- r -

• r() : core::scoring::packing::Ball
• R() : core::scoring::ResidualDipolarCoupling
• R_PARAM() : core::scoring::APBSConfig::R_PARAM
• radius() : core::scoring::packing::Ball , core::scoring::packstat::CavityBall
• radius_for_attype() : core::pack::interaction_graph::RotamerDots
• Rama2BOffset() : core::scoring::Rama2BOffset
• Rama2BOffsetEnergy() : core::scoring::methods::Rama2BOffsetEnergy
• rama_bin_probability_left() : core::scoring::Ramachandran2B
• rama_bin_probability_right() : core::scoring::Ramachandran2B
• rama_probability() : core::scoring::Ramachandran
• 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
• 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_missing_coords() : core::io::pdb::FileData , 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_lower() : core::conformation::symmetry::SymDof
• range2_upper() : core::conformation::symmetry::SymDof
• range_check() : core::environment::FoldTreeSketch , core::scoring::dssp::StrandPairing
• 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_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_index() : core::kinematics::Jump
• rb_jump() : core::pack::task::operation::RestrictToInterface
• RDAT() : core::io::rna::RDAT
• RDC() : core::scoring::RDC
• rdc_from_pose() : core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• RDC_Rohl() : core::scoring::RDC_Rohl
• reactivity() : 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 >
• read_bbdep_table() : core::scoring::methods::IdealParametersDatabase
• read_bbind_continuous_minimization_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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::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::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 , core::coarse::CoarseEtable
• 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 > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , 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 > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > , 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 >
• 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_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_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_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 >
• read_rotameric_data() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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
• 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
• 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
• 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
• ref_pose_for() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• reference_conformation() : core::environment::DofPassport
• 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
• 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 >
• 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
• rel_deriv_dev() : core::optimization::SimpleDerivCheckResult
• 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
• release_buffers() : core::scoring::ResidualDipolarCoupling
• 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_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::NamedAtomPairConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::SequenceProfileConstraint
• RemarkInfo() : core::pose::RemarkInfo
• remarks() : core::pose::PDBInfo
• rematchResToPatterson() : core::scoring::electron_density::ElectronDensity
• remember_unrecognized_res() : 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_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_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
• 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
• 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
• representative_atom_name() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• 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
• 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::RDC_Rohl
• res1() : core::scoring::CSA , core::scoring::DC , core::scoring::RDC
• res1_data() : core::scoring::hbonds::HBondResPairMinData , core::scoring::methods::LKB_ResPairMinData
• res2() : core::scoring::CSA , core::scoring::DC , core::scoring::RDC
• res2_data() : core::scoring::hbonds::HBondResPairMinData , core::scoring::methods::LKB_ResPairMinData
• res3() : core::scoring::CSA
• res6() : core::scoring::methods::ProQ_Energy
• 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_index() : core::scoring::methods::dfire::DFIRE_Potential
• res_inds() : core::scoring::disulfides::DisulfMinData
• res_labels() : core::scoring::packstat::SimplePDB
• res_list() : core::pose::full_model_info::FullModelInfo
• res_min_data() : core::scoring::MinimizationNode
• res_moved() : core::scoring::Energies
• res_name() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• res_num() : core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• res_pair_min_data() : core::scoring::MinimizationEdge
• res_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_type_linking_constraint_energy() : core::scoring::constraints::ConstraintEdge
• rescale() : core::sequence::SequenceProfile
• rescale_fastscoring_temp_bins() : core::scoring::electron_density::ElectronDensity
• ResConnID() : core::chemical::ResConnID
• 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_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
• ResfileContents() : core::pack::task::ResfileContents
• ResfileReaderException() : core::pack::task::ResfileReaderException
• ResFilterComposition() : core::pack::task::operation::ResFilterComposition
• 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
• resi2() : core::scoring::motif::ResPairMotif
• 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
• resid_2_moltenres() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , 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_for_entry() : core::scoring::trie::CPDataCorrespondence
• ResidualDipolarCoupling() : core::scoring::ResidualDipolarCoupling
• ResidualDipolarCoupling_Rohl() : core::scoring::ResidualDipolarCoupling_Rohl
• ResidualDipolarCouplingEnergy() : core::scoring::methods::ResidualDipolarCouplingEnergy
• ResidualDipolarCouplingEnergy_Rohl() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• ResidualDipolarCouplingEnergyRigidSegments() : core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• residue() : core::conformation::Conformation , core::conformation::parametric::Parameters
• Residue() : core::conformation::Residue
• residue() : core::conformation::UltraLightResidue , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::pose::Pose , core::scoring::func::ConformationXYZ , core::scoring::func::FourPointsFunc , core::scoring::func::ResiduePairXYZ , core::scoring::func::ResidueXYZ , core::scoring::func::XYZ_Func
• residue_() : core::conformation::Conformation
• 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_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::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , 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::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , 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::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , 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_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_id_for_atom() : core::chemical::ResidueType
• residue_connection_is_polymeric() : core::chemical::ResidueType
• residue_connection_partner() : core::conformation::Residue
• residue_connections_for_atom() : core::chemical::ResidueType
• residue_cop() : core::conformation::Conformation , core::conformation::parametric::Parameters
• 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::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_hbonds() : core::scoring::hbonds::HBondSet
• residue_id() : core::conformation::AtomGraphVertexData
• residue_in_chains() : core::scoring::methods::PoissonBoltzmannEnergy
• residue_indices() : core::pack::task::operation::OperateOnCertainResidues
• 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_neighbors_updated() : core::scoring::Energies
• 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_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::CSD_TorsionEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::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_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• residue_total_energies() : core::scoring::Energies
• residue_total_energy() : core::scoring::Energies
• residue_type() : core::conformation::Conformation , core::pose::Pose
• residue_type_param_set() : core::scoring::methods::MMBondAngleEnergy
• residue_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueType , core::conformation::Residue , core::import_pose::ImportPoseOptions
• residue_type_set_tag() : core::chemical::ResidueLoaderOptions
• residue_types() : core::chemical::ResidueTypeSet
• 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
• 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
• 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
• ResidueName3Is() : core::pack::task::operation::ResidueName3Is
• ResidueName3Isnt() : core::pack::task::operation::ResidueName3Isnt
• ResidueNblistData() : core::scoring::ResidueNblistData
• 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
• 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_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_insert() : core::conformation::Conformation
• residues_moved_begin() : core::kinematics::ResidueCoordinateChangeList
• residues_moved_end() : core::kinematics::ResidueCoordinateChangeList
• residues_replace() : core::conformation::Conformation
• 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
• ResidueType() : core::chemical::ResidueType
• ResidueTypeConstraint() : core::scoring::constraints::ResidueTypeConstraint
• ResidueTypeFilter() : core::pack::task::operation::ResidueTypeFilter
• ResidueTypeKinWriter() : core::chemical::ResidueTypeKinWriter
• ResidueTypeLinkingConstraint() : core::scoring::constraints::ResidueTypeLinkingConstraint
• ResidueTypeSet() : core::chemical::ResidueTypeSet
• 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
• ResLvlTaskOperationFactory() : core::pack::task::operation::ResLvlTaskOperationFactory
• ResLvlTaskOperationRegistrator() : core::pack::task::operation::ResLvlTaskOperationRegistrator< T >
• resnum() : core::sequence::Sequence
• resnum_to_rosetta_num() : core::io::raw_data::DisulfideFile
• 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 >
• 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
• RestrictToInterface() : core::pack::task::operation::RestrictToInterface
• RestrictYSDesign() : core::pack::task::operation::RestrictYSDesign
• restype_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• restype_index() : core::pack::scmin::ResidueAtomTreeCollectionMomento
• restypeinfo() : core::scoring::FACTSResidueInfo
• 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
• 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_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
• revoke_all_access() : core::environment::DofPassport
• reweighters_begin() : core::pack::task::IGEdgeReweightContainer
• reweighters_end() : core::pack::task::IGEdgeReweightContainer
• RG_Energy() : core::scoring::methods::RG_Energy
• RG_Energy_Fast() : core::scoring::methods::RG_Energy_Fast
• RG_Energy_RNA() : core::scoring::rna::RG_Energy_RNA
• RG_Local_MinData() : core::scoring::methods::RG_Local_MinData
• RG_LocalEnergy() : core::scoring::methods::RG_LocalEnergy
• RG_MinData() : core::scoring::methods::RG_MinData
• rho() : core::scoring::packing::HolesParamsRes , core::scoring::packstat::PackingScore
• right_cdf() : core::scoring::Ramachandran2B
• right_cdf_for_torsion_bin() : core::scoring::Ramachandran2B
• rigid_perturb_vector() : core::scoring::MembranePotential
• RigidBodySilentStruct() : core::io::silent::RigidBodySilentStruct
• RigidBodySilentStructCreator() : core::io::silent::RigidBodySilentStructCreator
• RigidDistanceVisitor() : core::chemical::RigidDistanceVisitor
• 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_intensity() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_radius() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• ring_size() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::RingConformerSet
• RingConformerSet() : core::chemical::RingConformerSet
• ringness() : core::chemical::Bond
• rings() : core::chemical::ResidueType
• 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
• RMS_Energy() : core::scoring::methods::RMS_Energy
• rmsd() : core::fragment::FragmentRmsd
• rna() : core::import_pose::ImportPoseOptions
• RNA_AtomVDW() : core::scoring::rna::RNA_AtomVDW
• rna_backbone_backbone_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_backbone_backbone_pair_energy_one_way() : 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_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_BaseBaseEnergy() : core::scoring::rna::RNA_BaseBaseEnergy
• rna_bond_geometry_energy() : core::scoring::constraints::ConstraintEdge
• 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_CentroidInfo() : core::scoring::rna::RNA_CentroidInfo
• 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_CS_parameters() : core::scoring::rna::chemical_shift::RNA_CS_parameters
• RNA_CS_residue_parameters() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• rna_data() : core::scoring::rna::data::RNA_DataInfo
• rna_data_info() : core::scoring::rna::RNA_ScoringInfo
• 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_LowResolutionPotential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• RNA_DMS_Potential() : core::scoring::rna::data::RNA_DMS_Potential
• 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_FilteredBaseBaseInfo() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• RNA_FittedTorsionInfo() : core::chemical::rna::RNA_FittedTorsionInfo
• RNA_FullAtomStackingEnergy() : core::scoring::rna::RNA_FullAtomStackingEnergy
• RNA_FullAtomVDW_BasePhosphate() : core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
• 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_LowResolutionPotential() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_Mg_Energy() : 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_PairwiseLowResolutionEnergy() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• rna_raw_base_base_info() : core::scoring::rna::RNA_ScoringInfo
• RNA_RawBaseBaseInfo() : core::scoring::rna::RNA_RawBaseBaseInfo
• rna_reactivities() : core::scoring::rna::data::RNA_DataInfo
• RNA_Reactivity() : core::scoring::rna::data::RNA_Reactivity
• rna_repulsive_pair_energy() : core::scoring::rna::RNA_LowResolutionPotential
• rna_repulsive_pair_energy_one_way() : core::scoring::rna::RNA_LowResolutionPotential
• RNA_ResidueLevelTask() : core::pack::task::rna::RNA_ResidueLevelTask
• RNA_ResidueType() : core::chemical::rna::RNA_ResidueType
• RNA_ScoringInfo() : core::scoring::rna::RNA_ScoringInfo
• RNA_SilentStruct() : core::io::silent::RNA_SilentStruct
• RNA_SilentStructCreator() : core::io::silent::RNA_SilentStructCreator
• RNA_SugarCloseEnergy() : core::scoring::rna::RNA_SugarCloseEnergy
• 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_terminal_res() : core::pose::full_model_info::FullModelInfo
• 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_Energy() : core::scoring::rna::RNA_VDW_Energy
• root() : core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::Node
• root_atom() : core::chemical::ResidueType
• root_from_code() : core::chemical::carbohydrates::CarbohydrateInfo
• rot_freq() : core::pack::annealer::SimAnnealerBase
• rot_perturb_vector() : core::scoring::MembranePotential
• rot_to_pack() : core::pack::annealer::RotamerAssigningAnnealer
• rot_well() : core::pack::dunbrack::DunbrackRotamerSampleData
• rotAlign2DPose() : core::scoring::electron_density::ElectronDensity
• rotamer() : core::conformation::RotamerSetBase , core::pack::dunbrack::RotamericData< T > , 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_aa() : core::chemical::ResidueType
• rotamer_couplings() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_couplings_exist() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_energy() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• rotamer_energy_deriv() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• rotamer_energy_deriv_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• rotamer_energy_deriv_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• 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_links() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_links_exist() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• rotamer_operations() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• rotamer_probability() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotamer_ref() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• 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_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 >
• RotamerAssigningAnnealer() : core::pack::annealer::RotamerAssigningAnnealer
• RotamerConstraint() : core::pack::dunbrack::RotamerConstraint
• RotamerDescriptor() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• RotamerDescriptorAtom() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT >
• RotamerDots() : core::pack::interaction_graph::RotamerDots
• RotamerDotsCache() : core::pack::interaction_graph::RotamerDotsCache
• RotamerDotsRadiusData() : core::pack::interaction_graph::RotamerDotsRadiusData
• RotamerExplosion() : core::pack::task::operation::RotamerExplosion
• RotamericData() : core::pack::dunbrack::RotamericData< T >
• RotamericSingleResidueDunbrackLibrary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• RotamericSingleResiduePeptoidLibrary() : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
• RotamerLibrary() : core::pack::dunbrack::RotamerLibrary
• RotamerLibraryScratchSpace() : core::pack::dunbrack::RotamerLibraryScratchSpace
• RotamerOperation() : core::pack::rotamer_set::RotamerOperation
• rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >
• RotamerSet() : core::pack::rotamer_set::RotamerSet
• RotamerSet_() : core::pack::rotamer_set::RotamerSet_
• RotamerSetBase() : core::conformation::RotamerSetBase
• RotamerSetOperation() : core::pack::rotamer_set::RotamerSetOperation
• RotamerSets() : core::pack::rotamer_set::RotamerSets
• RotamerSetsBase() : core::pack::rotamer_set::RotamerSetsBase
• RotamerSubset() : core::pack::rotamer_set::RotamerSubset
• RotamerSubsets() : core::pack::rotamer_set::RotamerSubsets
• RotamerTrie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• rotation() : core::kinematics::Stub
• rotation_by_axis() : core::kinematics::Jump
• rotation_by_matrix() : core::kinematics::Jump
• rotE() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecophipsi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotE_dsecopsi() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >
• rotid_on_moltenresidue() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• 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
• rotwell() : core::pack::dunbrack::DunbrackRotamer< S, 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
• rows() : core::sequence::DP_Matrix
• RPM_FilterStats() : core::scoring::motif::RPM_FilterStats
• rsa_feature() : core::scoring::methods::ProQ_Energy
• rsa_sc_feature() : core::scoring::methods::ProQ_Energy
• rsd() : core::id::AtomID , core::id::DOF_ID , core::id::NamedAtomID , core::id::TorsionID , core::optimization::AtomNode , core::optimization::DOF_Node , core::scoring::AtomNeighbor
• rsd1() : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• rsd2() : core::id::JumpID , core::scoring::etable::ResResEnergyInvoker< Evaluator >
• rsd_library_already_loaded() : core::pack::dunbrack::RotamerLibrary
• rsd_rsd_energy() : core::scoring::dna::DirectReadoutPotential
• rsigma_dot_initializer() : core::scoring::SecondaryStructurePotential
• rswitch() : core::scoring::constraints::BoundFunc
• rt() : core::kinematics::Jump
• RT() : core::kinematics::RT
• rt() : core::scoring::motif::ResPairMotif
• rt6() : core::scoring::motif::Xfrag
• 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_constant_temp_rotamer_substitutions() : core::pack::annealer::MultiCoolAnnealer
• run_quench() : core::pack::annealer::MultiCoolAnnealer
• run_quench_cycles() : core::pack::annealer::FASTERAnnealer