- r -

• R : numeric::xyzTransform< typename >
• r : Solver::SolutionInfo
• R_ : numeric::BodyPosition< typename >
• R_fresh_ : numeric::BodyPosition< typename >
• radius : basic::sampling::orientations::QuatDBMetadata , test.Workshop9_my_shapes.MyCircle
• radius_ : numeric::geometry::hashing::Ball , numeric::sphericalVector< typename >
• rama_id : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• rama_terms : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• random_mover : app.surface_docking.movers.FullAtomRelax
• randomize_button : app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame
• randomize_first : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow
• randomize_loops_bool : app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame
• rank_ : utility::SimulateMPI
• raw_buffer : yaml.reader.Reader
• raw_decode : yaml.reader.Reader
• raw_utf8_ : utility::json_spirit::Generator< Value_type, Ostream_type >
• read_buffer : boost_adaptbx::python::streambuf
• read_counts_ : utility::io::FileContentsMap
• read_limit_ : utility::io::FileContentsMap
• real_indices_ : numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >
• real_options_ : basic::resource_manager::JobOptions
• real_vector_options_ : basic::resource_manager::JobOptions
• real_vectors_ : utility::options::OptionCollection
• reals_ : utility::options::OptionCollection
• reason : yaml.reader.ReaderError
• reason_ : utility::json_spirit::Error_position
• recent_history_queue_ : utility::recent_history_queue
• recognized_aa : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• recover_low : app.pyrosetta_toolkit.window_main.IO.GUIOutput.GUIOutput
• recursive_objects : yaml.constructor.BaseConstructor
• Red : basic::Tracer
• ref_cycles : app.surface_docking.movers.FullAtomRelax
• ref_pose_ : FitMover
• refChain : loadPDB.chainType
• reference : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceResults , tools.CppParser.CppClass , tools.CppParser.CppFunction
• reference_columns_ : basic::database::schema_generator::ForeignKey
• reference_path : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown , app.pyrosetta_toolkit.window_main.menu.Menus
• reference_pose : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• reference_sequence : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• reference_table_ : basic::database::schema_generator::ForeignKey
• ReferenceSection : tools.CppParser.ClangXML
• refine_cycles : app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• refine_repack_cycles : app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• refine_stage_ : PhProtocol
• refLine : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• refuse_unexpected_files_ : utility::io::FileContentsMap
• region : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceInfo , app.pyrosetta_toolkit.modules.Region.Region , app.pyrosetta_toolkit.modules.Structure.CDR
• region_chain : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• region_end : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• region_sequence : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• region_start : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• regional_score_class : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• regional_scoring : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• regions : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown , app.pyrosetta_toolkit.modules.Region.Regions , app.pyrosetta_toolkit.modules.Structure.CDR , app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• relevant_ : utility::options::OptionCollection
• reload_pdb_button : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager
• remAlt : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• remH20 : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• remHet : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• remove_alternates_var : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• remove_hetatm_var : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• remove_trailing_zeros_ : utility::json_spirit::Generator< Value_type, Ostream_type >
• remove_variant_button : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• remove_waters_var : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• RemovePatchButton : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• repack_connection : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMover , app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow
• repack_connection_and_insert : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMover
• repack_connection_and_piece : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow
• repack_interface : app.pyrosetta_toolkit.modules.protocols.DockingProtocols.LowResWrapper
• repack_only : app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• repeatable_max_occurs_ : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• repeatable_min_occurs_ : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• repeats : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• replace_res_and_atoms_button : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• replace_res_and_atoms_var : app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow
• report_ : basic::Reporter
• represented_objects : yaml.representer.BaseRepresenter
• required : yaml.scanner.SimpleKey
• requiredTypes : tools.CppParser.CppClass
• res1 : calccontacts.resContact
• res2 : calccontacts.resContact
• res_to_loose_ : ExposedStrandMover
• resaa : loadPDB.PDBres
• reservoir_ : numeric::random::WeightedReservoirSampler< T >
• Reset : basic::Tracer
• resfile : app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper , app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• resfilename : pyrosetta.toolbox.generate_resfile.ResfileWriter , toolbox.generate_resfile.ResfileWriter
• resi_ : sidechain_cst_3.Residue
• resid : loadPDB.new_PDBatom , loadPDB.PDBatom , loadPDB.PDBres
• resid_ : numeric::geometry::hashing::Ball
• resid_2_chain_and_resid_ : HPatchByChainNPDCalculator
• residue_chain : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• residue_chain_vectors_ : utility::options::OptionCollection
• residue_definitions : app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow , app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• residue_energy_of_Eterm : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• residue_energy_total : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• residue_resnum : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• residue_rosetta_resnum : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• residue_string : app.pyrosetta_toolkit.pyrosetta_toolkit.main_window , app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• residue_types_ : ResidueTypeBenchmark
• residues : app.pyrosetta_toolkit.modules.Structure.CDR
• RESIDUES_aliased : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• resinfo : app.pyrosetta_toolkit.modules.definitions.restype_definitions.definitions
• resn_ : sidechain_cst_3.Residue
• resnum : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow , loadPDB.PDBres
• ResNum : PDBInfo.PDB
• resnum_column : app.pyrosetta_toolkit.window_modules.insert_bfactor.InsertBFactor.InsertBFactor
• resnum_entry : app.pyrosetta_toolkit.window_modules.insert_bfactor.InsertBFactor.InsertBFactor
• resnum_label : app.pyrosetta_toolkit.window_modules.insert_bfactor.InsertBFactor.InsertBFactor
• resolver_exact_paths : yaml.resolver.BaseResolver
• resolver_prefix_paths : yaml.resolver.BaseResolver
• resource_configurations_ : basic::resource_manager::LazyResourceManager
• resource_locators_ : basic::resource_manager::LazyResourceManager
• resource_options_ : basic::resource_manager::LazyResourceManager
• resource_options_tag : basic::resource_manager::ResourceConfiguration
• resource_tag : basic::resource_manager::ResourceConfiguration
• resource_tag_lists_ : basic::resource_manager::LazyResourceManager
• resource_tags_ : basic::resource_manager::LazyResourceManager
• resources_ : basic::resource_manager::ResourceManager
• rest_expression_token_ : numeric::expression_parser::ArithmeticASTRestExpression
• rest_term_token_ : numeric::expression_parser::ArithmeticASTRestTerm
• restrict_access : options_class.Option
• restricted_access_ : utility::options::Option
• restrictions_ : utility::tag::XMLSchemaRestriction
• ResTyp : PDBInfo.PDB
• restype : loadPDB.new_PDBatom , loadPDB.PDBatom , loadPDB.PDBres
• restype_info : app.pyrosetta_toolkit.modules.definitions.restype_definitions.definitions
• restype_var : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• restypes : app.pyrosetta_toolkit.modules.definitions.restype_definitions.definitions
• result : app.pyrosetta_toolkit.window_modules.vicinity_options.vicinity_window.vicinityrelaxwindow , basic::ExecutionResult
• result_ : PerformanceBenchmark
• results : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• returnType : tools.CppParser.CppFunction
• rho : decision_function , Solver::SolutionInfo , svm_model
• right_ : numeric::ClusteringTreeNode
• right_child_ : numeric::kdtree::KDNode
• rings_ : utility::graph::RingDetection< Graph >
• RmLoopButton : app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame
• rms_ : CAtrace
• rmsdOPT : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• rmsdOPTIONS : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• rmsdP : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• rmses : FragmentAssemblyMover
• roc_curve_ : numeric::RocCurve
• roc_point_vector_ : numeric::RocCurve
• root1_ : numeric::Polynomial_1d
• root2_ : numeric::Polynomial_1d
• root_ : numeric::kdtree::KDTree
• root_context : yaml.emitter.Emitter
• root_module : binder::Config
• rosetta_libs : BuildPackagedBindings.ModuleBuilder
• rosetta_read_state : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.Properties
• rosetta_script_ : XMLParseBenchmark
• rotamer_energy : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• rotamer_probabilty : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• rotamer_prot_stats_ : PhProtocol
• rotate_info_ : LigandDockBench
• rotid_ : ScoreFragInfo
• rotidx_ : ScoreFragInfo
• rotlist_ : numeric::UniformRotationSampler
• rotsets_ : InteractionGraphPerformanceBenchmark
• rounds : app.pyrosetta_toolkit.window_main.IO.GUIOutput.GUIOutput
• rounds_entry : app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame
• rounds_label : app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame
• rounds_options_menu : app.pyrosetta_toolkit.window_main.menu.Menus
• RoundVar : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• row : app.pyrosetta_toolkit.modules.prettytable.prettytable_test.BuildEquivelanceTest
• row1 : PyMOLPyRosettaServer.Matrix
• row2 : PyMOLPyRosettaServer.Matrix
• row3 : PyMOLPyRosettaServer.Matrix
• row_list_ : basic::database::insert_statement_generator::InsertGenerator
• rowcount : app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable
• rows : app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable
• rt_min : app.surface_docking.movers.FullAtomRelax
• runtime_libpaths : BuildBindings.ModuleBuilder , BuildPackagedBindings.ModuleBuilder