Here is a list of all namespace members with links to the namespace documentation for each member:

- r -

• R : core::scoring
• r1 : protocols::hybridization
• R1_PARA : core::scoring::nmr
• r2 : protocols::hybridization
• R2_PARA : core::scoring::nmr
• R2quat() : protocols::simple_filters
• R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• R3z : protocols::sic_dock::scores
• R3z1() : protocols::sic_dock::scores
• R3z2() : protocols::sic_dock::scores
• R3z3() : protocols::sic_dock::scores
• R_PEPTOID : core::chemical
• Ra : core::chemical::element
• radius_of_gyration() : core::pose
• RadiusOfGyrationFeaturesCOP : protocols::features
• RadiusOfGyrationFeaturesOP : protocols::features
• RAINBOW_COLOR : protocols::viewer::graphics_states_param
• RAINBOW_CPK_COLOR : protocols::viewer::graphics_states_param
• rama : core::scoring
• rama2b : core::scoring
• rama2b_lr : core::scoring::methods
• Rama2bPerturberCOP : protocols::kinematic_closure::perturbers
• Rama2bPerturberOP : protocols::kinematic_closure::perturbers
• rama_list_pred() : protocols::relax
• rama_prepro : core::scoring
• rama_prepro_check : protocols::generalized_kinematic_closure::filter
• rama_ref : core::scoring
• Rama_Table_Type : core::scoring
• Ramachandran2BCOP : core::scoring
• Ramachandran2BOP : core::scoring
• ramachandran_method : core::scoring::methods
• RamachandranCOP : core::scoring
• RamachandranEnergy2BCOP : core::scoring::methods
• RamachandranEnergy2BCreator_registrator : core::init
• RamachandranEnergy2BOP : core::scoring::methods
• RamachandranEnergyCOP : core::scoring::methods
• RamachandranEnergyCreator_registrator : core::init
• RamachandranEnergyOP : core::scoring::methods
• RamachandranHash : protocols::features
• RamachandranOP : core::scoring
• RamaCheck1BCOP : protocols::loops::loop_closure::ccd
• RamaCheck1BOP : protocols::loops::loop_closure::ccd
• RamaCheck2BCOP : protocols::loops::loop_closure::ccd
• RamaCheck2BOP : protocols::loops::loop_closure::ccd
• RamaCheckBaseCOP : protocols::loops::loop_closure::ccd
• RamaCheckBaseOP : protocols::loops::loop_closure::ccd
• RamaMutationSelectorCOP : protocols::cyclic_peptide
• RamaMutationSelectorOP : protocols::cyclic_peptide
• RamaPerturberCOP : protocols::kinematic_closure::perturbers
• RamaPerturberOP : protocols::kinematic_closure::perturbers
• ramaprepro_lr : core::scoring::methods
• RamaPreProCOP : core::scoring
• RamaPreProEnergyAP : core::scoring::methods
• RamaPreProEnergyCAP : core::scoring::methods
• RamaPreProEnergyCOP : core::scoring::methods
• RamaPreProEnergyCreator_registrator : core::init
• RamaPreProEnergyOP : core::scoring::methods
• RamaPreProOP : core::scoring
• RamaScoreCOP : protocols::frag_picker::scores
• RamaScoreOP : protocols::frag_picker::scores
• ramp_minpack_loop() : protocols::mpi_refinement
• ramp_minpack_pose() : protocols::mpi_refinement
• RampingFuncCOP : protocols::moves
• RampingFuncOP : protocols::moves
• RampingMoverCOP : protocols::moves
• RampingMoverOP : protocols::moves
• rand_rot() : core::scoring::packstat
• RANDOM : core::conformation::symmetry
• random : protocols::rigid
• random_chunk : protocols::hybridization
• random_conformer_tracer() : protocols::ligand_docking
• random_connection() : protocols::ligand_docking
• random_delay() : core::init
• random_reorientation_matrix() : protocols::geometry
• random_rotation() : core::scoring::motif , protocols::simple_moves
• random_selector : protocols::generalized_kinematic_closure::selector
• RANDOM_SIDE : protocols::forge::build::SegmentInsertConnectionScheme
• RandomConformerMoverCOP : protocols::ligand_docking
• RandomConformerMoverOP : protocols::ligand_docking
• RandomGapSolutionPickerCOP : protocols::backbone_moves::local_backbone_mover::gap_solution_pickers
• RandomGapSolutionPickerOP : protocols::backbone_moves::local_backbone_mover::gap_solution_pickers
• RandomGlycanFoliageSelectorCOP : core::select::residue_selector
• RandomGlycanFoliageSelectorOP : core::select::residue_selector
• randomize : protocols::generalized_kinematic_closure::perturber
• randomize_alpha_backbone_by_rama : protocols::generalized_kinematic_closure::perturber
• randomize_backbone_by_bins : protocols::generalized_kinematic_closure::perturber
• randomize_backbone_by_rama_prepro : protocols::generalized_kinematic_closure::perturber
• randomize_dihedral : protocols::generalized_kinematic_closure::perturber
• randomize_missing_coords() : core::io::pose_from_sfr
• randomize_selected_atoms() : protocols::comparative_modeling
• RandomizeBBByRamaPreProCOP : protocols::backbone_moves
• RandomizeBBByRamaPreProOP : protocols::backbone_moves
• RandomMoverCOP : protocols::moves
• RandomMoverOP : protocols::moves
• RandomMutationCOP : protocols::protein_interface_design::movers
• RandomMutationOP : protocols::protein_interface_design::movers
• RandomOmegaFlipMoverCOP : protocols::simple_moves
• RandomOmegaFlipMoverOP : protocols::simple_moves
• RandomPositionRotationMoverCOP : protocols::membrane
• RandomPositionRotationMoverOP : protocols::membrane
• RandomPositionTranslationMoverCOP : protocols::membrane
• RandomPositionTranslationMoverOP : protocols::membrane
• RandomResidueSelectorCOP : core::select::residue_selector
• RandomResidueSelectorOP : core::select::residue_selector
• RandomSolutionsCOP : protocols::kinematic_closure::solution_pickers
• RandomSolutionsOP : protocols::kinematic_closure::solution_pickers
• RandomSymmetrySliderCOP : protocols::symmetry
• RandomSymmetrySliderOP : protocols::symmetry
• RandomTorsionMoverCOP : protocols::simple_moves
• RandomTorsionMoverOP : protocols::simple_moves
• RandomTorsionPoseFolderCOP : protocols::denovo_design::components
• RandomTorsionPoseFolderOP : protocols::denovo_design::components
• Range : core::fragment
• range() : protocols::sic_dock
• RangeFilterCOP : protocols::simple_filters
• RangeFilterOP : protocols::simple_filters
• RangeRelaxMoverCOP : protocols::relax
• RangeRelaxMoverOP : protocols::relax
• RationalMonteCarloCOP : protocols::simple_moves::rational_mc
• RationalMonteCarloOP : protocols::simple_moves::rational_mc
• RationalMonteCarloTrigger : protocols::simple_moves::rational_mc
• RawStructOP : core::io::raw_data
• Rb : core::chemical::element
• RB1 : core::id
• RB2 : core::id
• RB3 : core::id
• RB4 : core::id
• RB5 : core::id
• RB6 : core::id
• RB_DEFAULT : protocols::rbsegment_relax
• rb_grid_rotamer_trials_atr_rep() : protocols::ligand_docking
• rb_grid_score_atr_rep() : protocols::ligand_docking
• RB_HELIX : protocols::rbsegment_relax
• RB_SHEET : protocols::rbsegment_relax
• RBConsIt : protocols::rbsegment_relax
• RBfitResultDB : protocols::electron_density
• RBInMoverCOP : protocols::splice
• RBInMoverOP : protocols::splice
• RBIt : protocols::rbsegment_relax
• RBOutMoverCOP : protocols::splice
• RBOutMoverOP : protocols::splice
• RBSegmentMoverOP : protocols::rbsegment_relax
• RBSegmentOP : protocols::rbsegment_relax
• RBSegmentRelax_main() : protocols
• RBSegmentRelaxImplOP : protocols
• RBSegmentType : protocols::rbsegment_relax
• rcl1 : core::scoring::rna::chemical_shift
• rcl2 : core::scoring::rna::chemical_shift
• rcl3 : core::scoring::rna::chemical_shift
• RDAT_VERSION_NUM_STRING : core::io::rna
• RDATCOP : core::io::rna
• RDATOP : core::io::rna
• rdc : core::scoring
• rdc_D_const() : core::scoring::nmr::rdc
• rdc_D_max() : core::scoring::nmr::rdc
• rdc_erf() : core::scoring::nmr::rdc
• rdc_ideal_bond_length() : core::scoring::nmr::rdc
• RDC_lines_collection : protocols::scoring
• RDC_NORM_TYPE : core::scoring::nmr
• rdc_rohl : core::scoring
• rdc_scaling_factor_toCH() : core::scoring::nmr::rdc
• rdc_scaling_factor_toNH() : core::scoring::nmr::rdc
• rdc_segments : core::scoring
• RDC_TYPE : core::scoring::nmr
• RDC_TYPE_CACB : core::scoring::nmr
• RDC_TYPE_CACO : core::scoring::nmr
• RDC_TYPE_CAHA : core::scoring::nmr
• RDC_TYPE_CAHN : core::scoring::nmr
• RDC_TYPE_COHN : core::scoring::nmr
• rdc_type_from_atom_names() : core::scoring::nmr
• RDC_TYPE_NCA : core::scoring::nmr
• RDC_TYPE_NCO : core::scoring::nmr
• RDC_TYPE_NH : core::scoring::nmr
• RDCDataAP : core::scoring::nmr::rdc
• RDCDataCAP : core::scoring::nmr::rdc
• RDCDataCOP : core::scoring::nmr::rdc
• RDCDataOP : core::scoring::nmr::rdc
• RDCEnergyAP : protocols::nmr::rdc
• RDCEnergyCAP : protocols::nmr::rdc
• RDCEnergyCOP : protocols::nmr::rdc
• RDCEnergyOP : protocols::nmr::rdc
• RDCMultiSetAP : core::scoring::nmr::rdc
• RDCMultiSetCAP : core::scoring::nmr::rdc
• RDCMultiSetCOP : core::scoring::nmr::rdc
• RDCMultiSetOP : core::scoring::nmr::rdc
• RDCSingleAP : core::scoring::nmr::rdc
• RDCSingleCAP : core::scoring::nmr::rdc
• RDCSingleCOP : core::scoring::nmr::rdc
• RDCSingleOP : core::scoring::nmr::rdc
• RDCSingleSetAP : core::scoring::nmr::rdc
• RDCSingleSetCAP : core::scoring::nmr::rdc
• RDCSingleSetCOP : core::scoring::nmr::rdc
• RDCSingleSetOP : core::scoring::nmr::rdc
• RDCTensorAP : core::scoring::nmr::rdc
• RDCTensorCAP : core::scoring::nmr::rdc
• RDCTensorCOP : core::scoring::nmr::rdc
• RDCTensorOP : core::scoring::nmr::rdc
• RDFBaseOP : protocols::ligand_docking::rdf
• RDFFunctionCreatorCOP : protocols::ligand_docking::rdf
• RDFFunctionCreatorOP : protocols::ligand_docking::rdf
• RDFResultList : protocols::ligand_docking::rdf
• Re : core::chemical::element
• ReactionSite : protocols::enzymatic_movers
• read1() : protocols::cluster
• read_additional_pdb_data() : core::import_pose
• read_alignment_file() : core::sequence
• read_all_alignments() : core::sequence
• read_all_poses() : core::import_pose
• read_aln() : core::sequence
• read_alternative_3_letter_codes_from_database_file() : core::io
• read_atom_selection_from_string() : core::io::nmr
• read_binary() : core::io::serialization
• read_biounit() : protocols::sic_dock
• read_body() : protocols::hydrate
• read_bytes() : core::io::serialization
• read_center_normal_from_cmd() : protocols::membrane
• read_center_normal_from_tag() : protocols::membrane
• read_checkpoint_log() : protocols::rna::movers , protocols::stepwise::monte_carlo::mover
• read_codes_and_roots_from_database_file() : core::chemical::carbohydrates
• read_comment_pdb() : core::pose
• read_conformers_from_database_file_for_ring_size() : core::chemical::rings
• read_cp_tables_from_db() : core::scoring::elec
• read_ddg_predictions_file() : core::io::PositionDdGInfo
• read_disulf_pairing_list() : protocols::jumping
• read_DNA_rotlib() : core::pack::rotamer_set
• read_enzyme_data_from_file() : core::enzymes
• read_extra_data() : core::io::mmtf
• read_extra_residues() : protocols::comparative_modeling
• read_fasta_file() : core::sequence
• read_fasta_file_and_concatenate() : core::sequence
• read_fasta_file_return_str() : core::sequence
• read_fasta_file_section() : core::sequence
• read_fasta_file_str() : core::sequence
• read_file_into_string() : protocols::cyclic_peptide_predict
• read_fold_tree_from_file() : protocols::backrub
• read_fragment_candidates() : protocols::frag_picker
• read_frags() : protocols::topology_broker
• read_Gaussian_parameters_from_database_file() : core::scoring::carbohydrates
• read_general_aln() : core::sequence
• read_general_aln_file() : core::sequence
• read_glycan_sequence_file() : core::chemical::carbohydrates
• read_gridsearch_values_from_string() : core::io::nmr
• read_grishin_aln_file() : core::sequence
• read_H3_cter_fragment() : protocols::antibody_legacy
• read_H3_seq() : protocols::splice
• read_header() : protocols::hydrate
• read_hyfile() : protocols::hydrate
• read_in_database_file() : core::io::nmr
• read_in_mutations() : protocols
• read_key_value_pair_from_line() : core::io::nmr
• read_lines_from_file() : update_ResidueType_enum_files
• read_linkage_conformers_from_database_file() : core::chemical::carbohydrates
• read_loop_fragments() : protocols::loops
• read_minor_helix_params() : protocols::helical_bundle
• read_model_file() : protocols::legacy_sewing
• read_motifs_binary() : core::scoring::motif
• read_native_residue_file() : protocols::legacy_sewing
• read_nomenclature_table_from_database_file() : core::chemical::carbohydrates
• read_pairing_list() : core::scoring::dssp , protocols::jumping
• read_pcs_datafile() : core::io::nmr
• read_pcs_dataset_params_list() : core::io::nmr
• read_pdb_seq() : protocols::splice
• read_peptide_design_file() : protocols::cyclic_peptide_predict
• read_pose_from_file() : protocols::enzdes::enzutil
• read_pre_datafile() : core::io::nmr
• read_pre_dataset_params_list() : core::io::nmr
• read_psipred_ss2_file() : core::pose
• read_rama_map_file_shapovalov() : core::chemical::mainchain_potential
• read_RBSegment_file() : protocols::rbsegment_relax
• read_rdc_datafile() : core::io::nmr
• read_rdc_dataset_params_list() : core::io::nmr
• read_rdc_tensor_values_from_string() : core::io::nmr
• read_record_definitions_from_file() : core::io::pdb
• read_rigid_core() : protocols::abinitio::abscript
• read_ring_sizes_and_morphemes_from_database_file() : core::chemical::carbohydrates
• read_selection_group_from_string() : core::io::nmr
• read_short_names_to_iupac_format_string() : core::chemical::carbohydrates
• read_ss2() : protocols::mpi_refinement
• read_std_frags_from_cmd() : core::fragment
• read_stoopid() : core::scoring::packstat
• read_template_scores() : protocols::cluster
• read_topology_file() : core::chemical
• read_xfrag_binary() : core::scoring::motif
• read_xfres_binary() : core::scoring::motif
• ReadMode : core::scoring
• ReadPoseExtraScoreFilterCOP : protocols::simple_filters
• ReadPoseExtraScoreFilterOP : protocols::simple_filters
• ReadResfileAndObeyLengthEventsCreator_registrator : core::init
• ReadResfileAndObeyLengthEventsOP : core::pack::task::operation
• ReadResfileCreator_registrator : core::init
• ReadResfileFromDBOP : protocols::task_operations
• ReadResfileOP : core::pack::task::operation
• readValueOrDie() : core::scoring::func
• READY : protocols::forge::build::BuildInstructionState
• Real : core , protocols::fldsgn::potentials::sspot , protocols::flxbb , protocols::moves , protocols::protein_interface_design::movers , protocols::protein_interface_design , protocols::rosetta_scripts , protocols::sic_dock , protocols::sic_dock::scores
• Real4 : core::pack::dunbrack
• Real5 : core::pack::dunbrack
• Real6 : protocols::match
• real6_to_rt() : core::scoring::motif
• real_regex_pattern() : protocols::docking::membrane , protocols::qsar
• real_to_uint16() : core::scoring::motif
• real_to_uint8() : core::scoring::motif
• real_to_virtual() : core::chemical
• RealAngleToShort() : protocols::loophash
• RealCIter : core::scoring::packstat
• RealIter : core::scoring::packstat
• REALLY_BAD_SCORE() : protocols::loops::loop_closure::ccd
• RealMetricCOP : core::simple_metrics
• RealMetricCreatorCOP : core::simple_metrics
• RealMetricCreatorOP : core::simple_metrics
• RealMetricOP : core::simple_metrics
• RealPerturbationType : core::conformation::parametric
• RealResidueAdjacentIter : core::chemical
• RealResidueAdjacentIterPair : core::chemical
• RealResidueED : core::chemical
• RealResidueEIter : core::chemical
• RealResidueGraph : core::chemical
• RealResidueOutEdgeIter : core::chemical
• RealResidueOutEdgeIterPair : core::chemical
• RealResidueVD : core::chemical
• RealResidueVIter : core::chemical
• RealResidueVIterPair : core::chemical
• Reals : core::scoring::motif , core::scoring::packstat , protocols::kinmatch , protocols::sasa_scores , protocols::sic_dock , protocols::sic_dock::scores
• RealValuedParameterAP : core::conformation::parametric
• RealValuedParameterCAP : core::conformation::parametric
• RealValuedParameterCAPs : core::conformation::parametric
• RealValuedParameterCOP : core::conformation::parametric
• RealValuedParameterCOPs : core::conformation::parametric
• RealValuedParameterOP : core::conformation::parametric
• RealValuedParameterOPs : core::conformation::parametric
• RealVectorValuedParameterAP : core::conformation::parametric
• RealVectorValuedParameterCAP : core::conformation::parametric
• RealVectorValuedParameterCAPs : core::conformation::parametric
• RealVectorValuedParameterCOP : core::conformation::parametric
• RealVectorValuedParameterCOPs : core::conformation::parametric
• RealVectorValuedParameterOP : core::conformation::parametric
• RealVectorValuedParameterOPs : core::conformation::parametric
• rebuild_disulfide() : core::util
• rebuild_fa_disulfides() : core::util
• rebuild_loops_until_closed() : protocols::comparative_modeling
• rebuild_missing_atoms() : protocols::denovo_design
• RECCES_MoverCOP : protocols::recces
• RECCES_MoverOP : protocols::recces
• RECCES_OptionsCOP : protocols::recces::options
• RECCES_OptionsOP : protocols::recces::options
• RECCES_ParametersCOP : protocols::recces::params
• RECCES_ParametersOP : protocols::recces::params
• recces_pose_setup() : protocols::recces
• recenter() : core::conformation::symmetry
• Record : core::io::pdb
• RecordDef : core::io::pdb
• RecordType : core::io::pdb
• RecoverSideChainsMoverCOP : protocols::comparative_modeling
• RecoverSideChainsMoverOP : protocols::comparative_modeling
• recreate_task() : protocols::enzdes::enzutil
• recursive_multiple_disulfide_former() : protocols::forge::remodel
• recursively_access_all_attributes() : protocols::rosetta_scripts
• reduce : core::scoring::sasa
• reduced_size() : protocols::scoring::methods::pcs2
• ref : core::scoring
• REF_2015 : core::scoring
• ref_nc : core::scoring
• ref_spectrum : core::scoring::saxs
• reference_e_method : core::scoring::methods
• reference_from_restype_ptr() : core::conformation
• ReferenceEnergyCOP : core::scoring::methods
• ReferenceEnergyCreator_registrator : core::init
• ReferenceEnergyNoncanonicalCOP : core::scoring::methods
• ReferenceEnergyNoncanonicalCreator_registrator : core::init
• ReferenceEnergyNoncanonicalOP : core::scoring::methods
• ReferenceEnergyOP : core::scoring::methods
• ReferencePoseAP : core::pose::reference_pose
• ReferencePoseCAP : core::pose::reference_pose
• ReferencePoseCAPs : core::pose::reference_pose
• ReferencePoseCOP : core::pose::reference_pose
• ReferencePoseCOPs : core::pose::reference_pose
• ReferencePoseOP : core::pose::reference_pose
• ReferencePoseOPs : core::pose::reference_pose
• ReferencePoseSetAP : core::pose::reference_pose
• ReferencePoseSetCAP : core::pose::reference_pose
• ReferencePoseSetCAPs : core::pose::reference_pose
• ReferencePoseSetCOP : core::pose::reference_pose
• ReferencePoseSetCOPs : core::pose::reference_pose
• ReferencePoseSetOP : core::pose::reference_pose
• ReferencePoseSetOPs : core::pose::reference_pose
• REFINE() : protocols::loops::loop_mover
• refine_all_cdr_loops() : protocols::tcr
• refine_cdr3_loops() : protocols::tcr
• refine_cdr_loop() : protocols::tcr
• refine_mindis_with_xyzHash() : protocols::sic_dock
• refine_tcr_cdr_loops() : protocols::tcr
• RefineBetaBarrelCOP : protocols::antibody
• RefineBetaBarrelOP : protocols::antibody
• RefinementResultDB : protocols::electron_density
• RefTag : core::import_pose::atom_tree_diffs
• RefTags : core::import_pose::atom_tree_diffs
• reg_AndJumpSelectorCreator : core::init
• reg_AndResidueSelectorCreator : core::init
• reg_AsymmetricUnitSelectorCreator : core::init
• reg_BinSelectorCreator : core::init
• reg_BondedResidueSelectorCreator : core::init
• reg_ChainSelectorCreator : core::init
• reg_ClashBasedShellSelectorCreator : core::init
• reg_CloseContactResidueSelectorCreator : core::init
• reg_CustomBaseTypePackerPaletteCreator : core::init
• reg_DefaultPackerPaletteCreator : core::init
• reg_DensityFitResidueSelectorCreator : core::init
• reg_FalseResidueSelectorCreator : core::init
• reg_GlycanLayerSelectorCreator : core::init
• reg_GlycanResidueSelectorCreator : core::init
• reg_GlycanSequonsSelectorCreator : core::init
• reg_InterchainJumpSelectorCreator : core::init
• reg_InterGroupInterfaceByVectorSelectorCreator : core::init
• reg_JumpDownstreamSelectorCreator : core::init
• reg_JumpIndexSelectorCreator : core::init
• reg_JumpUpstreamSelectorCreator : core::init
• reg_LayerSelectorCreator : core::init
• reg_NeighborhoodResidueSelectorCreator : core::init
• reg_NoDesignPackerPaletteCreator : core::init
• reg_NotJumpSelectorCreator : core::init
• reg_NotResidueSelectorCreator : core::init
• reg_NumNeighborsSelectorCreator : core::init
• reg_OrJumpSelectorCreator : core::init
• reg_OrResidueSelectorCreator : core::init
• reg_PhiSelectorCreator : core::init
• reg_PrimarySequenceNeighborhoodSelectorCreator : core::init
• reg_RandomGlycanFoliageSelectorCreator : core::init
• reg_RandomResidueSelectorCreator : core::init
• reg_ResidueIndexSelectorCreator : core::init
• reg_ResidueInMembraneSelectorCreator : core::init
• reg_ResidueInSequenceMotifSelectorCreator : core::init
• reg_ResidueNameSelectorCreator : core::init
• reg_ResiduePDBInfoHasLabelSelectorCreator : core::init
• reg_ResiduePropertySelectorCreator : core::init
• reg_ResidueSpanSelectorCreator : core::init
• reg_ScoreTermValueBasedSelectorCreator : core::init
• reg_SecondaryStructureSelectorCreator : core::init
• reg_SliceResidueSelectorCreator : core::init
• reg_SSElementSelectorCreator : core::init
• reg_SymmetricalResidueSelectorCreator : core::init
• reg_TrueResidueSelectorCreator : core::init
• regenerate_graph_vertex_index() : core::chemical
• regex_usable() : core::select::residue_selector
• RegionCOP : protocols::nonlocal
• RegionOP : protocols::nonlocal
• register1() : protocols::init
• register2() : protocols::init
• register3() : protocols::init
• register4() : protocols::init
• register_common_options() : protocols::abinitio
• register_creators() : protocols::init
• register_cutoff() : protocols::abinitio
• register_options() : protocols::evaluation , protocols::jd2
• register_options_broker() : protocols::abinitio
• register_options_universal_main() : protocols::jobdist
• register_unpublished_author_info() : core::pack::annealer
• RegisterShift : protocols::denovo_design::components
• RegisterShifts : protocols::denovo_design::components
• regular_edges_within_interval() : protocols::forge::methods
• regular_facet_containing_position() : protocols::forge::methods
• reinitialize_mingraph_neighborhood_for_residue() : core::pack
• reject : protocols::hotspot_hashing
• REJECTED : protocols::monte_carlo
• rel_per_res_sc_sasa() : core::scoring::sasa
• RelativeConnectRightAP : protocols::forge::build
• RelativeConnectRightCAP : protocols::forge::build
• RelativeConnectRightCOP : protocols::forge::build
• RelativeConnectRightOP : protocols::forge::build
• RelativePoseFilterCOP : protocols::calc_taskop_filters
• RelativePoseFilterOP : protocols::calc_taskop_filters
• RelativeSegmentCOP : protocols::protein_interface_design::filters
• RelativeSegmentOP : protocols::protein_interface_design::filters
• RelativeSequencePositionAP : protocols::forge::build
• RelativeSequencePositionCAP : protocols::forge::build
• RelativeSequencePositionCOP : protocols::forge::build
• RelativeSequencePositionOP : protocols::forge::build
• RELAX : protocols::abinitio
• relax : protocols::antibody::design
• Relax_main() : protocols::relax
• relax_pose() : protocols::relax
• RelaxProtocolBaseAP : protocols::relax
• RelaxProtocolBaseCAP : protocols::relax
• RelaxProtocolBaseCOP : protocols::relax
• RelaxProtocolBaseOP : protocols::relax
• RelaxScriptFileContentsCOP : protocols::relax
• RelaxScriptFileContentsOP : protocols::relax
• RelaxScriptManagerCOP : protocols::relax
• RelaxScriptManagerOP : protocols::relax
• ReleaseConstraintFromResidueMoverCOP : protocols::fold_from_loops::movers
• ReleaseConstraintFromResidueMoverOP : protocols::fold_from_loops::movers
• remap_cis_omega_torsion_bins_to_trans() : core::conformation
• remap_names_on_geometry() : core::io::pose_from_sfr
• remap_rb_segments() : protocols::rbsegment_relax
• remap_vect() : core::chemical
• REMARK : core::io::pdb
• RemarksCOP : core::io
• RemarksOP : core::io
• remodel_fold_tree_to_account_for_insertion() : core::kinematics
• remodel_generic_taskfactory() : protocols::forge::methods
• remodel_tcr_cdr_loops() : protocols::tcr
• RemodelConstraintGeneratorAP : protocols::forge::remodel
• RemodelConstraintGeneratorCAP : protocols::forge::remodel
• RemodelConstraintGeneratorCOP : protocols::forge::remodel
• RemodelConstraintGeneratorOP : protocols::forge::remodel
• RemodelEnzdesCstModuleOP : protocols::forge::remodel
• RemodelGlobalFrame_AP : protocols::forge::remodel
• RemodelGlobalFrame_CAP : protocols::forge::remodel
• RemodelGlobalFrame_COP : protocols::forge::remodel
• RemodelGlobalFrame_OP : protocols::forge::remodel
• RemodelLigandHandler_AP : protocols::forge::remodel
• RemodelLigandHandler_CAP : protocols::forge::remodel
• RemodelLigandHandler_COP : protocols::forge::remodel
• RemodelLigandHandler_OP : protocols::forge::remodel
• RemodelLoopMoverAP : protocols::forge::remodel
• RemodelLoopMoverCAP : protocols::forge::remodel
• RemodelLoopMoverCOP : protocols::forge::remodel
• RemodelLoopMoverOP : protocols::forge::remodel
• RemodelLoopMoverPoseFolderCOP : protocols::denovo_design::components
• RemodelLoopMoverPoseFolderOP : protocols::denovo_design::components
• RemodelMover_AP : protocols::forge::remodel
• RemodelMover_CAP : protocols::forge::remodel
• RemodelMover_COP : protocols::forge::remodel
• RemodelMover_OP : protocols::forge::remodel
• RemodelRotamerLinksOP : protocols::forge::remodel
• REMOVE : protocols::enzdes
• remove_all_anchors_and_ENF() : protocols::hydrate
• remove_all_enzdes_constraints() : protocols::enzdes::enzutil
• remove_all_jump_atoms() : protocols::denovo_design
• remove_all_variant_types() : protocols::stepwise::modeler::rna
• remove_all_virtual_phosphates() : protocols::stepwise::modeler::rna
• remove_and_store_bracketed() : core::pose::rna
• remove_bracketed() : core::pose::rna
• remove_carbohydrate_branch_point_variants() : core::pose::carbohydrates
• remove_chain_break_jump_point() : protocols::stepwise::legacy::modeler::rna
• remove_chain_break_variants() : protocols::stepwise::modeler::rna
• remove_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• remove_constraint_from_residue_constraints() : core::scoring::constraints
• remove_constraints_of_type() : core::scoring::constraints
• remove_coordinate_constraints_from_pose() : protocols::protein_interface_design
• remove_cut() : protocols::jumping
• remove_cutpoint() : protocols::forge::methods
• remove_cutpoint_closed() : core::import_pose
• remove_cutpoint_variants() : core::util , protocols::forge::methods , protocols::loops
• remove_cutpoint_variants_for_ccd() : protocols::grafting
• remove_cutpoints() : protocols::forge::methods
• remove_cutpoints_closed() : core::import_pose
• remove_file() : protocols::stepwise::modeler::rna
• remove_high_energy_water_molecules() : protocols::hydrate
• remove_hotspot_constraints_from_pose() : protocols::hotspot_hashing
• remove_ligand_canonical_residues() : core::pose
• remove_lower_terminus_type_from_conformation_residue() : core::conformation
• remove_lower_terminus_type_from_pose_residue() : core::pose
• remove_mg_bound_waters() : protocols::magnesium
• remove_missing_density() : protocols::loops
• remove_missing_jump_atoms() : protocols::denovo_design
• remove_models_from_dssp() : protocols::legacy_sewing
• remove_non_buried_wat() : protocols::hydrate
• remove_non_protein_residues() : protocols::toolbox::pose_manipulation
• remove_nonbb_constraints() : core::scoring::constraints
• remove_nonprotein_residues() : core::pose
• remove_register_shift_single_pair() : protocols::fldsgn::filters
• remove_register_shifts() : protocols::fldsgn::filters
• remove_remark_header_for_geomcst() : protocols::enzdes::enzutil
• remove_residues() : protocols::hybridization
• remove_set1_elements_from_set2() : protocols::rna::movers
• remove_short_chunks() : protocols::loops
• remove_silent_file_if_it_exists() : core::io::silent
• remove_small_gaps() : protocols::loops
• remove_terminal_phosphates() : protocols::stepwise::modeler::rna::phosphate
• remove_terminus_variant_types_for_rna() : core::import_pose::libraries
• remove_upper_lower_variants_from_RNA() : core::pose::rna
• remove_upper_terminus_type_from_conformation_residue() : core::conformation
• remove_upper_terminus_type_from_pose_residue() : core::pose
• remove_variant_type_from_conformation_residue() : core::conformation
• remove_variant_type_from_pose_residue() : core::pose
• remove_variant_type_from_residue() : core::pose
• remove_virtual_O2Prime_hydrogen() : protocols::stepwise::modeler::rna
• remove_virtual_residues() : core::pose
• remove_virtual_rna_residue_variant_type() : core::pose::rna
• remove_waters_except_mg_bound() : protocols::magnesium
• remove_whitespaces() : core::scoring::rna::chemical_shift
• RemoveConstraintsCOP : protocols::constraint_generator
• RemoveConstraintsOP : protocols::constraint_generator
• RemoveLigandFilterOP : protocols::enzdes
• rename_atoms() : core::chemical
• renumber_pdbinfo_based_on_conf_chains() : core::pose
• renumber_with_pdb_info() : protocols::hybridization
• reorder_chains() : protocols::denovo_design::components
• reorder_full_model_info_after_append() : core::pose::full_model_info
• reorder_full_model_info_after_delete() : core::pose::full_model_info
• reorder_full_model_info_after_prepend() : core::pose::full_model_info
• reorder_glycan_residues() : core::io
• reorder_membrane_foldtree() : protocols::membrane
• reorder_moving_res_list_after_delete() : core::pose::full_model_info
• reorder_moving_res_list_after_insert() : core::pose::full_model_info
• reorder_pose() : core::import_pose
• reorder_res_list_after_append() : core::pose::full_model_info
• reorder_res_list_after_delete() : core::pose::full_model_info
• reorder_res_list_after_prepend() : core::pose::full_model_info
• reorder_root_partition_res() : core::pose
• reorder_with_first_non_mobile_as_root() : protocols::ligand_docking
• reorient_extended_fibril() : protocols::fibril
• repack : protocols::antibody::design
• repack_connection_and_residues_in_movemap() : protocols::grafting
• repack_connection_and_residues_in_movemap_and_piece() : protocols::grafting
• repack_connection_and_residues_in_movemap_and_piece_and_neighbors() : protocols::grafting
• repack_these_residues() : protocols::toolbox::pose_manipulation
• repack_this_residue() : protocols::toolbox::pose_manipulation
• repackable_residues() : core::pack
• repackable_residues_dup() : core::pack
• RepackingRefinerCOP : protocols::loop_modeling::refiners
• RepackingRefinerOP : protocols::loop_modeling::refiners
• RepackSidechainsMoverCOP : protocols::minimization_packing
• RepackSidechainsMoverOP : protocols::minimization_packing
• RepackTrialCOP : protocols::loops::loop_mover::refine
• RepackTrialOP : protocols::loops::loop_mover::refine
• RepeatMoverCOP : protocols::moves
• RepeatMoverOP : protocols::moves
• RepeatParameterFilterCOP : protocols::simple_filters
• RepeatParameterFilterOP : protocols::simple_filters
• RepeatPropagationMoverCOP : protocols::simple_moves
• RepeatPropagationMoverOP : protocols::simple_moves
• RepeatProteinRelaxCOP : protocols::simple_moves
• RepeatProteinRelaxOP : protocols::simple_moves
• RepGridTracer() : protocols::qsar::scoring_grid
• REPL_PHOSPHATE : core::chemical
• replace() : protocols::forge::methods
• replace_conformation_residue_copying_existing_coordinates() : core::conformation
• replace_file() : protocols::monte_carlo
• replace_pose_residue_copying_existing_coordinates() : core::pose
• replace_region() : protocols::grafting
• replace_residue_in_atom_tree() : core::conformation
• replace_residue_keeping_all_atom_positions() : protocols::toolbox::match_enzdes_util
• replace_substr() : core::kinematics
• replace_underscores_with_spaces() : core::chemical::carbohydrates
• replaced_symmetric_foldtree_with_new_monomer() : core::conformation::symmetry
• ReplaceRegionMoverCOP : protocols::grafting
• ReplaceRegionMoverOP : protocols::grafting
• ReplicaExchangeMC_COP : protocols::moves
• ReplicaExchangeMC_OP : protocols::moves
• ReplicateFilterCOP : protocols::filters
• ReplicateFilterOP : protocols::filters
• ReplicateTaskAP : core::pack::task::operation
• ReplicateTaskCAP : core::pack::task::operation
• ReplicateTaskCOP : core::pack::task::operation
• ReplicateTaskOP : core::pack::task::operation
• REPLONLY : core::chemical
• REPLS_BB : core::chemical
• report_application_command() : core::init
• report_batch_inconsistency() : protocols::jd2::archive
• report_coordinate_constraints() : protocols::splice
• report_des_pack_res() : protocols::splice
• report_designable_packable_residues() : protocols::splice
• report_heading_directions_of_all_AA_in_a_strand() : protocols::features::strand_assembly
• report_tag_error() : protocols::jd2::archive
• report_unfolded() : protocols::fold_from_loops::utils
• report_value_error() : protocols::jd2::archive
• ReportCOP : protocols::features
• ReportOP : protocols::features
• ReportToDBCOP : protocols::features
• ReportToDBOP : protocols::features
• ReportXYZCOP : protocols::simple_moves
• ReportXYZOP : protocols::simple_moves
• represent_residue_selector() : core::select::residue_selector
• RepresentativeOutputterMap : protocols::jd3::standard
• REPULSIVE : core::chemical
• RepulsiveOnlyMoverCOP : protocols::simple_moves
• RepulsiveOnlyMoverOP : protocols::simple_moves
• REQUEST_SYMMETRIZE_BY_INTERSECTION : core::pack::task
• REQUEST_SYMMETRIZE_BY_UNION : core::pack::task
• requires_CB_mapping() : core::scoring::constraints
• reroot() : core::pose
• reroot_based_on_full_model_info() : protocols::stepwise::modeler
• reroot_restype() : core::chemical
• res1_pointed_at_res2() : core::select::util
• res_filter_schema_w_attributes() : core::pack::task::operation
• res_in_chain() : core::pose
• res_lvl_task_op_schema_empty() : core::pack::task::operation
• res_lvl_task_op_schema_w_attributes() : core::pack::task::operation
• res_matrix : protocols::splice
• res_res_min_distance() : protocols::simple_filters
• res_rmsd() : protocols::protein_interface_design::filters , protocols::simple_filters
• res_type_constraint : core::scoring
• res_type_linking_constraint : core::scoring
• resample() : core::scoring::electron_density
• RESAMPLE : protocols::stepwise::monte_carlo::mover
• RESAMPLE_INTERNAL_LOCAL : protocols::stepwise::monte_carlo::mover
• ResampleMoverCOP : protocols::stepwise::monte_carlo::mover
• ResampleMoverCreatorCOP : protocols::stepwise::monte_carlo::mover
• ResampleMoverCreatorOP : protocols::stepwise::monte_carlo::mover
• ResampleMoverOP : protocols::stepwise::monte_carlo::mover
• rescale_scorefxn() : protocols::stepwise::modeler::rna
• ResElecGroup : core::scoring::elec
• reset_x() : protocols::toolbox
• ResetBaselineMoverCOP : protocols::monte_carlo
• ResetBaselineMoverOP : protocols::monte_carlo
• ResetFoldTreeCOP : protocols::simple_moves
• ResetFoldTreeOP : protocols::simple_moves
• ResetFullModelInfoMoverCOP : protocols::simple_moves
• ResetFullModelInfoMoverOP : protocols::simple_moves
• ResfileCommandCOP : core::pack::task
• ResfileCommandOP : core::pack::task
• ResfileCommandOperationCOP : protocols::task_operations
• ResfileCommandOperationOP : protocols::task_operations
• ResfileContentsCOP : core::pack::task
• ResfileContentsOP : core::pack::task
• ResFilterCOP : core::pack::task::operation
• ResFilterCreatorCOP : core::pack::task::operation
• ResFilterCreatorOP : core::pack::task::operation
• ResFilterFactoryCOP : core::pack::task::operation
• ResFilterFactoryOP : core::pack::task::operation
• ResFilterOP : core::pack::task::operation
• ResHashMapCOP : protocols::mean_field
• ResHashMapOP : protocols::mean_field
• ResIdCOP : protocols::moves
• ResIdOP : protocols::moves
• resids() : core::select
• ResidualDipolarCoupling_RohlCOP : core::scoring
• ResidualDipolarCoupling_RohlOP : core::scoring
• ResidualDipolarCouplingCOP : core::scoring
• ResidualDipolarCouplingEnergy_RohlCreator_registrator : core::init
• ResidualDipolarCouplingEnergyCreator_registrator : core::init
• ResidualDipolarCouplingEnergyOP : core::scoring::methods
• ResidualDipolarCouplingEnergyRigidSegmentsOP : protocols::scoring::methods
• ResidualDipolarCouplingOP : core::scoring
• ResidualDipolarCouplingRigidSegmentsCOP : protocols::scoring
• ResidualDipolarCouplingRigidSegmentsOP : protocols::scoring
• RESIDUE_ALTERNATIVE : protocols::toolbox
• RESIDUE_ALTERNATIVE_COMB : protocols::toolbox
• RESIDUE_APPLIER : protocols::stepwise::screener
• residue_burial_filter_tracer() : protocols::simple_filters
• residue_center_of_mass() : core::conformation::symmetry , core::pose
• RESIDUE_COLOR : protocols::viewer::graphics_states_param
• RESIDUE_CONTACT : protocols::stepwise::screener
• RESIDUE_CPK_COLOR : protocols::viewer::graphics_states_param
• residue_cutoff() : protocols::abinitio
• residue_distance_filter_tracer() : protocols::simple_filters
• residue_entries_to_pose() : protocols::indexed_structure_store
• residue_fast_pair_energy_attached_H() : core::scoring
• residue_gws_string() : core::io::carbohydrates
• residue_is_bulge() : core::pose::rna
• residue_is_compatible() : protocols::denovo_design::components
• residue_is_floppy() : protocols::sic_dock
• RESIDUE_LIST : protocols::toolbox
• residue_near_water() : core::scoring::hbonds , protocols::hydrate
• residue_packer_states() : protocols::rosetta_scripts
• residue_point_graph_from_conformation() : core::conformation
• residue_range_gws_string() : core::io::carbohydrates
• residue_rebuild_checkpoint_namer() : protocols::stepwise::monte_carlo::mover
• residue_rebuild_log_namer() : protocols::stepwise::monte_carlo::mover
• residue_rmsd_nosuper() : core::scoring
• residue_rmsd_super() : core::scoring
• residue_rotamer_recovery() : core::pack
• residue_sc_rmsd_no_super() : core::scoring , protocols::hotspot_hashing
• residue_selector_single_from_line() : core::chemical
• residue_subset() : protocols::pose_metric_calculators
• residue_type_all_patches_name() : core::chemical
• residue_type_base_name() : core::chemical
• residue_type_bases_identical() : core::chemical
• residue_types_from_saccharide_sequence() : core::pose
• residue_types_from_saccharide_sequence_recursive() : core::pose
• residue_types_from_sequence() : core::pose
• residue_types_identical() : core::chemical
• ResidueAlternativeSetCOP : protocols::stepwise::sampler::copy_dofs
• ResidueAlternativeSetOP : protocols::stepwise::sampler::copy_dofs
• ResidueAlternativeStepWiseSamplerCombCOP : protocols::stepwise::sampler::copy_dofs
• ResidueAlternativeStepWiseSamplerCombOP : protocols::stepwise::sampler::copy_dofs
• ResidueAlternativeStepWiseSamplerCOP : protocols::stepwise::sampler::copy_dofs
• ResidueAlternativeStepWiseSamplerOP : protocols::stepwise::sampler::copy_dofs
• ResidueAP : core::conformation
• ResidueArrayAnnealableEnergyCOP : core::scoring::annealing
• ResidueArrayAnnealableEnergyOP : core::scoring::annealing
• ResidueArrayAnnealingEvaluatorOP : core::pack::interaction_graph
• ResidueAtomTreeCollectionCOP : core::pack::scmin
• ResidueAtomTreeCollectionMomentoCOP : core::pack::scmin
• ResidueAtomTreeCollectionMomentoOP : core::pack::scmin
• ResidueAtomTreeCollectionOP : core::pack::scmin
• ResidueBurialFeaturesCOP : protocols::features
• ResidueBurialFeaturesOP : protocols::features
• ResidueCAP : core::conformation
• ResidueCAPs : core::conformation
• ResidueCartBondedParametersAP : core::scoring::methods
• ResidueCartBondedParametersCAP : core::scoring::methods
• ResidueCartBondedParametersCOP : core::scoring::methods
• ResidueCartBondedParametersOP : core::scoring::methods
• ResidueConformationFeaturesCOP : protocols::features
• ResidueConformationFeaturesOP : protocols::features
• ResidueConstraintsCOP : core::scoring::constraints
• ResidueConstraintsOP : core::scoring::constraints
• ResidueContactScreenerCOP : protocols::stepwise::screener
• ResidueContactScreenerOP : protocols::stepwise::screener
• ResidueCoordinateChangeListOP : core::kinematics
• ResidueCOP : core::conformation , core::scoring::nmr
• ResidueCOPs : core::conformation
• ResidueCouplingConstraintCOP : core::scoring::constraints
• ResidueCouplingConstraintOP : core::scoring::constraints
• ResidueDataCacheIndex : core::conformation::residue_datacache
• ResidueDecompositionByChainCalculatorCOP : protocols::pose_metric_calculators
• ResidueDecompositionByChainCalculatorOP : protocols::pose_metric_calculators
• ResidueDepthDataCOP : protocols::simple_filters
• ResidueDepthDataOP : protocols::simple_filters
• ResidueElements : protocols::environment::claims
• ResidueExclParamsCOP : core::scoring
• ResidueExclParamsOP : core::scoring
• ResidueFeatureCOP : protocols::comparative_modeling::features
• ResidueFeatureOP : protocols::comparative_modeling::features
• ResidueFeaturesCOP : protocols::features
• ResidueFeaturesOP : protocols::features
• ResidueGraph : core::chemical
• ResidueGridScoresFeaturesCOP : protocols::features
• ResidueGridScoresFeaturesOP : protocols::features
• ResidueHasPropertyCreator_registrator : core::init
• ResidueHasPropertyOP : core::pack::task::operation
• ResidueIdentifier : protocols::loops
• ResidueIEFilterCOP : protocols::simple_filters
• ResidueIEFilterOP : protocols::simple_filters
• ResidueIndexDescriptionCOP : core::pose
• ResidueIndexDescriptionOP : core::pose
• ResidueIndexIsCreator_registrator : core::init
• ResidueIndexIsntCreator_registrator : core::init
• ResidueIndexIsntOP : core::pack::task::operation
• ResidueIndexIsOP : core::pack::task::operation
• ResidueIndexList : core::kinematics
• ResidueIndexSelectorCOP : core::select::residue_selector
• ResidueIndexSelectorOP : core::select::residue_selector
• ResidueInMembraneSelectorCOP : core::select::residue_selector
• ResidueInMembraneSelectorOP : core::select::residue_selector
• ResidueInSequenceMotifSelectorCOP : core::select::residue_selector
• ResidueInSequenceMotifSelectorOP : core::select::residue_selector
• ResidueKinWriterCOP : core::conformation
• ResidueKinWriterOP : core::conformation
• ResidueLabelsToPymolSelectionMoverCOP : protocols::fold_from_loops::movers
• ResidueLabelsToPymolSelectionMoverOP : protocols::fold_from_loops::movers
• ResidueLacksPropertyCreator_registrator : core::init
• ResidueLacksPropertyOP : core::pack::task::operation
• ResidueListIterator : core::kinematics
• ResidueListStepWiseSamplerCOP : protocols::stepwise::sampler::copy_dofs
• ResidueListStepWiseSamplerOP : protocols::stepwise::sampler::copy_dofs
• ResidueMaskOP : protocols::constel
• ResidueMatcherCOP : core::conformation
• ResidueMatcherOP : core::conformation
• ResidueName3IsCreator_registrator : core::init
• ResidueName3IsntCreator_registrator : core::init
• ResidueName3IsntOP : core::pack::task::operation
• ResidueName3IsOP : core::pack::task::operation
• ResidueNameSelectorCOP : core::select::residue_selector
• ResidueNameSelectorOP : core::select::residue_selector
• ResidueNblistDataCOP : core::scoring
• ResidueNblistDataOP : core::scoring
• ResidueNeighborConstIteratorCOP : core::scoring
• ResidueNeighborConstIteratorOP : core::scoring
• ResidueNeighborIteratorCOP : core::scoring
• ResidueNeighborIteratorOP : core::scoring
• ResidueNetworkCOP : protocols::toolbox
• ResidueNetworkOP : protocols::toolbox
• ResidueOP : core::conformation , core::scoring::nmr
• ResidueOPs : core::conformation
• ResiduePair : protocols::denovo_design::components
• ResiduePairEvalType : core::pack::interaction_graph
• ResiduePairJumpCOP : protocols::jumping
• ResiduePairJumpOP : protocols::jumping
• ResiduePairJumpSetupCOP : protocols::jumping
• ResiduePairJumpSetupOP : protocols::jumping
• ResiduePairJumpSetupSingleCOP : protocols::jumping
• ResiduePairJumpSetupSingleOP : protocols::jumping
• ResiduePairJumpSingleCOP : protocols::jumping
• ResiduePairJumpSingleOP : protocols::jumping
• ResiduePairNeighborListCOP : core::scoring
• ResiduePairNeighborListOP : core::scoring
• ResiduePairs : protocols::denovo_design::components , protocols::fldsgn
• ResiduePDBIndexIsntOP : core::pack::task::operation
• ResiduePDBIndexIsOP : core::pack::task::operation
• ResiduePDBInfoHasLabelCreator_registrator : core::init
• ResiduePDBInfoHasLabelOP : core::pack::task::operation
• ResiduePDBInfoHasLabelSelectorCOP : core::select::residue_selector
• ResiduePDBInfoHasLabelSelectorOP : core::select::residue_selector
• ResidueProbDesignOperationCOP : protocols::task_operations
• ResidueProbDesignOperationOP : protocols::task_operations
• ResiduePropertiesCOP : core::chemical
• ResiduePropertiesOP : core::chemical
• ResidueProperty : core::chemical
• ResiduePropertySelectorCOP : core::select::residue_selector
• ResiduePropertySelectorOP : core::select::residue_selector
• ResidueRangesAP : core::select::residue_selector
• ResidueRangesCAP : core::select::residue_selector
• ResidueRangesCOP : core::select::residue_selector
• ResidueRangesOP : core::select::residue_selector
• ResidueReplacementRebuildMoverCOP : protocols::ncbb
• ResidueReplacementRebuildMoverOP : protocols::ncbb
• residues_downstream_of_jump() : core::kinematics
• residues_in_interface_tracer() : protocols::simple_filters
• residues_interact() : core::scoring::methods
• residues_upstream_of_jump() : core::kinematics
• ResidueScoresFeaturesCOP : protocols::features
• ResidueScoresFeaturesOP : protocols::features
• ResidueSecondaryStructureFeaturesCOP : protocols::features
• ResidueSecondaryStructureFeaturesOP : protocols::features
• ResidueSelection : core::scoring
• ResidueSelectionVector : core::scoring
• ResidueSelectorAP : core::select::residue_selector
• ResidueSelectorCAP : core::select::residue_selector
• ResidueSelectorCOP : core::select::residue_selector
• ResidueSelectorCreatorCOP : core::select::residue_selector
• ResidueSelectorCreatorOP : core::select::residue_selector
• ResidueSelectorOP : core::select::residue_selector
• ResidueSpanSelectorCOP : core::select::residue_selector
• ResidueSpanSelectorOP : core::select::residue_selector
• ResidueSubset : core::select::residue_selector
• ResidueSubsetAP : core::select::residue_selector
• ResidueSubsetCAP : core::select::residue_selector
• ResidueSubsetCOP : core::select::residue_selector
• ResidueSubsetOP : core::select::residue_selector
• ResidueSummaryMetricCOP : core::simple_metrics::metrics
• ResidueSummaryMetricOP : core::simple_metrics::metrics
• ResidueTorsionRestraintsCOP : protocols::ligand_docking
• ResidueTorsionRestraintsOP : protocols::ligand_docking
• ResidueTotalScoresFeaturesCOP : protocols::features
• ResidueTotalScoresFeaturesOP : protocols::features
• ResidueTypeAP : core::chemical
• ResidueTypeBaseAP : core::chemical
• ResidueTypeBaseCAP : core::chemical
• ResidueTypeBaseCOP : core::chemical
• ResidueTypeBaseOP : core::chemical
• ResidueTypeCAP : core::chemical
• ResidueTypeCAPs : core::chemical
• ResidueTypeConstraintCOP : core::scoring::constraints
• ResidueTypeConstraintGeneratorCOP : protocols::constraint_generator
• ResidueTypeConstraintGeneratorOP : protocols::constraint_generator
• ResidueTypeConstraintMoverCOP : protocols::constraint_movers
• ResidueTypeConstraintMoverOP : protocols::constraint_movers
• ResidueTypeConstraintOP : core::scoring::constraints
• ResidueTypeCOP : core::chemical
• ResidueTypeCOPs : core::chemical
• ResidueTypeFinderCOP : core::chemical
• ResidueTypeFinderOP : core::chemical
• ResidueTypeKinWriterCOP : core::chemical
• ResidueTypeKinWriterOP : core::chemical
• ResidueTypeLinkingConstraintCOP : core::scoring::constraints
• ResidueTypeLinkingConstraintOP : core::scoring::constraints
• ResidueTypeOP : core::chemical
• ResidueTypeOPs : core::chemical
• ResidueTypeResFilterCreator_registrator : core::init
• ResidueTypeSelectorOP : core::chemical
• ResidueTypeSelectorSingleOP : core::chemical
• ResidueTypeSetCacheCOP : core::chemical
• ResidueTypeSetCacheOP : core::chemical
• ResidueTypeSetCAP : core::chemical
• ResidueTypeSetCOP : core::chemical
• ResidueTypeSetOP : core::chemical
• ResidueTypesFeaturesCOP : protocols::features
• ResidueTypesFeaturesOP : protocols::features
• ResidueVectorAP : core::select::residue_selector
• ResidueVectorCAP : core::select::residue_selector
• ResidueVectorCOP : core::select::residue_selector
• ResidueVectorOP : core::select::residue_selector
• ResidueVicinityInfoCOP : protocols::forge::remodel
• ResidueVicinityInfoOP : protocols::forge::remodel
• ResidueVicinityRCGCAP : protocols::forge::remodel
• ResidueVicinityRCGOP : protocols::forge::remodel
• resize_and_add_if_not_empty() : core::io::mmtf
• ResLvlTaskOperationCOP : core::pack::task::operation
• ResLvlTaskOperationCreatorCOP : core::pack::task::operation
• ResLvlTaskOperationCreatorOP : core::pack::task::operation
• ResLvlTaskOperationFactoryCOP : core::pack::task::operation
• ResLvlTaskOperationFactoryOP : core::pack::task::operation
• ResLvlTaskOperationOP : core::pack::task::operation
• ResMap : core::pose , protocols::stepwise::modeler::protein
• resnums_from_bool_mask() : core::pack::task::residue_selector
• resnums_from_task() : core::pack::task::residue_selector
• ResolutionSwitcherCOP : protocols::abinitio
• ResolutionSwitcherOP : protocols::abinitio
• ResonanceAP : protocols::noesy_assign
• ResonanceCAP : protocols::noesy_assign
• ResonanceCOP : protocols::noesy_assign
• ResonanceListAP : protocols::noesy_assign
• ResonanceListCAP : protocols::noesy_assign
• ResonanceListCOP : protocols::noesy_assign
• ResonanceListOP : protocols::noesy_assign
• ResonanceOP : protocols::noesy_assign
• resource_deallocation_msg : protocols::jd3::deallocation
• RESOURCE_MANAGED_JOB : protocols::jd2::JobInputterInputSource
• ResourceDeallocationMessageCOP : protocols::jd3::deallocation
• ResourceDeallocationMessageOP : protocols::jd3::deallocation
• RespairInteractionsCOP : core::scoring::custom_pair_distance
• RespairInteractionsOP : core::scoring::custom_pair_distance
• ResPairMinimizationDataCOP : core::scoring
• ResPairMinimizationDataOP : core::scoring
• ResPairMotifPtrs : core::scoring::motif
• ResPairMotifsMap : core::scoring::motif
• ResPairMotifsStringMap : core::scoring::motif
• resSeq : protocols::loops
• ResSingleMinimizationDataCOP : core::scoring
• ResSingleMinimizationDataOP : core::scoring
• restore_pose_from_rbsegs() : protocols::rbsegment_relax
• restore_residues() : protocols::forge::methods
• restore_sc12_settings : core::init
• restrain_ligand_nbr_atom() : protocols::ligand_docking
• restrict_dna_rotamers() : protocols::dna
• restrict_prec() : core::io::pose_to_sfr
• restrict_to_canonical_aas() : protocols::multistate_design
• restrict_to_protein_residues() : protocols::ligand_docking
• restrict_to_single_sequence() : protocols::dna
• RestrictAbsentCanonicalAASCreator_registrator : core::init
• RestrictAbsentCanonicalAASExceptNativeRLTCreator_registrator : core::init
• RestrictAbsentCanonicalAASOP : core::pack::task::operation
• RestrictAbsentCanonicalAASRLTCreator_registrator : core::init
• RestrictAbsentCanonicalAASRLTOP : core::pack::task::operation
• RestrictByCalculatorsOperationCOP : protocols::task_operations
• RestrictByCalculatorsOperationOP : protocols::task_operations
• RestrictChainToRepackingOperationCOP : protocols::task_operations
• RestrictChainToRepackingOperationOP : protocols::task_operations
• RestrictConservedLowDdgOperationOP : protocols::task_operations
• RestrictDesignToProteinDNAInterfaceOP : protocols::dna
• RestrictIdentitiesAtAlignedPositionsOperationCOP : protocols::task_operations
• RestrictIdentitiesAtAlignedPositionsOperationOP : protocols::task_operations
• RestrictIdentitiesOperationCOP : protocols::task_operations
• RestrictIdentitiesOperationOP : protocols::task_operations
• RestrictInteractionGraphThreadsOperationCOP : core::pack::task::operation
• RestrictInteractionGraphThreadsOperationCreator_registrator : core::init
• RestrictInteractionGraphThreadsOperationOP : core::pack::task::operation
• RestrictInterGroupVectorOperationCOP : protocols::task_operations
• RestrictInterGroupVectorOperationOP : protocols::task_operations
• RestrictNativeResiduesOperationOP : protocols::task_operations
• RestrictNonSurfaceToRepackingOperationOP : protocols::task_operations
• RestrictOperationsBaseCOP : protocols::task_operations
• RestrictOperationsBaseOP : protocols::task_operations
• RestrictResiduesToRepackingOperationCOP : protocols::task_operations
• RestrictResiduesToRepackingOperationOP : protocols::task_operations
• RestrictResidueToRepackingCreator_registrator : core::init
• RestrictResidueToRepackingOP : core::pack::task::operation
• RestrictToAlignedSegmentsOperationCOP : protocols::task_operations
• RestrictToAlignedSegmentsOperationOP : protocols::task_operations
• RestrictToCDRH3LoopOP : protocols::task_operations
• RestrictToCDRsAndNeighborsCOP : protocols::antibody::task_operations
• RestrictToCDRsAndNeighborsOP : protocols::antibody::task_operations
• RestrictToInterfaceCOP : protocols::simple_task_operations
• RestrictToInterfaceOP : protocols::simple_task_operations
• RestrictToInterfaceOperationCOP : protocols::task_operations
• RestrictToInterfaceOperationOP : protocols::task_operations
• RestrictToInterfaceVectorOperationCOP : protocols::task_operations
• RestrictToInterfaceVectorOperationOP : protocols::task_operations
• RestrictToLoopsAndNeighborsOP : protocols::simple_task_operations
• RestrictToLoopsOP : protocols::simple_task_operations
• RestrictToMoveMapChiOperationOP : protocols::task_operations
• RestrictToNeighborhoodOperationCOP : protocols::task_operations
• RestrictToNeighborhoodOperationOP : protocols::task_operations
• RestrictToRepackingCreator_registrator : core::init
• RestrictToRepackingOP : core::pack::task::operation
• RestrictToRepackingRLTCreator_registrator : core::init
• RestrictToRepackingRLTOP : core::pack::task::operation
• RestrictToResiduePropertiesCreator_registrator : core::init
• RestrictToResiduePropertiesOP : core::pack::task::operation
• RestrictToSpecifiedBaseResidueTypesCreator_registrator : core::init
• RestrictToSpecifiedBaseResidueTypesOP : core::pack::task::operation
• RestrictToTerminiOperationCOP : protocols::task_operations
• RestrictToTerminiOperationOP : protocols::task_operations
• RestrictYSDesignCreator_registrator : core::init
• RestrictYSDesignOP : core::pack::task::operation
• Restype_Variants_VariantStrings_Exceptions : core::chemical
• ResTypeFragmentMoverCOP : protocols::simple_moves
• ResTypeFragmentMoverOP : protocols::simple_moves
• RestypeInfoGraph : core::io::pose_from_sfr
• ResTypeSequence : protocols::dna
• ResTypeSequences : protocols::dna
• result_to_five_ss_models() : protocols::legacy_sewing
• result_to_models() : protocols::legacy_sewing
• ResultIndex : protocols::jd3
• ResultOutputterCOP : protocols::jd3::output
• ResultOutputterOP : protocols::jd3::output
• RESULTS : core::scoring::sc
• retain_top() : core::fragment
• retrieve_assignment() : protocols::noesy_assign
• retrieve_base_partner_from_pose() : core::scoring::dna
• retrieve_base_partner_from_pose_inline() : core::scoring::methods
• retrieve_centroid_scatter_from_pose() : core::scoring::fiber_diffraction
• retrieve_connection_architect() : protocols::denovo_design::connection
• retrieve_const_ss_info_from_pose() : core::scoring
• retrieve_coordinates() : core::scoring
• retrieve_CSA_from_pose() : core::scoring
• retrieve_DC_from_pose() : core::scoring
• retrieve_denovo_architect() : protocols::denovo_design::architects
• retrieve_fa_scatter_from_pose() : core::scoring::fiber_diffraction
• retrieve_lkb_resdata() : core::scoring::lkball
• retrieve_lkb_rotamer_set_info() : core::scoring::lkball
• retrieve_mp_pairdata() : core::scoring::methods
• retrieve_mp_resdata() : core::scoring::methods
• retrieve_mp_resdata_ptr() : core::scoring::methods
• retrieve_mp_residue_info() : core::scoring::methods
• retrieve_nonconst_mp_pairdata() : core::scoring::methods
• retrieve_nonconst_mp_resdata() : core::scoring::methods
• retrieve_nonconst_mp_residue_info() : core::scoring::methods
• retrieve_nonconst_ss_info_from_pose() : core::scoring
• retrieve_nonconst_vdw_pairdata() : core::scoring::methods
• retrieve_nonconst_vdw_resdata() : core::scoring::methods
• retrieve_nonconst_vdw_residue_info() : core::scoring::methods
• retrieve_RDC_from_pose() : core::scoring
• retrieve_RDC_ROHL_from_pose() : core::scoring
• retrieve_RDC_segments_from_pose() : protocols::scoring
• retrieve_residue_num_of_rkde() : protocols::features::strand_assembly
• retrieve_vdw_pairdata() : core::scoring::methods
• retrieve_vdw_resdata() : core::scoring::methods
• retrieve_vdw_resdata_ptr() : core::scoring::methods
• retrieve_vdw_residue_info() : core::scoring::methods
• RetrieveStoredTaskOperationCOP : protocols::task_operations
• RetrieveStoredTaskOperationOP : protocols::task_operations
• return_nearest_residue() : core::conformation::symmetry , core::pose
• return_region() : protocols::grafting
• ReturnResidueSubsetSelectorCOP : core::select::residue_selector
• ReturnResidueSubsetSelectorOP : core::select::residue_selector
• ReturnSidechainMoverCOP : protocols::simple_moves
• ReturnSidechainMoverOP : protocols::simple_moves
• retype_is_aromatic() : core::chemical
• REVDAT : core::io::pdb
• reverse_chains() : protocols::denovo_design::components
• reverse_lengths() : protocols::denovo_design::components
• reverse_orientations() : protocols::denovo_design::components
• Reversions : protocols::dna
• revert_to_pre_talaris_2013_defaults() : core::init
• revise_root_and_moving_res() : protocols::stepwise::modeler
• revise_root_and_moving_res_list() : protocols::stepwise::modeler
• Rf : core::chemical::element
• RFd_like : protocols::fldsgn::topology
• Rg : core::chemical::element
• rg : core::scoring
• RG_Energy_FastCreator_registrator : core::init
• RG_Energy_RNACreator_registrator : core::init
• rg_local : core::scoring
• RG_Local_MinDataOP : core::scoring::methods
• RG_LocalEnergyCreator_registrator : core::init
• RG_MinDataOP : core::scoring::methods
• Rh : core::chemical::element
• RHIJU_COLOR : protocols::viewer::graphics_states_param
• RID_SourceCOP : core::pose
• RID_SourceOP : core::pose
• RIGID_BODY : protocols::toolbox
• rigid_body_move() : protocols::toolbox::pose_manipulation
• RIGID_BODY_WITH_RESIDUE_ALTERNATIVES : protocols::toolbox
• RIGID_BODY_WITH_RESIDUE_LIST : protocols::toolbox
• RigidBodyDeterministicSpinMoverCOP : protocols::rigid
• RigidBodyDeterministicSpinMoverOP : protocols::rigid
• RigidBodyDofPerturbMoverCOP : protocols::rigid
• RigidBodyDofPerturbMoverOP : protocols::rigid
• RigidBodyDofRandomizeMoverCOP : protocols::rigid
• RigidBodyDofRandomizeMoverOP : protocols::rigid
• RigidBodyDofRandomTransMoverCOP : protocols::rigid
• RigidBodyDofRandomTransMoverOP : protocols::rigid
• RigidBodyDofSeqPerturbMoverCOP : protocols::rigid
• RigidBodyDofSeqPerturbMoverOP : protocols::rigid
• RigidBodyDofSeqRandomizeMoverCOP : protocols::rigid
• RigidBodyDofSeqRandomizeMoverOP : protocols::rigid
• RigidBodyDofSeqTransMoverCOP : protocols::rigid
• RigidBodyDofSeqTransMoverOP : protocols::rigid
• RigidBodyDofTransMoverCOP : protocols::rigid
• RigidBodyDofTransMoverOP : protocols::rigid
• RigidBodyInfoCOP : protocols::docking
• RigidBodyInfoOP : protocols::docking
• RigidBodyMotionMoverCOP : protocols::rigid
• RigidBodyMotionMoverOP : protocols::rigid
• RigidBodyMoverCOP : protocols::rigid
• RigidBodyMoverOP : protocols::rigid
• RigidBodyMoveRSOCOP : protocols::toolbox::rotamer_set_operations
• RigidBodyMoveRSOOP : protocols::toolbox::rotamer_set_operations
• RigidBodyPerturbMoverCOP : protocols::rigid
• RigidBodyPerturbMoverOP : protocols::rigid
• RigidBodyPerturbNoCenterMoverCOP : protocols::rigid
• RigidBodyPerturbNoCenterMoverOP : protocols::rigid
• RigidBodyPerturbRandomJumpMoverCOP : protocols::rigid
• RigidBodyPerturbRandomJumpMoverOP : protocols::rigid
• RigidBodyRandomizeMoverCOP : protocols::rigid
• RigidBodyRandomizeMoverOP : protocols::rigid
• RigidBodyRandomTMHMoverCOP : protocols::topology_broker
• RigidBodyRandomTMHMoverOP : protocols::topology_broker
• RigidBodySilentStructCreator_registrator : core::init
• RigidBodySpinMoverCOP : protocols::rigid
• RigidBodySpinMoverOP : protocols::rigid
• RigidBodyStepWiseSamplerCOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerValueRangeCOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerValueRangeOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerWithResidueAlternativesCOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerWithResidueAlternativesOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerWithResidueListCOP : protocols::stepwise::sampler::rigid_body
• RigidBodyStepWiseSamplerWithResidueListOP : protocols::stepwise::sampler::rigid_body
• RigidBodyTiltMoverCOP : protocols::rigid
• RigidBodyTiltMoverOP : protocols::rigid
• RigidBodyTransMoverCOP : protocols::rigid
• RigidBodyTransMoverOP : protocols::rigid
• RigidChunkClaimerAP : protocols::topology_broker
• RigidChunkClaimerCAP : protocols::topology_broker
• RigidChunkClaimerCOP : protocols::topology_broker
• RigidChunkClaimerOP : protocols::topology_broker
• RigidChunkCMCOP : protocols::abinitio::abscript
• RigidChunkCMOP : protocols::abinitio::abscript
• RigidLigandBuilderCOP : protocols::match::downstream
• RigidLigandBuilderOP : protocols::match::downstream
• RigidScoreCOP : protocols::sic_dock
• RigidScoreOP : protocols::sic_dock
• RigidSearchMoverCOP : protocols::ligand_docking
• RigidSearchMoverOP : protocols::ligand_docking
• RIGVD : core::io::pose_from_sfr
• ring_close : core::scoring
• RING_CONFORMERS : protocols::toolbox
• ring_current_effect() : core::scoring::rna::chemical_shift
• ring_current_effect_individual_ring() : core::scoring::rna::chemical_shift
• RING_HYBRID : core::chemical
• ring_pos() : core::scoring::rna::chemical_shift
• RingClosureEnergyCOP : core::scoring::methods
• RingClosureEnergyCreator_registrator : core::init
• RingClosureEnergyOP : core::scoring::methods
• RingConformationMoverCOP : protocols::simple_moves
• RingConformationMoverOP : protocols::simple_moves
• RingConformerSetCOP : core::chemical::rings
• RingConformerSetOP : core::chemical::rings
• RingPlaneFlipMoverCOP : protocols::carbohydrates
• RingPlaneFlipMoverOP : protocols::carbohydrates
• RingSaturationType : core::chemical::rings
• rlto_datamap_category() : core::pack::task::operation
• RM_BB : core::scoring::motif
• RM_PH : core::scoring::motif
• RM_PO : core::scoring::motif
• RM_SC : core::scoring::motif
• RM_Type : core::scoring::motif
• RM_Type_NONE : core::scoring::motif
• rm_variant() : protocols::environment
• rmANGLE : core::scoring
• rmATOM : core::scoring
• rmBOND : core::scoring
• rmIMPROPER : core::scoring
• rmNONE : core::scoring
• rms : core::scoring
• rms_at_all_corresponding_atoms() : core::scoring
• rms_at_corresponding_atoms() : core::scoring
• rms_at_corresponding_atoms_no_super() : core::scoring
• rms_at_corresponding_heavy_atoms() : core::scoring
• RMS_EnergyCreator_registrator : core::init
• rms_error_with_noise() : core::import_pose::atom_tree_diffs
• RMSD() : protocols::cluster::calibur
• rmsd_all : core::scoring
• rmsd_all_heavy : core::scoring
• rmsd_atom_total : core::scoring
• rmsd_atoms : core::scoring
• RMSD_FRAG_STORE : protocols::loops::loop_closure::ccd
• rmsd_no_super() : core::scoring
• rmsd_no_super_subset() : core::scoring
• rmsd_over_residue_list() : protocols::stepwise::modeler::rna
• rmsd_protein_bb_ca : core::scoring
• rmsd_protein_bb_heavy : core::scoring
• rmsd_protein_bb_heavy_including_O : core::scoring
• rmsd_sc : core::scoring
• rmsd_sc_heavy : core::scoring
• rmsd_with_super() : core::scoring
• rmsd_with_super_subset() : core::scoring
• RmsdFromResidueSelectorFilterCOP : protocols::fold_from_loops::filters
• RmsdFromResidueSelectorFilterOP : protocols::fold_from_loops::filters
• RMSDMetricCOP : core::simple_metrics::metrics
• RMSDMetricOP : core::simple_metrics::metrics
• RMSwrapper() : protocols::simple_filters
• rmTORSION : core::scoring
• Rn : core::chemical::element
• RNA : core::chemical
• RNA_AddDeleteMonteCarloOP : protocols::stepwise::monte_carlo::rna
• RNA_AnalyticLoopCloserOP : protocols::stepwise::legacy::modeler::rna
• RNA_ANTI_CHI : core::pose::full_model_info
• RNA_AtomVDWCOP : core::scoring::rna
• RNA_AtomVDWOP : core::scoring::rna
• RNA_AtrRepCheckerCOP : protocols::stepwise::modeler::rna::checker
• RNA_AtrRepCheckerOP : protocols::stepwise::modeler::rna::checker
• RNA_AtrRepScreenerCOP : protocols::stepwise::legacy::screener
• RNA_AtrRepScreenerOP : protocols::stepwise::legacy::screener
• rna_backbone_backbone : core::scoring
• rna_base_axis : core::scoring
• rna_base_axis_pairwise : core::scoring
• rna_base_backbone : core::scoring
• rna_base_pair : core::scoring
• rna_base_pair_pairwise : core::scoring
• rna_base_stack : core::scoring
• rna_base_stack_axis : core::scoring
• rna_base_stack_axis_pairwise : core::scoring
• rna_base_stack_pairwise : core::scoring
• rna_base_stagger : core::scoring
• rna_base_stagger_pairwise : core::scoring
• RNA_BaseCentroidCheckerCOP : protocols::stepwise::modeler::rna::checker
• RNA_BaseCentroidCheckerOP : protocols::stepwise::modeler::rna::checker
• RNA_BasePairHandlerCOP : core::import_pose
• RNA_BasePairHandlerOP : core::import_pose
• RNA_BasePairList : core::pose::rna
• RNA_BaseStackList : core::pose::rna
• RNA_BasicOptionsCOP : core::import_pose::options
• RNA_BasicOptionsOP : core::import_pose::options
• RNA_BLOCK_STACK_ABOVE : core::pose::full_model_info
• RNA_BLOCK_STACK_BELOW : core::pose::full_model_info
• rna_bond_geometry : core::scoring
• RNA_BULGE : core::pose::full_model_info
• rna_bulge : core::scoring
• RNA_BulgeEnergyCreator_registrator : core::init
• RNA_CentroidInfoOP : core::scoring::rna
• RNA_CHAIN_CLOSABLE_GEOMETRY : protocols::stepwise::screener
• RNA_CHAIN_CLOSABLE_GEOMETRY_RESIDUE_BASED : protocols::stepwise::screener
• RNA_CHAIN_CLOSABLE_GEOMETRY_STUB_BASED : protocols::stepwise::screener
• RNA_CHAIN_CLOSURE : protocols::stepwise::screener
• RNA_ChainClosableGeometryCheckerCOP : protocols::stepwise::modeler::rna::checker
• RNA_ChainClosableGeometryCheckerOP : protocols::stepwise::modeler::rna::checker
• RNA_ChainClosableGeometryResidueBasedScreenerCOP : protocols::stepwise::screener
• RNA_ChainClosableGeometryResidueBasedScreenerOP : protocols::stepwise::screener
• RNA_ChainClosableGeometryScreenerCOP : protocols::stepwise::screener
• RNA_ChainClosableGeometryScreenerOP : protocols::stepwise::screener
• RNA_ChainClosableGeometryStubBasedScreenerCOP : protocols::stepwise::screener
• RNA_ChainClosableGeometryStubBasedScreenerOP : protocols::stepwise::screener
• RNA_ChainClosureCheckerCOP : protocols::stepwise::modeler::rna::checker
• RNA_ChainClosureCheckerOP : protocols::stepwise::modeler::rna::checker
• RNA_ChainClosureScreenerCOP : protocols::stepwise::screener
• RNA_ChainClosureScreenerOP : protocols::stepwise::screener
• rna_chem_map : core::scoring
• rna_chem_map_lores : core::scoring
• rna_chem_shift : core::scoring
• RNA_ChemicalMappingEnergyCOP : core::scoring::rna::data
• RNA_ChemicalMappingEnergyCreator_registrator : core::init
• RNA_ChemicalMappingEnergyOP : core::scoring::rna::data
• RNA_ChemicalShiftPotentialCOP : core::scoring::rna::chemical_shift
• RNA_ChemicalShiftPotentialOP : core::scoring::rna::chemical_shift
• RNA_CHI : protocols::toolbox
• RNA_ChiStepWiseSamplerOP : protocols::stepwise::sampler::rna
• RNA_ChunkLibraryCOP : core::import_pose::libraries
• RNA_ChunkLibraryOP : core::import_pose::libraries
• RNA_CSA_JobDistributorCOP : protocols::rna::setup
• RNA_CSA_JobDistributorOP : protocols::rna::setup
• RNA_Data : core::pose::rna
• rna_data_backbone : core::scoring
• rna_data_base : core::scoring
• RNA_DataBackboneEnergyCreator_registrator : core::init
• RNA_DataInfoAP : core::pose::rna
• RNA_DataInfoOP : core::pose::rna
• RNA_DataReaderOP : core::io::rna
• RNA_DeNovoJobOutputterOP : protocols::jd2
• RNA_DeNovoMasterMoverCOP : protocols::rna::denovo::movers
• RNA_DeNovoMasterMoverOP : protocols::rna::denovo::movers
• RNA_DeNovoOptimizerCOP : protocols::rna::movers
• RNA_DeNovoOptimizerOP : protocols::rna::movers
• RNA_DeNovoParametersCOP : core::import_pose
• RNA_DeNovoParametersOP : core::import_pose
• RNA_DeNovoPoseInitializerCOP : protocols::rna::denovo
• RNA_DeNovoPoseInitializerOP : protocols::rna::denovo
• RNA_DeNovoProtocolCOP : protocols::rna::denovo
• RNA_DeNovoProtocolMoverCOP : protocols::rna::denovo::movers
• RNA_DeNovoProtocolMoverOP : protocols::rna::denovo::movers
• RNA_DeNovoProtocolOP : protocols::rna::denovo
• RNA_DeNovoProtocolOptionsCOP : core::import_pose::options
• RNA_DeNovoProtocolOptionsOP : core::import_pose::options
• RNA_DeNovoSetupCOP : core::import_pose
• RNA_DeNovoSetupOP : core::import_pose
• RNA_DMS_LowResolutionPotentialCOP : core::scoring::rna::data
• RNA_DMS_LowResolutionPotentialOP : core::scoring::rna::data
• RNA_DMS_PotentialCOP : core::scoring::rna::data
• RNA_DMS_PotentialOP : core::scoring::rna::data
• rna_dna_match() : core::chemical::rna
• RNA_ELEC_NBLIST : core::scoring::EnergiesCacheableDataType
• rna_elec_pair_nblist : core::scoring
• rna_elec_weight() : core::scoring::elec
• RNA_EnergyMethodOptionsCOP : core::scoring::rna
• RNA_EnergyMethodOptionsOP : core::scoring::rna
• rna_fa_atr_base : core::scoring
• RNA_FA_ElecEnergyCreator_registrator : core::init
• rna_fa_rep_base : core::scoring
• RNA_FilteredBaseBaseInfoOP : core::pose::rna
• RNA_FittedTorsionInfoOP : core::chemical::rna
• RNA_FragmentHomologyExclusionCOP : core::fragment::rna
• RNA_FragmentHomologyExclusionOP : core::fragment::rna
• RNA_FragmentMonteCarloCOP : protocols::rna::denovo
• RNA_FragmentMonteCarloOP : protocols::rna::denovo
• RNA_FragmentMonteCarloOptionsCOP : core::import_pose::options
• RNA_FragmentMonteCarloOptionsOP : core::import_pose::options
• RNA_FragmentMonteCarloOutputterCOP : protocols::rna::denovo::output
• RNA_FragmentMonteCarloOutputterOP : protocols::rna::denovo::output
• RNA_FragmentMoverOP : protocols::rna::denovo::movers
• RNA_FragmentsCOP : core::fragment::rna
• RNA_FragmentsOP : core::fragment::rna
• RNA_FullAtomStackingEnergyCreator_registrator : core::init
• RNA_FullAtomVDW_BasePhosphateCOP : core::scoring::rna
• RNA_FullAtomVDW_BasePhosphateCreator_registrator : core::init
• RNA_FullAtomVDW_BasePhosphateOP : core::scoring::rna
• RNA_HelixAssemblerOP : core::import_pose
• RNA_HelixMoverOP : protocols::rna::denovo::movers
• RNA_HIRES_WTS : core::scoring
• RNA_IdealCoordOP : core::pose::rna
• RNA_InfoAP : core::chemical::rna
• RNA_InfoCAP : core::chemical::rna
• RNA_InfoCOP : core::chemical::rna
• RNA_InfoOP : core::chemical::rna
• RNA_JobDistributorCOP : protocols::rna::setup
• RNA_JobDistributorOP : protocols::rna::setup
• rna_jr_suite : core::scoring
• RNA_JR_SuiteEnergyCreator_registrator : core::init
• RNA_JumpLibraryCOP : core::import_pose::libraries
• RNA_JumpLibraryOP : core::import_pose::libraries
• RNA_JumpMoverCOP : core::import_pose
• RNA_JumpMoverOP : core::import_pose
• RNA_KIC : protocols::toolbox
• RNA_KIC_SamplerOP : protocols::stepwise::sampler::rna
• RNA_KINEMATIC_CLOSER : protocols::toolbox
• RNA_KinematicCloserOP : protocols::stepwise::sampler::rna
• RNA_LibraryManagerCOP : core::import_pose::libraries
• RNA_LibraryManagerOP : core::import_pose::libraries
• RNA_LJ_BaseEnergyCreator_registrator : core::init
• RNA_LoopCloserCOP : protocols::rna::movers
• RNA_LoopCloserOP : protocols::rna::movers
• RNA_LORES_PLUS_HIRES_WTS : core::scoring
• RNA_LORES_WTS : core::scoring
• RNA_LowResolutionPotentialCOP : core::scoring::rna
• RNA_LowResolutionPotentialOP : core::scoring::rna
• rna_mg_point : core::scoring
• rna_mg_point_indirect : core::scoring
• RNA_MgPointEnergyCreator_registrator : core::init
• RNA_MinimizerOP : protocols::rna::denovo::movers
• RNA_MinimizerOptionsCOP : core::import_pose::options
• RNA_MinimizerOptionsOP : core::import_pose::options
• RNA_MonteCarloJobDistributorCOP : protocols::rna::setup
• RNA_MonteCarloJobDistributorOP : protocols::rna::setup
• rna_motif : core::scoring
• rna_motif_bonus : core::scoring::rna
• RNA_MotifCOP : core::scoring::rna
• RNA_MotifOP : core::scoring::rna
• RNA_MotifsCOP : core::scoring::rna
• RNA_MotifsOP : core::scoring::rna
• RNA_MotifType : core::scoring::rna
• RNA_NORTH_SUGAR : core::pose::full_model_info
• rna_nts() : core::chemical::rna
• RNA_NUCLEOSIDE : protocols::toolbox
• RNA_NucleosideStepWiseSamplerOP : protocols::stepwise::sampler::rna
• RNA_O2PrimeMoverOP : protocols::stepwise::monte_carlo::rna
• RNA_PairingTemplateList : core::import_pose::libraries
• RNA_PairingTemplateMap : core::import_pose::libraries
• RNA_PairingTemplateOP : core::import_pose::libraries
• RNA_PairwiseLowResolutionEnergyCreator_registrator : core::init
• rna_partition : core::scoring
• RNA_PartitionEnergyCreator_registrator : core::init
• RNA_RawBaseBaseInfoAP : core::pose::rna
• RNA_RawBaseBaseInfoOP : core::pose::rna
• RNA_Reactivities : core::pose::rna
• RNA_ReactivityAP : core::pose::rna
• RNA_ReactivityOP : core::pose::rna
• RNA_ReactivityType : core::pose::rna
• RNA_RelaxerOP : protocols::rna::denovo::movers
• rna_repulsive : core::scoring
• rna_residue_name_to_num() : core::scoring::rna
• rna_residue_type_to_num() : core::scoring::rna
• RNA_ResidueLevelTaskCOP : core::pack::task::rna
• RNA_ResidueLevelTaskOP : core::pack::task::rna
• rna_rg : core::scoring
• RNA_SAMPLE_SUGAR : core::pose::full_model_info
• rna_scoring_info_from_pose() : core::scoring::rna
• RNA_ScoringInfoOP : core::scoring::rna
• RNA_SecStructCOP : core::pose::rna
• RNA_SecStructLegacyInfoOP : core::pose::rna::secstruct_legacy
• RNA_SecStructOP : core::pose::rna
• RNA_SilentStructCreator_registrator : core::init
• RNA_SilentStructOP : core::io::silent
• RNA_SOUTH_SUGAR : core::pose::full_model_info
• rna_stub_coord_hack : core::scoring
• rna_stub_coord_lr : core::scoring::methods
• RNA_StubCoordinateEnergyCreator_registrator : core::init
• RNA_SUGAR : protocols::toolbox
• rna_sugar_close : core::scoring
• RNA_SugarCloseEnergyCOP : core::scoring::rna
• RNA_SugarCloseEnergyCreator_registrator : core::init
• RNA_SugarCloseEnergyOP : core::scoring::rna
• RNA_SugarStepWiseSamplerOP : protocols::stepwise::sampler::rna
• rna_suite : core::scoring
• RNA_SUITE : protocols::toolbox
• rna_suite_lr : core::scoring::methods
• RNA_SuiteEnergyCreator_registrator : core::init
• RNA_SuiteNameOP : core::pose::rna
• RNA_SuitePotentialCOP : core::scoring::rna
• RNA_SuitePotentialOP : core::scoring::rna
• RNA_SuiteStepWiseSamplerOP : protocols::stepwise::sampler::rna
• RNA_SYN_CHI : core::pose::full_model_info
• RNA_TERMINAL : core::pose::full_model_info
• RNA_Torsion : core::chemical::rna
• rna_torsion : core::scoring
• rna_torsion_sc : core::scoring
• RNA_TorsionEnergyCOP : core::scoring::rna
• RNA_TorsionEnergyCreator_registrator : core::init
• RNA_TorsionEnergyOP : core::scoring::rna
• RNA_TorsionMoverOP : protocols::stepwise::monte_carlo::rna
• RNA_TorsionPotentialCOP : core::scoring::rna
• RNA_TorsionPotentialOP : core::scoring::rna
• RNA_TorsionScreenerOP : protocols::stepwise::sampler::screener
• rna_vdw : core::scoring
• RNA_VDW_BinCheckerCOP : protocols::stepwise::modeler::rna::checker
• RNA_VDW_BinCheckerOP : protocols::stepwise::modeler::rna::checker
• RNA_VDW_EnergyCreator_registrator : core::init
• RNAIdealizeMoverCOP : protocols::rna::movers
• RNAIdealizeMoverOP : protocols::rna::movers
• RNAseH : protocols::fldsgn::topology
• RNAThreadAndMinimizeMoverCOP : protocols::rna::movers
• RNAThreadAndMinimizeMoverOP : protocols::rna::movers
• rnp_aa_to_rna_backbone : core::scoring
• rnp_base_pair : core::scoring
• rnp_env : core::scoring
• RNP_HighResMoverOP : protocols::rna::denovo::movers
• RNP_LowResEnergyCreator_registrator : core::init
• RNP_LowResPairDistEnergyCreator_registrator : core::init
• RNP_LowResPairDistPotentialOP : core::scoring::rna
• RNP_LowResPotentialOP : core::scoring::rna
• RNP_LowResStackDataOP : core::scoring::rna
• RNP_LowResStackEnergyCreator_registrator : core::init
• rnp_pair : core::scoring
• rnp_pair_dist : core::scoring
• rnp_stack : core::scoring
• rnp_stack_xy : core::scoring
• rnp_vdw : core::scoring
• rolling_score() : protocols::frag_picker::scores
• RollMoverCOP : protocols::rigid
• RollMoverOP : protocols::rigid
• rootj() : core::scoring::fiber_diffraction
• ROSETTA : protocols::cluster::calibur
• ROSETTA_LIBRARY_DOMAIN : core::import_pose::libraries
• rosetta_recharge_fullatom() : core::chemical
• rosetta_retype_fullatom() : core::chemical
• RosettaScriptsParserCOP : protocols::rosetta_scripts
• RosettaScriptsParserOP : protocols::rosetta_scripts
• RosI : protocols::fldsgn::topology
• RosO : protocols::fldsgn::topology
• Rot : core::scoring::packstat
• rot1 : protocols::jumping
• rot2 : protocols::jumping
• rot_mat() : protocols::forge::remodel
• rot_matrix : protocols::splice
• rot_pose() : protocols::matdes , protocols::sic_dock
• rot_sample_from_name() : core::pack::task
• rotamer_from_chi() : core::pack::dunbrack
• rotamer_from_chi_02() : core::pack::dunbrack
• rotamer_information_from_PDB_stream() : core::pack::rotamers
• rotamer_recovery() : core::pack
• rotamer_sampling_data_xml_schema_attributes() : core::pack::task::operation
• rotamer_trials() : core::pack
• RotamerAssigningAnnealerOP : core::pack::annealer
• RotamerBin : core::pack::rotamer_set
• RotamerBins : core::pack::rotamer_set
• RotamerBoltzCalculatorCOP : protocols::pose_metric_calculators
• RotamerBoltzCalculatorOP : protocols::pose_metric_calculators
• RotamerBoltzmannWeight2COP : protocols::calc_taskop_filters
• RotamerBoltzmannWeight2OP : protocols::calc_taskop_filters
• RotamerBoltzmannWeightFeaturesCOP : protocols::features
• RotamerBoltzmannWeightFeaturesOP : protocols::features
• RotamerBoltzmannWeightFilterCOP : protocols::calc_taskop_filters
• RotamerBoltzmannWeightFilterOP : protocols::calc_taskop_filters
• RotamerConstraintCOP : core::pack::dunbrack
• RotamerConstraintOP : core::pack::dunbrack
• RotamerCouplingsCOP : core::pack::rotamer_set
• RotamerCouplingsOP : core::pack::rotamer_set
• RotamerDNAHBondFilterOP : protocols::dna
• RotamerDotsCOP : core::pack::interaction_graph
• RotamerDotsOP : core::pack::interaction_graph
• RotamerExplosionCreator_registrator : core::init
• RotamerExplosionOP : core::pack::task::operation
• RotamerFeaturesCOP : protocols::features
• RotamerFeaturesOP : protocols::features
• rotameric_chi_mimic_EX_flags : protocols::match::upstream
• rotameric_chi_partition_sd_range : protocols::match::upstream
• rotameric_chi_step_by_value : protocols::match::upstream
• rotameric_chi_step_wi_sd_range : protocols::match::upstream
• RotamericSingleResidueDunbrackLibraryParserCOP : core::pack::dunbrack
• RotamericSingleResidueDunbrackLibraryParserOP : core::pack::dunbrack
• RotamerIDSize : core::scoring::hbonds::graph
• RotamerizeMoverCOP : protocols::minimization_packing
• RotamerizeMoverOP : protocols::minimization_packing
• RotamerLibraryCOP : core::pack::dunbrack
• RotamerLibraryOP : core::pack::dunbrack
• RotamerLibraryScratchSpaceCOP : core::pack::dunbrack
• RotamerLibraryScratchSpaceOP : core::pack::dunbrack
• RotamerLibrarySpecificationCOP : core::chemical::rotamers
• RotamerLibrarySpecificationCreatorCOP : core::chemical::rotamers
• RotamerLibrarySpecificationCreatorOP : core::chemical::rotamers
• RotamerLibrarySpecificationOP : core::chemical::rotamers
• RotamerLinksCOP : core::pack::rotamer_set
• RotamerLinksOP : core::pack::rotamer_set
• RotamerOperationCOP : core::pack::rotamer_set
• RotamerOperationOP : core::pack::rotamer_set
• RotamerOperations : core::pack::rotamer_set
• RotamerProbabilities : protocols::pose_metric_calculators
• RotamerProbability : protocols::pose_metric_calculators
• RotamerRecoveryCOP : protocols::rotamer_recovery
• RotamerRecoveryFactoryCOP : protocols::rotamer_recovery
• RotamerRecoveryFactoryOP : protocols::rotamer_recovery
• RotamerRecoveryFeaturesCOP : protocols::features
• RotamerRecoveryFeaturesOP : protocols::features
• RotamerRecoveryMoverCOP : protocols::rotamer_recovery
• RotamerRecoveryMoverOP : protocols::rotamer_recovery
• RotamerRecoveryOP : protocols::rotamer_recovery
• RotamerReporterCOP : protocols::rotamer_recovery
• RotamerReporterSimpleCOP : protocols::rotamer_recovery
• RotamerReporterSQLiteCOP : protocols::rotamer_recovery
• Rotamers : core::pack::rotamer_set
• rotamers_for_trials() : protocols::ligand_docking
• RotamerSetBaseCOP : core::conformation
• RotamerSetBaseOP : core::conformation
• RotamerSetCOP : core::pack::rotamer_set
• RotamerSetFactoryOP : core::pack::rotamer_set
• RotamerSetOP : core::pack::rotamer_set
• RotamerSetOperationCOP : core::pack::rotamer_set
• RotamerSetOperationOP : core::pack::rotamer_set
• RotamerSetsBaseCOP : core::pack_basic
• RotamerSetsBaseOP : core::pack_basic
• RotamerSetsCOP : core::pack::rotamer_set
• RotamerSetsFactoryOP : core::pack::rotamer_set
• RotamerSetsOP : core::pack::rotamer_set
• RotamerSetsOperationCOP : core::pack::rotamer_set
• RotamerSetsOperationOP : core::pack::rotamer_set
• RotamerSetVector : core::pack::rotamer_set::symmetry
• RotamerSubsetsCOP : core::pack::rotamer_set
• RotamerSubsetsOP : core::pack::rotamer_set
• RotamerTracer() : protocols::RotamerDump
• RotamerTrialsMinMoverCOP : protocols::minimization_packing
• RotamerTrialsMinMoverOP : protocols::minimization_packing
• RotamerTrialsMoverCOP : protocols::minimization_packing
• RotamerTrialsMoverOP : protocols::minimization_packing
• RotamerTrialsRefinerCOP : protocols::loop_modeling::refiners
• RotamerTrialsRefinerOP : protocols::loop_modeling::refiners
• RotamerTrieBaseCOP : core::scoring::trie
• RotamerTrieBaseOP : core::scoring::trie
• RotamerVector : core::pack::rotamers
• ROTATE() : core::scoring , protocols::cluster::calibur
• rotate() : protocols::cluster::calibur
• ROTATE() : protocols::evaluation
• rotate() : protocols::toolbox::rigid_body
• ROTATE() : protocols::toolbox
• rotate_anchor_to_x_axis() : core::pose::symmetry
• rotate_into_nucleobase_frame() : protocols::toolbox::sample_around
• rotate_into_phosphate_frame() : protocols::toolbox::sample_around
• rotate_vec() : protocols::toolbox
• RotateCOP : protocols::ligand_docking
• RotateCOPs : protocols::ligand_docking
• RotateJumpAxisMoverCOP : protocols::rigid
• RotateJumpAxisMoverOP : protocols::rigid
• RotateOP : protocols::ligand_docking
• RotateOPs : protocols::ligand_docking
• rotates_tracer() : protocols::ligand_docking
• RotatesCOP : protocols::ligand_docking
• RotatesCOPs : protocols::ligand_docking
• RotateSegmentMoverCOP : protocols::denovo_design::movers
• RotateSegmentMoverOP : protocols::denovo_design::movers
• RotatesOP : protocols::ligand_docking
• RotatesOPs : protocols::ligand_docking
• rotation_matrix_from_euler_angles() : core::scoring::nmr
• RotationMoverCOP : protocols::membrane
• RotationMoverOP : protocols::membrane
• RotBoltzWeight_subelement_ct_name() : protocols::calc_taskop_filters
• RotDataVec : protocols::make_rot_lib
• RotLibdbCOP : protocols::splice
• RotLibdbOP : protocols::splice
• RotLibOutCOP : protocols::splice
• RotLibOutOP : protocols::splice
• RotMatrixCOP : protocols::mean_field
• RotMatrixOP : protocols::mean_field
• RotPair : core::scoring::packstat
• rots_from_pose() : protocols::comparative_modeling
• RotSetOperationList : core::pack::rotamer_set
• RotSetOperationListIterator : core::pack::rotamer_set
• RotSetsOperationList : core::pack::rotamer_set
• RotSetsOperationListIterator : core::pack::rotamer_set
• RotVec : protocols::make_rot_lib
• RotVector : core::pack::dunbrack
• round() : protocols::noesy_assign
• round_to_float() : protocols::features::strand_assembly
• round_to_Real() : protocols::features::strand_assembly
• round_to_Size() : protocols::features::strand_assembly
• RPM_Type : core::scoring::motif
• rpm_type1() : core::scoring::motif
• rpm_type2() : core::scoring::motif
• RPM_Type_NONE : core::scoring::motif
• RPT_end_of_list : core::conformation::parametric
• RPT_gaussian : core::conformation::parametric
• RPT_uniform : core::conformation::parametric
• RPT_unknown_type : core::conformation::parametric
• RRComparerAutomorphicRMSDCOP : protocols::rotamer_recovery
• RRComparerAutomorphicRMSDOP : protocols::rotamer_recovery
• RRComparerChiDiffCOP : protocols::rotamer_recovery
• RRComparerChiDiffOP : protocols::rotamer_recovery
• RRComparerCOP : protocols::rotamer_recovery
• RRComparerCreatorCOP : protocols::rotamer_recovery
• RRComparerCreatorOP : protocols::rotamer_recovery
• RRComparerElecDensDiffCOP : protocols::rotamer_recovery
• RRComparerElecDensDiffOP : protocols::rotamer_recovery
• RRComparerOP : protocols::rotamer_recovery
• RRComparerRotBinsCOP : protocols::rotamer_recovery
• RRComparerRotBinsOP : protocols::rotamer_recovery
• RRProtocolCOP : protocols::rotamer_recovery
• RRProtocolCreatorCOP : protocols::rotamer_recovery
• RRProtocolCreatorOP : protocols::rotamer_recovery
• RRProtocolMinPackCOP : protocols::rotamer_recovery
• RRProtocolMinPackOP : protocols::rotamer_recovery
• RRProtocolMoverCOP : protocols::rotamer_recovery
• RRProtocolMoverOP : protocols::rotamer_recovery
• RRProtocolOP : protocols::rotamer_recovery
• RRProtocolPackRotamersCOP : protocols::rotamer_recovery
• RRProtocolPackRotamersOP : protocols::rotamer_recovery
• RRProtocolReferenceStructureCOP : protocols::rotamer_recovery
• RRProtocolReferenceStructureOP : protocols::rotamer_recovery
• RRProtocolRelaxCOP : protocols::rotamer_recovery
• RRProtocolRelaxOP : protocols::rotamer_recovery
• RRProtocolRotamerTrialsCOP : protocols::rotamer_recovery
• RRProtocolRotamerTrialsOP : protocols::rotamer_recovery
• RRProtocolRTMinCOP : protocols::rotamer_recovery
• RRProtocolRTMinOP : protocols::rotamer_recovery
• RRReporterCreatorCOP : protocols::rotamer_recovery
• RRReporterCreatorOP : protocols::rotamer_recovery
• RRReporterHumanCOP : protocols::rotamer_recovery
• RRReporterHumanOP : protocols::rotamer_recovery
• RRReporterOP : protocols::rotamer_recovery
• RRReporterSimpleOP : protocols::rotamer_recovery
• RRReporterSQLiteOP : protocols::rotamer_recovery
• rsd_closest_to_chain_com() : protocols::membrane
• rsd_closest_to_chain_tm_com() : protocols::membrane
• rsd_closest_to_pose_tm_com() : protocols::membrane
• rsd_op() : protocols::denovo_design::components
• rsd_set_from_cmd_line() : core::chemical
• rsigma : core::scoring
• Rsmn2x2 : protocols::fldsgn::topology
• Rsmn3x3 : protocols::fldsgn::topology
• Rsmn3x3_Half : protocols::fldsgn::topology
• rt6_rt6_bb_dis2() : core::scoring::motif
• rt6_rt6_bb_dis2_explicit_stupid() : core::scoring::motif
• rt6_rt6_dis2() : core::scoring::motif
• RT_from_epos() : protocols::jumping
• rt_to_real6() : core::scoring::motif
• RTAP : core::kinematics
• rtas_subelement_ct_naming_function() : protocols::task_operations
• RTConstraintCOP : core::scoring::constraints
• RTConstraintOP : core::scoring::constraints
• RTOP : core::kinematics
• Ru : core::chemical::element
• run_boinc_debug() : protocols::abinitio
• run_command() : protocols::frag_picker
• run_metrics() : core::simple_metrics
• run_shear_min_pack() : protocols::carbohydrates
• Run_WriteToDB_sandwich() : protocols::features::strand_assembly
• runpsipred_name_mangle_check() : core::io::external
• RunSimpleMetricsMoverCOP : protocols::analysis::simple_metrics
• RunSimpleMetricsMoverOP : protocols::analysis::simple_metrics
• RuntimeFeaturesCOP : protocols::features
• RuntimeFeaturesOP : protocols::features
• rvec : core::scoring , protocols::toolbox
• rvec5 : core::scoring