core::scoring::FACTSPoseInfo , core::scoring::FACTSPotential , core::scoring::FACTSResidueInfo , core::scoring::FACTSRotamerSetInfo
• residue() : core::scoring::func::ConformationXYZ
• Residue : core::scoring::func::FourPointsFunc
• residue() : core::scoring::func::FourPointsFunc , core::scoring::func::ResiduePairXYZ , core::scoring::func::ResidueXYZ
• Residue : core::scoring::func::XYZ_Func
• residue() : core::scoring::func::XYZ_Func
• Residue : core::scoring::GenBornPoseInfo , core::scoring::GenBornPotential , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• residue : core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::Atom
• Residue : core::scoring::WaterAdductHBondPotential
• residue1 : core::scoring::motif::MotifHit
• residue2 : core::scoring::motif::MotifHit
• residue_() : core::conformation::Conformation , core::conformation::UltraLightResidue
• residue_action() : core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AUTO , core::pack::task::EMPTY , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NC , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::POLAR , core::pack::task::RESET , core::pack::task::ResfileCommand , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC
• RESIDUE_APPEND : core::conformation::signals::LengthEvent
• residue_atom_pair_energy() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_backbone_backbone() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_sidechain_backbone() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_sidechain_sidechain() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEvaluator
• residue_atom_pair_energy_sidechain_whole() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEvaluator
• residue_atomtree_collection() : core::pack::scmin::AtomTreeCollection
• residue_atomtree_collection_op() : core::pack::scmin::AtomTreeCollection
• residue_change_id_ : core::kinematics::ResidueCoordinateChangeList
• residue_connect_atom_index() : core::chemical::ResidueType , core::conformation::Residue
• residue_connection() : core::chemical::ResidueType , core::conformation::Residue
• residue_connection_conn_id() : core::conformation::Residue
• residue_connection_data_ : core::scoring::etable::etrie::CountPairDataGeneric
• residue_connection_id_for_atom() : core::chemical::ResidueType
• residue_connection_is_polymeric() : core::chemical::ResidueType
• residue_connection_partner() : core::conformation::Residue
• residue_connections_ : core::chemical::ResidueType
• residue_connections_for_atom() : 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_cop() : core::conformation::Conformation , core::conformation::parametric::Parameters
• residue_dEdN_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• RESIDUE_DELETE : core::conformation::signals::LengthEvent
• residue_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• residue_E_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_energy() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPTerminiPenalty , core::scoring::methods::BurialEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::pHEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::nv::NVscore , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SugarCloseEnergy
• residue_energy_ext() : core::scoring::methods::OneBodyEnergy
• residue_fast_pair_energy_attached_H() : core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
• residue_forms_disulfide() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• 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_hbonds() : core::scoring::hbonds::HBondSet
• residue_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_hsasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2
• residue_id() : core::conformation::AtomGraphVertexData
• residue_id_ : core::conformation::AtomGraphVertexData
• residue_identifier_type : core::pack::task::ResfileContents
• residue_in_chains() : core::scoring::methods::PoissonBoltzmannEnergy
• residue_indices() : core::pack::task::operation::OperateOnCertainResidues
• residue_indices_ : core::pack::task::operation::OperateOnCertainResidues
• residue_info() : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• residue_info_ : core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• residue_is_surface() : core::scoring::solid_surface::SurfaceEnergies
• residue_iterated_on() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• residue_list_ : core::conformation::parametric::Parameters
• residue_N_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• residue_neighbors_updated() : core::scoring::Energies
• residue_numbers_ : core::io::silent::SilentStruct
• residue_numbers_into_pose() : core::io::silent::SilentStruct
• residue_op() : core::conformation::Conformation
• residue_pair_constraint_exists() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_ : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_begin() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_end() : core::scoring::constraints::ConstraintSet
• residue_pair_constraints_exists() : core::scoring::constraints::ConstraintSet
• residue_pair_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy
• residue_pair_energy_aro_aro() : core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::hackaro::HackAroEnergy
• residue_pair_energy_ext() : core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::StackElecEnergy
• residue_pair_energy_one_way() : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::StackElecEnergy
• residue_pair_energy_sorted() : core::scoring::methods::CartesianBondedEnergy
• RESIDUE_PREPEND : core::conformation::signals::LengthEvent
• 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_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• residue_selection_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::PreventRepacking
• residue_selector_ : core::pack::task::operation::OperateOnResidueSubset
• residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• residue_tasks_ : core::pack::task::PackerTask_
• residue_torsions_need_updating_ : core::conformation::Conformation
• residue_total_energies() : core::scoring::Energies
• residue_total_energies_ : core::scoring::Energies
• residue_total_energies_uptodate_ : core::scoring::Energies
• residue_total_energy() : core::scoring::Energies
• residue_total_energy_ : core::scoring::Energies
• residue_total_energy_uptodate_ : core::scoring::Energies
• residue_type() : core::conformation::Conformation , core::pose::Pose , core::scoring::methods::LKB_ResidueInfo
• 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_param_set() : core::scoring::methods::MMBondAngleEnergy
• residue_type_rotamers_begin_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• residue_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueType , core::conformation::Residue , core::import_pose::ImportPoseOptions
• residue_type_set_ : core::chemical::ResidueType , core::import_pose::ImportPoseOptions
• residue_type_set_tag() : core::chemical::ResidueLoaderOptions
• residue_type_set_tag_ : core::chemical::ResidueLoaderOptions
• residue_type_sets_ : core::chemical::ChemicalManager
• residue_types() : core::chemical::ResidueTypeSet
• residue_types_ : core::chemical::ResidueTypeSet , core::scoring::BB_Pos
• residue_types_const_ : core::chemical::ResidueTypeSet
• residue_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• residue_xyz_change_list_begin() : core::kinematics::AtomTree
• residue_xyz_change_list_end() : core::kinematics::AtomTree
• residue_z_position() : core::conformation::membrane::MembraneInfo
• ResidueAtomTreeCollection() : core::pack::scmin::ResidueAtomTreeCollection
• ResidueAtomTreeCollectionMomento() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• ResidueCartBondedParameters() : core::scoring::methods::ResidueCartBondedParameters
• ResidueConnection() : core::chemical::ResidueConnection
• ResidueCoordinateChangeList() : core::kinematics::ResidueCoordinateChangeList
• ResidueCoords : core::io::pdb::FileData
• ResidueCOP : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• ResidueDatabaseIO() : core::chemical::ResidueDatabaseIO
• ResidueHasProperty() : core::pack::task::operation::ResidueHasProperty
• ResidueIndexIs() : core::pack::task::operation::ResidueIndexIs
• ResidueIndexIsnt() : core::pack::task::operation::ResidueIndexIsnt
• ResidueIndexSelector() : core::pack::task::residue_selector::ResidueIndexSelector
• ResidueIndices : core::pack::task::operation::OperateOnCertainResidues
• ResidueInformation() : core::io::pdb::ResidueInformation
• ResidueKey() : core::pose::PDBPoseMap::ResidueKey
• ResidueKinWriter() : core::conformation::ResidueKinWriter
• ResidueLacksProperty() : core::pack::task::operation::ResidueLacksProperty
• ResidueLevelTask_() : core::pack::task::ResidueLevelTask_
• ResidueLoader() : core::chemical::ResidueLoader
• ResidueLoaderOptions() : core::chemical::ResidueLoaderOptions
• ResidueMap : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T >
• ResidueMatcherCOP : core::pack::rotamer_set::RotamerCouplings
• ResidueName3Is() : core::pack::task::operation::ResidueName3Is
• ResidueName3Isnt() : core::pack::task::operation::ResidueName3Isnt
• ResidueNameSelector() : core::pack::task::residue_selector::ResidueNameSelector
• ResidueNblistData() : core::scoring::ResidueNblistData
• ResidueOP : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo
• ResiduePairConstraints : core::scoring::constraints::ConstraintSet
• ResiduePairConstraintsIterator : core::scoring::constraints::ConstraintSet
• ResiduePairNeighborList() : core::scoring::ResiduePairNeighborList
• ResiduePairXYZ() : core::scoring::func::ResiduePairXYZ
• ResiduePDBIndexIs() : core::pack::task::operation::ResiduePDBIndexIs
• ResiduePDBIndexIsnt() : core::pack::task::operation::ResiduePDBIndexIsnt
• ResiduePDBInfoHasLabel() : core::pack::task::operation::ResiduePDBInfoHasLabel
• ResiduePDBInfoLacksLabel() : core::pack::task::operation::ResiduePDBInfoLacksLabel
• ResidueProperties() : core::chemical::ResidueProperties
• ResidueRecord() : core::pose::PDBInfo::ResidueRecord
• ResidueRecords : core::pose::PDBInfo
• residues() : core::fragment::picking_old::vall::VallSection , core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::packing::HolesParamsRes
• residues_ : core::conformation::Conformation , core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::scoring::packing::HolesParamsRes
• residues_adjacent_for_subunit_pair() : core::pack::interaction_graph::SymmOnTheFlyEdge
• residues_append() : core::conformation::Conformation
• residues_delete() : core::conformation::Conformation
• residues_for_atom_name_remapping() : core::io::pdb::FileDataOptions
• residues_for_atom_name_remapping_ : core::io::pdb::FileDataOptions
• residues_info_ : core::scoring::methods::LKB_ResiduesInfo
• residues_insert() : core::conformation::Conformation
• residues_moved_begin() : core::kinematics::ResidueCoordinateChangeList
• residues_moved_end() : core::kinematics::ResidueCoordinateChangeList
• residues_replace() : core::conformation::Conformation
• residues_to_prevent_ : core::pack::task::operation::PreventRepacking
• residues_to_restrict_to_repacking_ : core::pack::task::operation::RestrictResidueToRepacking
• ResidueSelector() : core::pack::task::residue_selector::ResidueSelector
• ResidueSelectorFactory() : core::pack::task::residue_selector::ResidueSelectorFactory
• ResidueSelectorRegistrator() : core::pack::task::residue_selector::ResidueSelectorRegistrator< T >
• ResidueSelectorSingle() : core::chemical::ResidueSelectorSingle
• ResidueSpan : core::indexed_structure_store::FragmentLookup
• ResidueTemps : core::io::pdb::FileData
• ResidueType() : core::chemical::ResidueType , core::conformation::Residue , core::pack::dunbrack::RotamerLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::scoring::methods::LK_BallEnergy
• ResidueTypeConstraint() : core::scoring::constraints::ResidueTypeConstraint
• ResidueTypeCOPList : core::pack::task::ResidueLevelTask
• ResidueTypeCOPListConstIter : core::pack::task::ResidueLevelTask
• ResidueTypeCOPListIter : core::pack::task::ResidueLevelTask
• ResidueTypeFilter() : core::pack::task::operation::ResidueTypeFilter
• ResidueTypeKinWriter() : core::chemical::ResidueTypeKinWriter
• ResidueTypeLinkingConstraint() : core::scoring::constraints::ResidueTypeLinkingConstraint
• ResidueTypeSet() : core::chemical::ResidueTypeSet
• ResidueTypeSets : core::chemical::ChemicalManager
• ResidueXYZ() : core::scoring::func::ResidueXYZ
• resize() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::indexed_structure_store::FragmentStore , core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::interaction_graph::RotamerDotsCache , core::pack::rotamer_set::RotamerCouplings , core::pack::rotamer_set::RotamerLinks , core::scoring::BB_Pos , core::scoring::dna::BasePartner , core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise , core::scoring::Helices , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::SS_Info , core::scoring::Strands
• resize_asu() : core::conformation::symmetry::SymmetryInfo
• resize_atom_records() : core::pose::PDBInfo
• resize_bb_donor_acceptor_arrays() : core::scoring::hbonds::HBondSet
• resize_chi() : core::io::silent::ProteinSilentStruct_Template< T >
• resize_residue_records() : core::pose::PDBInfo
• resl_params_ : core::scoring::packing::HolesEnergy
• resl_score : core::scoring::packing::HolesResult
• reslibraries_ : core::pack::dunbrack::RotamerLibrary
• reslibrary_iterator : core::pack::dunbrack::RotamerLibrary
• ResLibraryMap : core::pack::dunbrack::RotamerLibrary
• ResLvlTaskOperationFactory() : core::pack::task::operation::ResLvlTaskOperationFactory
• ResLvlTaskOperationRegistrator() : core::pack::task::operation::ResLvlTaskOperationRegistrator< T >
• ResMap : core::scoring::motif::MotifHits
• 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 , core::sequence::Sequence
• resnum_ : core::pack::task::operation::AppendResidueRotamerSet
• resnum_to_rosetta_num() : core::io::raw_data::DisulfideFile
• reso : core::scoring::electron_density::ElectronDensity
• resolve_jump() : core::environment::SequenceAnnotation
• resolve_seq() : core::environment::SequenceAnnotation
• resolve_store_path() : core::indexed_structure_store::StructureStoreManager
• resolve_trie_vs_path() : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::vdwaals::VDWTrieCountPair1B
• resolve_trie_vs_trie() : core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPair1BC4 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieCountPairBase , core::scoring::vdwaals::VDWTrieCountPair1B
• RespairInteractions() : core::scoring::custom_pair_distance::RespairInteractions
• ResPairMinimizationData() : core::scoring::ResPairMinimizationData
• ResPairMotif() : core::scoring::motif::ResPairMotif
• ResPairMotifMetaBinner() : core::scoring::motif::ResPairMotifMetaBinner
• ResPairMotifQuery() : core::scoring::motif::ResPairMotifQuery
• ResRangePredicate() : core::scoring::ResRangePredicate
• ResResEnergyInvoker() : core::scoring::etable::ResResEnergyInvoker< Evaluator >
• 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
• ResSingleMinimizationData() : core::scoring::ResSingleMinimizationData
• restrict_absent_canonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_absent_nas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_nonnative_canonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_to_repacking() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• restrict_to_residue() : core::pack::task::operation::DisallowIfNonnative
• restrict_to_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• RestrictAbsentCanonicalAAS() : core::pack::task::operation::RestrictAbsentCanonicalAAS
• RestrictAbsentCanonicalAASRLT() : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• RestrictYSDesign() : core::pack::task::operation::RestrictYSDesign
• 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_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
• restype_index_ : core::pack::scmin::ResidueAtomTreeCollectionMomento
• restypegroup_adjacency_ : core::pack::interaction_graph::SymmOnTheFlyEdge
• restypeinfo() : core::scoring::FACTSResidueInfo
• restypeinfo_ : core::scoring::FACTSResidueInfo
• ResTypePair : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• ResTypePairTuple : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• result : core::scoring::APBSWrapper
• results : core::scoring::sc::MolecularSurfaceCalculator
• retrieve() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T >
• retrieve_calculator() : core::pose::metrics::CalculatorFactory
• retrieve_energy() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• return_val_ : core::scoring::func::ConstantFunc
• revamp_weight_by_burial() : core::scoring::methods::PoissonBoltzmannEnergy
• reverse() : core::id::BondID , core::id::SequenceMapping , core::kinematics::Jump , core::kinematics::RT , core::scoring::dssp::Pairing
• reverse_ : core::import_pose::atom_tree_diffs::ScoreLessThanComparator
• reverse_in_place() : core::scoring::motif::ResPairMotif
• reverse_in_place_unsafe() : core::scoring::motif::ResPairMotif
• reverse_score_filter() : core::io::silent::SilentFileData
• reversed() : core::id::BondID , core::kinematics::Jump , core::scoring::motif::ResPairMotif
• revision_id() : core::scoring::constraints::ConstraintSet
• revision_id_ : core::scoring::constraints::ConstraintSet
• revision_id_current_ : core::scoring::constraints::ConstraintSet
• revoke_all_access() : core::environment::DofPassport
• reweight_ : core::scoring::methods::D2H_SA_Energy
• reweight_symm_interactions_ : core::conformation::symmetry::SymmetryInfo
• reweighters_begin() : core::pack::task::IGEdgeReweightContainer
• reweighters_end() : core::pack::task::IGEdgeReweightContainer
• rg : core::scoring::methods::RG_MinData
• rg_ : core::scoring::rna::RG_Energy_RNA
• RG_Energy_Fast() : core::scoring::methods::RG_Energy_Fast
• RG_Energy_RNA() : core::scoring::rna::RG_Energy_RNA
• RG_LOCAL_MINDATA : core::pose::datacache::CacheableDataType
• RG_Local_MinData() : core::scoring::methods::RG_Local_MinData
• RG_LocalEnergy() : core::scoring::methods::RG_LocalEnergy
• RG_MINDATA : core::pose::datacache::CacheableDataType
• RG_MinData() : core::scoring::methods::RG_MinData
• rho() : core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore
• 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_cylindrical_ : core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• 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_ : core::scoring::Ramachandran2B
• right_cdf_by_torsion_bin_ : core::scoring::Ramachandran2B
• right_cdf_for_torsion_bin() : core::scoring::Ramachandran2B
• right_ram_probabil_ : core::scoring::Ramachandran2B
• rigid_perturb_vector() : core::scoring::MembranePotential
• RigidBodySilentStruct() : core::io::silent::RigidBodySilentStruct
• RigidBodySilentStructCreator() : core::io::silent::RigidBodySilentStructCreator
• RigidDistanceVisitor() : core::chemical::RigidDistanceVisitor
• rinfo_ : core::io::pdb::GeometricRenameIsomorphismCallback
• ring_ : core::chemical::Bond
• ring_conformer_set() : core::chemical::ResidueType
• ring_current_coeff() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_height() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_height_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_intensity() : 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_radius_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_size() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::RingConformerSet
• ring_size_ : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::RingConformerSet
• RingConformerManager() : core::chemical::RingConformerManager
• RingConformerSet() : core::chemical::RingConformerSet
• ringness() : core::chemical::Bond
• rings() : core::chemical::ResidueType
• rings_and_their_edges_ : core::chemical::ResidueType
• RLTOC_Map : core::pack::task::operation::ResLvlTaskOperationFactory
• rltoc_map_ : core::pack::task::operation::ResLvlTaskOperationFactory
• rm_jump_neighbor() : core::environment::FoldTreeSketch::Node
• rm_neighbor() : core::environment::FoldTreeSketch::Node
• rm_peptide_neighbor() : core::environment::FoldTreeSketch::Node
• rm_seq_label() : core::environment::SequenceAnnotation
• Rmax : core::scoring::fiber_diffraction::FiberDiffraction
• rmax_ : core::scoring::func::MixtureFunc
• rms : core::scoring::motif::MotifHit
• RMS_Energy() : core::scoring::methods::RMS_Energy
• rms_target_ : core::scoring::methods::RMS_Energy
• rmsd() : core::fragment::FragmentRmsd
• rmsd_ : core::scoring::ResidualDipolarCoupling
• rmsd_history_ : core::scoring::methods::VallLookbackData
• rna() : core::import_pose::ImportPoseOptions
• rna_ : core::import_pose::ImportPoseOptions
• rna_anti_chi_res() : core::pose::full_model_info::FullModelInfo
• rna_atom_vdw_ : core::scoring::rna::RNA_VDW_Energy , core::scoring::ScoringManager
• RNA_AtomVDW() : core::scoring::rna::RNA_AtomVDW
• rna_axis_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_pair_energy_one_way() : 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_atoms() : core::chemical::rna::RNA_ResidueType
• rna_base_axis_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_backbone_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_backbone_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_backbone_xy_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_base_pair_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stack_axis_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stack_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_base_stagger_pairwise_pair_energy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• 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_bond_geometry_energy_ : core::scoring::constraints::ConstraintEdge
• rna_bulge_bonus_once_per_loop_ : core::scoring::rna::RNA_BulgeEnergy
• rna_bulge_res() : core::pose::full_model_info::FullModelInfo
• RNA_BulgeEnergy() : core::scoring::rna::RNA_BulgeEnergy
• rna_centroid_info() : core::scoring::rna::RNA_ScoringInfo
• rna_centroid_info_ : core::scoring::rna::RNA_ScoringInfo
• RNA_CentroidInfo() : core::scoring::rna::RNA_CentroidInfo
• 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_ChemicalMappingEnergy() : core::scoring::rna::data::RNA_ChemicalMappingEnergy
• RNA_ChemicalShiftEnergy() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy
• RNA_ChemicalShiftPotential() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• rna_cos_theta_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• rna_cos_theta_fade_zone_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• RNA_CS_parameters() : core::scoring::rna::chemical_shift::RNA_CS_parameters
• rna_cs_params_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• RNA_CS_residue_parameters() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• rna_data() : core::scoring::rna::data::RNA_DataInfo
• rna_data_ : core::scoring::rna::data::RNA_DataInfo
• rna_data_info() : core::scoring::rna::RNA_ScoringInfo
• rna_data_info_ : core::scoring::rna::RNA_ScoringInfo
• rna_data_info_with_conventional_numbering_ : core::io::rna::RNA_DataReader
• RNA_DataBackboneEnergy() : core::scoring::rna::data::RNA_DataBackboneEnergy
• RNA_DataInfo() : core::scoring::rna::data::RNA_DataInfo
• RNA_DataReader() : core::io::rna::RNA_DataReader
• RNA_Datum() : core::scoring::rna::data::RNA_Datum
• rna_dms_low_resolution_potential_ : core::scoring::ScoringManager
• RNA_DMS_LowResolutionPotential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• RNA_DMS_Potential() : core::scoring::rna::data::RNA_DMS_Potential
• rna_dms_potential_ : core::scoring::ScoringManager
• RNA_EnergyMethodOptions() : core::scoring::rna::RNA_EnergyMethodOptions
• rna_fa_elec_one_way() : core::scoring::elec::RNA_FA_ElecEnergy
• RNA_FA_ElecEnergy() : core::scoring::elec::RNA_FA_ElecEnergy
• rna_filtered_base_base_info() : core::scoring::rna::RNA_ScoringInfo
• rna_filtered_base_base_info_ : core::scoring::rna::RNA_ScoringInfo
• RNA_FilteredBaseBaseInfo() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• rna_fitted_torsion_info_ : core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionPotential
• RNA_FittedTorsionInfo() : core::chemical::rna::RNA_FittedTorsionInfo
• RNA_FullAtomStackingEnergy() : core::scoring::rna::RNA_FullAtomStackingEnergy
• RNA_FullAtomVDW_BasePhosphate() : core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
• rna_gaussian_variance_per_residue_ : core::scoring::loop_graph::LoopGraph
• RNA_IdealCoord() : core::pose::rna::RNA_IdealCoord
• RNA_JR_SuiteEnergy() : core::scoring::rna::RNA_JR_SuiteEnergy
• RNA_LJ_BaseEnergy() : core::scoring::rna::RNA_LJ_BaseEnergy
• rna_low_resolution_potential_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::ScoringManager
• RNA_LowResolutionPotential() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_Mg_Energy() : core::scoring::rna::RNA_Mg_Energy
• rna_mg_knowledge_based_potential_ : core::scoring::rna::RNA_Mg_Energy
• RNA_Mg_KnowledgeBasedPotential() : core::scoring::rna::RNA_Mg_KnowledgeBasedPotential
• rna_note_chi_controls_atom() : core::chemical::rna::RNA_ResidueType
• rna_options() : core::scoring::methods::EnergyMethodOptions
• rna_options_ : core::scoring::methods::EnergyMethodOptions
• RNA_PairwiseLowResolutionEnergy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_raw_base_base_info() : core::scoring::rna::RNA_ScoringInfo
• rna_raw_base_base_info_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_ScoringInfo
• RNA_RawBaseBaseInfo() : core::scoring::rna::RNA_RawBaseBaseInfo
• rna_reactivities() : core::scoring::rna::data::RNA_DataInfo
• rna_reactivities_ : core::scoring::rna::data::RNA_DataInfo
• RNA_Reactivity() : core::scoring::rna::data::RNA_Reactivity
• 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_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_pair_energy_one_way() : 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_ResidueLevelTask() : core::pack::task::rna::RNA_ResidueLevelTask
• RNA_ResidueType() : core::chemical::rna::RNA_ResidueType
• rna_sample_sugar_res() : core::pose::full_model_info::FullModelInfo
• RNA_SCORING_INFO : core::pose::datacache::CacheableDataType
• RNA_ScoringInfo() : core::scoring::rna::RNA_ScoringInfo
• RNA_SECSTRUCT_INFO : core::pose::datacache::CacheableDataType
• RNA_SilentStruct() : core::io::silent::RNA_SilentStruct
• RNA_SilentStructCreator() : core::io::silent::RNA_SilentStructCreator
• rna_stagger_ : core::scoring::rna::RNA_LowResolutionPotential
• rna_sugar_close_constraints_ : core::scoring::rna::RNA_SugarCloseEnergy
• RNA_SugarCloseEnergy() : 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_SuiteAssignment() : core::pose::rna::RNA_SuiteAssignment
• RNA_SuiteEnergy() : core::scoring::rna::RNA_SuiteEnergy
• RNA_SuiteInfo() : core::pose::rna::RNA_SuiteInfo
• RNA_SuiteName() : core::pose::rna::RNA_SuiteName
• RNA_SuitePotential() : core::scoring::rna::RNA_SuitePotential
• rna_syn_chi_res() : core::pose::full_model_info::FullModelInfo
• rna_task() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• rna_task_ : core::pack::task::ResidueLevelTask_
• rna_terminal_res() : core::pose::full_model_info::FullModelInfo
• rna_tight_torsions_ : core::chemical::rna::RNA_FittedTorsionInfo
• rna_torsion_potential_ : core::scoring::rna::RNA_TorsionEnergy
• RNA_TorsionEnergy() : core::scoring::rna::RNA_TorsionEnergy
• RNA_TorsionPotential() : core::scoring::rna::RNA_TorsionPotential
• RNA_type() : core::chemical::ResidueType , core::conformation::Residue
• rna_update_last_controlling_chi() : core::chemical::rna::RNA_ResidueType
• rna_vdw_atom_ : core::scoring::rna::RNA_AtomVDW
• RNA_VDW_Energy() : core::scoring::rna::RNA_VDW_Energy
• rna_vdw_parameter_ : core::scoring::rna::RNA_AtomVDW
• rna_verbose_ : core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_LowResolutionPotential
• root() : core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::Node
• root_ : core::chemical::RerootRestypeVisitor , core::conformation::symmetry::SymmData , core::kinematics::AtomTree
• root_atom() : core::chemical::ResidueType
• root_atom_ : core::chemical::ResidueType , core::scoring::methods::GoapRsdType
• root_from_code() : core::chemical::carbohydrates::CarbohydrateInfo
• rosetta_atom_name_ : core::chemical::AddAtomAlias
• rosetta_num : core::io::raw_data::DisulfideFile
• ROSETTA_SASA_radii_ : core::pack::interaction_graph::RotamerDotsRadiusData
• rot : core::pack::dunbrack::ChiSet
• rot_bin_ : core::pack::dunbrack::DunbrackConstraint
• rot_freq() : core::pack::annealer::SimAnnealerBase
• rot_freq_ : core::pack::annealer::SimAnnealerBase
• rot_perturb_vector() : core::scoring::MembranePotential
• rot_to_pack() : core::pack::annealer::RotamerAssigningAnnealer
• rot_to_pack_ : core::pack::annealer::RotamerAssigningAnnealer
• rot_vec_pos_ : core::pack::dunbrack::DunbrackConstraint
• rot_well() : core::pack::dunbrack::DunbrackRotamerSampleData
• rot_well_ : core::pack::dunbrack::DunbrackRotamerSampleData
• ROT_X : core::kinematics::Jump
• ROT_Y : core::kinematics::Jump
• ROT_Z : core::kinematics::Jump
• rotAlign2DPose() : core::scoring::electron_density::ElectronDensity
• rotamer() : core::conformation::RotamerSetBase , core::pack::dunbrack::RotamericData< T, N > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets
• rotamer_ : core::pack::dunbrack::RotamericData< T, N > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::InvRotamerDots , core::pack::interaction_graph::RotamerDots
• rotamer_aa() : core::chemical::ResidueType
• rotamer_aa_ : core::chemical::ResidueType
• rotamer_couplings() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_couplings_ : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::task::operation::SetRotamerCouplings , core::pack::task::PackerTask_
• rotamer_couplings_exist() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_energies_ : core::pack::interaction_graph::DoubleDensePDNode
• rotamer_energy() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• rotamer_energy_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• rotamer_energy_deriv_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• rotamer_energy_deriv_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• rotamer_for_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• rotamer_id() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• rotamer_id_ : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• rotamer_library_name_ : core::chemical::ResidueType
• rotamer_links() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_links_ : core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::task::operation::SetRotamerLinks , core::pack::task::PackerTask_
• rotamer_links_exist() : core::pack::task::PackerTask , 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 , core::pack::task::ResidueLevelTask_
• rotamer_operations_ : core::pack::task::ResidueLevelTask_
• rotamer_probability() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• rotamer_probability_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• rotamer_ref() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• 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_for_moltenres() : core::pack::rotamer_set::ContinuousRotamerSets
• rotamer_set_for_moltenresidue() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• rotamer_set_for_res() : core::pack::rotamer_set::ContinuousRotamerSets
• rotamer_set_for_residue() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• rotamer_set_operation_ : core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamerSet
• rotamer_set_operation_begin() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• rotamer_set_operation_end() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• rotamer_sets() : core::pack::annealer::RotamerAssigningAnnealer , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• 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
• RotamerAssigningAnnealer() : core::pack::annealer::RotamerAssigningAnnealer
• RotamerConstraint() : core::pack::dunbrack::RotamerConstraint
• RotamerCouplingsCOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::task::PackerTask
• RotamerCouplingsOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• RotamerDescriptor() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• RotamerDescriptorAtom() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT >
• RotamerDots() : core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache
• RotamerDotsCache() : core::pack::interaction_graph::RotamerDotsCache
• RotamerDotsRadiusData() : core::pack::interaction_graph::RotamerDotsRadiusData
• RotamerExplosion() : core::pack::task::operation::RotamerExplosion
• RotamericData() : core::pack::dunbrack::RotamericData< T, N >
• RotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• RotamericSingleResiduePeptoidLibrary() : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• rotamerid : core::pack::annealer::RotSub
• RotamerLibrary : core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::RotamerLibrary
• RotamerLibraryScratchSpace() : core::pack::dunbrack::RotamerLibraryScratchSpace
• RotamerLinksCOP : core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::task::PackerTask
• RotamerLinksOP : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerOperation() : core::pack::rotamer_set::RotamerOperation
• rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• rotamers_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , 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 >
• RotamerSet() : core::pack::rotamer_set::RotamerSet , core::scoring::FACTSRotamerSetInfo
• RotamerSet_() : core::pack::rotamer_set::RotamerSet_
• RotamerSetBase() : core::conformation::RotamerSetBase , core::scoring::GenBornRotamerSetInfo
• RotamerSetCOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerSetOperation() : core::pack::rotamer_set::RotamerSetOperation
• RotamerSets() : core::pack::rotamer_set::RotamerSets
• RotamerSetsBase() : core::pack::rotamer_set::RotamerSetsBase
• RotamerSetsBaseCOP : core::pack::annealer::SimAnnealerBase
• RotamerSetsCOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerSetVector : core::pack::rotamer_set::FixbbRotamerSets
• RotamersForAA : core::pack::rotamer_set::ContinuousRotamerSet
• RotamerSubset() : core::pack::rotamer_set::RotamerSubset
• RotamerSubsets() : core::pack::rotamer_set::RotamerSubsets
• RotamerTrie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• RotamerTrieBaseOP : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• rotation : core::kinematics::RT , core::kinematics::Stub
• rotation_by_axis() : core::kinematics::Jump
• rotation_by_matrix() : core::kinematics::Jump
• rotation_matrices_ : core::conformation::symmetry::SymmData
• rotid_on_moltenresidue() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• rotlib_ : core::pack::dunbrack::RotamerConstraint
• rotno_2_packed_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotno_2_packed_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotprob() : core::pack::dunbrack::RotamerLibraryScratchSpace
• rotprob_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• rots_for_nodes_ : core::pack::annealer::RotamerAssigningAnnealer
• rotsetops_ : core::pack::task::ResidueLevelTask_
• rotwell() : core::pack::dunbrack::DunbrackRotamer< S, N, P > , core::pack::dunbrack::RotamerLibraryScratchSpace
• rotwell_ : core::pack::dunbrack::DunbrackRotamer< S, N, P > , core::pack::dunbrack::RotamerLibraryScratchSpace
• rotwell_2_packed_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotwell_2_rotno() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• rotwell_exists_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• Row : core::sequence::DP_Matrix
• rows() : core::sequence::DP_Matrix
• rp : core::scoring::fiber_diffraction::Hankel , core::scoring::sc::MolecularSurfaceCalculator
• rp0 : core::scoring::fiber_diffraction::Hankel
• RPM_FilterStats() : core::scoring::motif::RPM_FilterStats
• rsa_class_pred_ : core::scoring::methods::ProQ_Energy
• rsa_feature() : 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
• rsa_sc_feature() : core::scoring::methods::ProQ_Energy
• Rscale_factor : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• rsd() : core::id::AtomID , core::id::DOF_ID , core::id::NamedAtomID , core::id::TorsionID , core::optimization::DOF_Node , core::scoring::AtomNeighbor
• rsd1() : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• 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 >
• 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_library_already_loaded() : core::pack::dunbrack::RotamerLibrary
• 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_rsd_energy() : core::scoring::dna::DirectReadoutPotential
• rsd_sasa_ : core::scoring::sasa::SasaCalc
• rsd_sasa_sc_ : core::scoring::sasa::SasaCalc
• rsd_type_ : core::conformation::Residue , core::scoring::methods::LKB_ResidueInfo
• 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
• rsigma_dot_initializer() : core::scoring::SecondaryStructurePotential
• Rsum_obs : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• rswitch() : core::scoring::constraints::BoundFunc
• rswitch_ : core::scoring::constraints::BoundFunc
• rt() : core::kinematics::Jump
• RT() : core::kinematics::RT , core::scoring::dna::DirectReadoutPotential
• rt() : core::scoring::motif::ResPairMotif
• rt6() : core::scoring::motif::Xfrag
• rt6_ : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfrag
• rt_ : core::fragment::DownJumpSRFD , core::kinematics::Jump
• RT_from_epos() : core::scoring::disulfides::RT_helper
• rtmin() : core::pack::RTMin
• RTMin() : core::pack::RTMin
• run() : core::optimization::AtomTreeMinimizer , core::optimization::CartesianMinimizer , core::optimization::GA_Minimizer , core::optimization::JJH_Minimizer , core::optimization::Minimizer , core::optimization::NelderMeadSimplex , core::optimization::ParticleSwarmMinimizer , core::optimization::symmetry::SymAtomTreeMinimizer , core::pack::annealer::DebuggingAnnealer , core::pack::annealer::FASTERAnnealer , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::MultiCoolAnnealer , core::pack::annealer::SimAnnealerBase
• run_ : core::scoring::sc::MolecularSurfaceCalculator
• run_constant_temp_rotamer_substitutions() : core::pack::annealer::MultiCoolAnnealer
• run_quench() : core::pack::annealer::MultiCoolAnnealer
• run_quench_cycles() : core::pack::annealer::FASTERAnnealer
• RV : core::scoring::electron_density::ElectronDensity
• rvec : core::scoring::ResidualDipolarCoupling
• rvec5 : core::scoring::ResidualDipolarCoupling