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

- r -

• r1 : basic::options::OptionKeys::motifs , motifs , test::Workshop3test
• r2 : basic::options::OptionKeys::motifs , motifs , test::Workshop3test
• R5C : test::Workshop2test
• R5CA : test::Workshop2test
• R5N : test::Workshop2test
• rad2deg : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• radial_disp : basic::options::OptionKeys::matdes , matdes
• RADIANS : numeric::conversions
• radians() : numeric::conversions
• radians_to_degrees : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• radius : basic::options::OptionKeys::cluster , basic::options::OptionKeys::score::fiber_diffraction , cluster , score::fiber_diffraction
• radius_cutoff : basic::options::OptionKeys::mp::lipid_acc , mp::lipid_acc
• radius_cutoffs : basic::options::OptionKeys::patterson , patterson
• radius_size : basic::options::OptionKeys::lh , lh
• rama : basic::options::OptionKeys::remodel , remodel
• rama2b_map : basic::options::OptionKeys::in::file , in::file
• rama_2b : basic::options::OptionKeys::loops::ccd , loops::ccd
• rama_B : basic::options::OptionKeys::frags , frags
• rama_C : basic::options::OptionKeys::frags , frags
• rama_cutoff : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• rama_map : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_average_L_flat : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_average_L_flat_stringent : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_average_L_flat : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_average_L_flat_stringent : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_gly_flat : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_gly_flat_stringent : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_pro_flat : basic::options::OptionKeys::corrections::score , corrections::score
• rama_map_sym_pro_flat_stringent : basic::options::OptionKeys::corrections::score , corrections::score
• rama_norm : basic::options::OptionKeys::frags , frags
• rama_not_squared : basic::options::OptionKeys::corrections::score , corrections::score
• rama_power : basic::options::OptionKeys::score , score
• rama_prepro_nobidentate : basic::options::OptionKeys::corrections::score , corrections::score
• rama_prepro_steep : basic::options::OptionKeys::corrections::score , corrections::score
• rama_sampling_table_by_res : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• ramady : basic::options::OptionKeys::relax , relax
• ramady_cutoff : basic::options::OptionKeys::relax , relax
• ramady_force : basic::options::OptionKeys::relax , relax
• ramady_max_rebuild : basic::options::OptionKeys::relax , relax
• ramady_rms_limit : basic::options::OptionKeys::relax , relax
• ramaneighbors : basic::options::OptionKeys::score , score
• ramp_chainbreaks : basic::options::OptionKeys::jumps , jumps
• ramp_constraints : basic::options::OptionKeys::relax , relax
• ramp_coord_cst : basic::options::OptionKeys::fold_cst , fold_cst
• ramp_fa_rep : basic::options::OptionKeys::flexPepDocking , basic::options::OptionKeys::loops , flexPepDocking , loops
• ramp_nativeness : basic::options::OptionKeys::optE , optE
• ramp_rama : basic::options::OptionKeys::flexPepDocking , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax::centroid , flexPepDocking , loops , relax::centroid
• ramp_repulsive : basic::options::OptionKeys::ddg , ddg
• ramp_vdw : basic::options::OptionKeys::relax::centroid , relax::centroid
• rand_checkpoint_file : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• rand_sleep() : utility
• RANDOM : app::pyrosetta_toolkit::modules::prettytable::prettytable
• random_conformer : basic::options::OptionKeys::docking::ligand , docking::ligand
• random_delay : basic::options::OptionKeys::run , run
• random_generator() : numeric::random
• random_grow_loops_by : basic::options::OptionKeys::loops , loops
• random_limit_cluster_size_percent : basic::options::OptionKeys::cluster , cluster
• random_loop : basic::options::OptionKeys::loops , loops
• random_move() : test::Workshop4test
• random_normal() : numeric::random
• random_order : basic::options::OptionKeys::loops , loops
• random_permutation() : numeric::random
• random_phi_psi_preturbation : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• random_point_on_unit_sphere() : numeric::random
• random_range() : numeric::random
• random_rot_start : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• random_rotation() : numeric::random
• random_rotation_angle() : numeric::random
• random_sequence() : pyrosetta::toolbox::mutants , toolbox::mutants
• random_sheets : basic::options::OptionKeys::jumps , jumps
• random_start() : antibody::design , basic::options::OptionKeys::antibody::design
• random_trans_start : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• random_translation() : numeric::random
• random_unit_quaternion() : numeric::random
• random_vector() : numeric::random
• random_vector_spherical() : numeric::random
• random_vector_unit_cube() : numeric::random
• random_xform() : numeric::random
• RandomGeneratorOP : numeric::random
• randomize1 : basic::options::OptionKeys::docking , docking , test::Workshop7test
• randomize2 : basic::options::OptionKeys::docking , docking , test::Workshop7test
• randomize_input_sequence() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• randomize_loops : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• randomize_missing : basic::options::OptionKeys::nonlocal , nonlocal
• randomize_missing_coords : basic::options::OptionKeys::run , run
• randomize_motif : basic::options::OptionKeys::dna::specificity , dna::specificity
• randomly_perturb_starting_free_weights : basic::options::OptionKeys::optE , optE
• range : basic::options::OptionKeys::relax::range , relax::range
• rank : basic::options::OptionKeys::sewing , sewing
• rank_by_bsasa : basic::options::OptionKeys::remodel , remodel
• Rargs : app::surface_docking::surface_docking
• ras : test::Workshop3test , test::Workshop4test
• raw : basic::options::OptionKeys::out::file , out::file
• raw_stats : basic::options::OptionKeys::packstat , packstat
• raw_utf8 : utility::json_spirit
• rb_file : basic::options::OptionKeys::RBSegmentRelax , basic::options::OptionKeys::SSrbrelax , RBSegmentRelax , SSrbrelax
• rb_mag : basic::options::OptionKeys::smhybrid , smhybrid
• rb_mover_stage1_weight : basic::options::OptionKeys::broker , broker
• rb_param_file : basic::options::OptionKeys::SSrbrelax , SSrbrelax
• rb_rot_magnitude : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rb_scorefxn : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• rb_trans_magnitude : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rbe : basic::options::OptionKeys::rbe , rbe
• rbMCM : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• RBSegmentRelax : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• rc : setup_pyrosetta
• rc_file_path : setup_pyrosetta
• RCFILE : setup_pyrosetta
• rdc : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::in::file , basic::options::OptionKeys::rdc , evaluation , in::file , rdc
• rdc_column : basic::options::OptionKeys::evaluation , evaluation
• rdc_target : basic::options::OptionKeys::evaluation , evaluation
• rdf : basic::options::OptionKeys::in::rdf , in::rdf
• read() : ObjexxFCL , utility::json_spirit
• read_binary() : ObjexxFCL
• read_input_list() : arls_impl
• read_mArray() : utility::json_spirit
• read_metric_value() : basic
• read_metric_value_scalar() : basic
• read_metric_value_template() : basic
• read_metric_value_vector1() : basic
• read_mObject() : utility::json_spirit
• read_or_throw() : utility::json_spirit
• read_probabilities_or_die() : numeric
• read_range() : utility::json_spirit
• read_range_or_throw() : utility::json_spirit
• READ_RCFILE : setup_pyrosetta
• read_row() : numeric
• read_stream() : utility::json_spirit
• read_stream_or_throw() : utility::json_spirit
• read_string() : utility::json_spirit
• read_string_or_throw() : utility::json_spirit
• read_structures_into_pool : basic::options::OptionKeys::mc , mc
• read_subset_of_global_option_collection() : basic::options
• read_vector() : utility::io
• readFASC() : app::pyrosetta_toolkit::modules::tools::analysis
• readonly : basic::options::OptionKeys::inout::dbms , inout::dbms
• readsome() : ObjexxFCL
• ready_set_only : basic::options::OptionKeys::rna::farna::erraser , rna::farna::erraser
• real : basic::options::OptionKeys::james , james
• Real : numeric , platform
• real2afteroption() : basic::options
• Real2string() : utility
• Real3 : numeric::geometry::hashing
• real3afteroption() : basic::options
• Real6 : numeric::geometry::hashing
• REAL_OPTION : utility::options
• real_regex_pattern() : utility::tag
• real_type : utility::json_spirit
• REAL_VECTOR_OPTION : utility::options
• realafteroption() : basic::options
• realign : basic::options::OptionKeys::edensity , edensity
• realign_domains : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• realign_domains_stage2 : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• REALLY_BIG_DISTANCE() : numeric::kdtree
• RealOption : basic::options
• RealOptionKey : basic::options
• RealVectorOption : basic::options
• RealVectorOptionKey : basic::options
• reassign_atom_types : basic::options::OptionKeys::chemical , chemical
• reassign_icoor : basic::options::OptionKeys::chemical , chemical
• rebuild_bulge_mode : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• rebuild_disulf : basic::options::OptionKeys::run , run
• recalculate_foldtree : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• receive_char_from_node() : utility
• receive_double_from_node() : utility
• receive_doubles_from_node() : utility
• receive_integer_from_anyone() : utility
• receive_integer_from_node() : utility
• receive_integers_from_node() : utility
• RECEIVE_MESSAGE_TAG : basic::mpi
• receive_string_from_node() : utility
• receptor_chain : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• recover_low : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• recover_low_in_stages() : abinitio , basic::options::OptionKeys::abinitio
• recover_nat_rot : basic::options::OptionKeys::optE , optE
• recover_side_chain_mover : test::T600_Docking
• recover_side_chains : basic::options::OptionKeys::cm , cm
• recover_sidechains : basic::options::OptionKeys::docking , docking , loops , loops_kic , test::T650_LoopsKIC , test::Workshop7test
• recurse_through_tree() : utility::tag
• RED : fmt
• redesign_complete : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_core : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_loops : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_pdb_list : sequence_recovery
• redesign_surface : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• reduce_rays : basic::options::OptionKeys::pocket_grid , pocket_grid
• reduced_couplings : basic::options::OptionKeys::rdc , rdc
• ref_cen_spectrum : basic::options::OptionKeys::score::saxs , score::saxs
• ref_fa_spectrum : basic::options::OptionKeys::score::saxs , score::saxs
• ref_lig : basic::options::OptionKeys::fingerprint , fingerprint
• ref_offset : basic::options::OptionKeys::score , score
• ref_offsets : basic::options::OptionKeys::score , score
• ref_pdb_list : basic::options::OptionKeys::pepspec , pepspec
• ref_pddf : basic::options::OptionKeys::score::saxs , score::saxs
• ref_spectrum : basic::options::OptionKeys::score::saxs , score::saxs
• ref_startstruct : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• refChain : calccontacts
• reference_pose : test::Workshop8test
• ReferenceCountCOP : utility::pointer
• ReferenceCountOP : utility::pointer
• refinable_lattice : basic::options::OptionKeys::cryst , cryst
• refine() : antibody , basic::options::OptionKeys::antibody , basic::options::OptionKeys::loops , basic::options::OptionKeys::smhybrid , loops , smhybrid
• refine_CCD_off() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• refine_cycles() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::TailSegment , FloppyTail , TailSegment
• refine_design_iterations : basic::options::OptionKeys::loops , loops
• refine_final_temp : basic::options::OptionKeys::loops , loops
• refine_h3() : antibody , basic::options::OptionKeys::antibody
• refine_init_temp : basic::options::OptionKeys::loops , loops
• refine_KIC_off() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• refine_native : basic::options::OptionKeys::rna::farna , rna::farna
• refine_only() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::loops , loops
• refine_outer_cycles : basic::options::OptionKeys::loops , loops
• refine_repack_cycles() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::TailSegment , FloppyTail , TailSegment
• refine_res : basic::options::OptionKeys::casp , casp
• refine_silent_file : basic::options::OptionKeys::rna::farna , rna::farna
• refine_temp() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• refstruct : basic::options::OptionKeys::lh , lh
• refweight_arg : local
• refweight_asp : local
• refweight_glu : local
• refweight_lys : local
• reg : test::G200_Module_Region
• reg_score : test::G205_Module_RegionalScoring
• regexs : ObjexxFCL
• region : test::G102_Functions_General
• region2 : test::G200_Module_Region
• region_def : basic::options::OptionKeys::contactMap , contactMap
• region_selection() : app::pyrosetta_toolkit::modules::help
• regions : test::G101_Functions_Output , test::G102_Functions_General
• register_version_with_core() : devel
• regs : test::G200_Module_Region
• reinitialize_CCD_torsions : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• reinitialize_mover_for_each_job : basic::options::OptionKeys::run , run
• reinitialize_mover_for_new_input : basic::options::OptionKeys::run , run
• rel : test::G200_Module_Region
• rel_sasa_cutoff : basic::options::OptionKeys::mp::lipid_acc , mp::lipid_acc
• relax() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize , basic::options::OptionKeys::loops , basic::options::OptionKeys::mp::mutate_relax , basic::options::OptionKeys::relax , cm::hybridize , loops , mp::mutate_relax , relax , test::T800_ClassicRelax , test::Workshop5test
• relax_failures() : abinitio , basic::options::OptionKeys::abinitio
• relax_frags_repeats : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• relax_input : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• relax_input_with_coordinate_constraints : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• relax_mover : basic::options::OptionKeys::cp , cp
• relax_p : test::T800_ClassicRelax
• relax_rna : basic::options::OptionKeys::rna::farna , rna::farna
• relax_sfxn : basic::options::OptionKeys::cp , cp
• relax_with_foldtree : basic::options::OptionKeys::loops , loops
• relax_with_jumps() : abinitio , basic::options::OptionKeys::abinitio
• RELERROR : numeric::kinematic_closure
• relevant_include() : binder
• remainder() : numeric , ObjexxFCL
• remainder_conversion() : numeric , ObjexxFCL
• remap_pdb_atom_names_for : basic::options::OptionKeys::in::file , in::file
• remember_unrecognized_res : basic::options::OptionKeys::in , in
• remember_unrecognized_water : basic::options::OptionKeys::in , in
• remodel() : antibody , basic::options::OptionKeys::antibody , basic::options::OptionKeys::loops , basic::options::OptionKeys::remodel , loops , remodel
• remodel_aggressiveness : basic::options::OptionKeys::enzdes , enzdes
• remodel_final_temp : basic::options::OptionKeys::loops , loops
• remodel_init_temp : basic::options::OptionKeys::loops , loops
• remodel_kic_attempts : basic::options::OptionKeys::loops , loops
• remodel_protocol : basic::options::OptionKeys::enzdes , enzdes
• remodel_secmatch : basic::options::OptionKeys::enzdes , enzdes
• remodel_trials : basic::options::OptionKeys::enzdes , enzdes
• RemodelLoopMover : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• remove_all_dssp : basic::options::OptionKeys::sewing , sewing
• remove_antigen() : antibody::design , basic::options::OptionKeys::antibody::design
• remove_any_dssp : basic::options::OptionKeys::sewing , sewing
• remove_duplicates : basic::options::OptionKeys::mh , mh
• remove_exit_callback() : utility
• remove_extended_loops : basic::options::OptionKeys::loops , loops
• remove_highest_energy_member : basic::options::OptionKeys::cluster , cluster
• remove_input_bb : basic::options::OptionKeys::pepspec , pepspec
• remove_obligate_pair : basic::options::OptionKeys::rna::farna , rna::farna
• remove_option_from_map() : basic::resource_manager
• remove_pair : basic::options::OptionKeys::rna::farna , rna::farna
• remove_singletons : basic::options::OptionKeys::cluster , cluster
• remove_ss_length_screen : basic::options::OptionKeys::run , run
• remove_tracer_default_args_and_vars() : exclude
• remove_trailing() : utility::json_spirit
• remove_trailing_zeros : utility::json_spirit
• removechain : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• RemoveListItem() : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• removeProtectedConstructos() : exclude
• rename : basic::options::OptionKeys::ms::checkpoint , ms::checkpoint
• renameandsave() : app::pyrosetta_toolkit::modules::tools::general_tools
• renumber_pdb : basic::options::OptionKeys::out::file , out::file
• rep_edge_files : basic::options::OptionKeys::smhybrid , smhybrid
• rep_ramp_cycles : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• repack : basic::options::OptionKeys::casp , basic::options::OptionKeys::rot_anl , casp , rot_anl
• repack_again : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range , mp::quickrelax , relax::range
• repack_and_minimize_decoys : basic::options::OptionKeys::optE , optE
• repack_and_minimize_input_structures : basic::options::OptionKeys::optE , optE
• repack_fragments : usec
• repack_mutation_only : basic::options::OptionKeys::mp::mutate_relax , mp::mutate_relax
• repack_only : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::packing , dna::design , packing
• repack_period : basic::options::OptionKeys::docking , basic::options::OptionKeys::loops , docking , loops
• repack_radius : basic::options::OptionKeys::mp::mutate_relax , mp::mutate_relax
• repack_rate : basic::options::OptionKeys::run , run
• repair_sidechains : basic::options::OptionKeys::in::file , in::file
• repeat : basic::options::OptionKeys::run , basic::options::OptionKeys::sewing , ObjexxFCL::format , run , sewing
• repeat_mover : test::Workshop5test
• repeat_structure : basic::options::OptionKeys::remodel , remodel
• repeat_swarm_optimization_until_fitness_improves : basic::options::OptionKeys::optE , optE
• replace() : binder
• replace_() : binder
• replace_environment_variables() : utility
• replace_in() : utility
• replace_init() : src
• replace_spaces() : utility
• replonly_loops : basic::options::OptionKeys::in , in
• replonly_residues : basic::options::OptionKeys::in , in
• report_format : basic::options::OptionKeys::peptide_deriver , peptide_deriver
• report_gzip : basic::options::OptionKeys::peptide_deriver , peptide_deriver
• report_system_error() : fmt
• report_unknown_type() : fmt::internal
• ReportCOP : basic
• ReportOP : basic
• request_bindings() : binder
• request_data_from_head_node() : basic::mpi
• REQUEST_MESSAGE_TAG : basic::mpi
• require_disulfides : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• require_frags_match_blueprint : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• required_active_site_atom_names : basic::options::OptionKeys::match , match
• required_name_attribute() : utility::tag
• reramp_cst_cycles : basic::options::OptionKeys::fold_cst , fold_cst
• reramp_iterations : basic::options::OptionKeys::fold_cst , fold_cst
• reramp_start_cstweight : basic::options::OptionKeys::fold_cst , fold_cst
• reread_all_structures() : archive , basic::options::OptionKeys::archive
• reroot_tree : basic::options::OptionKeys::remodel , remodel
• rerun() : abinitio , basic::options::OptionKeys::abinitio
• rerun_motifsearch : basic::options::OptionKeys::motifs , motifs
• res : app::delta_score_per_mutation
• res5 : test::T100_Basic
• res_design_bs : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• res_set : test::T880_Other
• resample : basic::options::OptionKeys::resample , resample
• rescale_cartesian() : PyMOLPyRosettaServer
• resclass_by_sasa : basic::options::OptionKeys::remodel , remodel
• rescore : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::in::file , basic::options::OptionKeys::optE::rescore , basic::options::OptionKeys::rescore , hotspot , in::file , optE::rescore , rescore
• rescore_single_pdb() : app::pyrosetta_toolkit::modules::tools::output
• reservoir_sample() : numeric::random
• reservoir_sample_accept_prob() : numeric::random
• reset_chain() : loadPDB
• resetChain() : loadPDB
• resetlists() : PDBInfo
• resfile : basic::options::OptionKeys::packing , packing
• resfile_dump : basic::options::OptionKeys::mh::dump , mh::dump
• resfile_min_pair_score : basic::options::OptionKeys::mh::dump , mh::dump
• resfile_min_tot_score : basic::options::OptionKeys::mh::dump , mh::dump
• resi : basic::options::OptionKeys::cmiles::jumping , cmiles::jumping
• residual_squared_of_points_to_plane() : numeric::geometry
• residue : basic::options::OptionKeys::hotspot , hotspot
• residue_1 : test::T220_AtomAtomPairEnergies
• residue_2 : test::T220_AtomAtomPairEnergies
• residue_buffer : clean_pdb_keep_ligand
• RESIDUE_CHAIN_VECTOR_OPTION : utility::options
• residue_invalid : clean_pdb_keep_ligand
• residue_letter : clean_pdb_keep_ligand
• residue_name : usec
• residue_pair_jump_file : basic::options::OptionKeys::jumps , jumps
• residue_scores : basic::options::OptionKeys::holes , basic::options::OptionKeys::packstat , holes , packstat
• residue_trim_file : basic::options::OptionKeys::motifs , motifs
• residue_type_set : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , in::file , out::file
• ResidueChainVectorOptionKey : basic::options
• ResidueList() : PDBInfo
• residues : basic::options::OptionKeys::willmatch , demo::D010_Pose_structure , demo::D020_Pose_scoring , willmatch
• residues_backbone_move : basic::options::OptionKeys::rigid , rigid
• residues_repack_only : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• residues_to_sample : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• resj : basic::options::OptionKeys::cmiles::jumping , cmiles::jumping
• resnum : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• resolution_cutoff_high : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• resolution_cutoff_low : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• resolution_cutoffs : basic::options::OptionKeys::patterson , patterson
• resolve_build_version() : setup
• resolve_context_and_name() : tools::CppParser
• resolve_db_partition() : basic::database
• Resource : basic::resource_manager
• resource_definition_files : basic::options::OptionKeys::jd2 , jd2
• ResourceDescription : basic::resource_manager
• ResourceLoaderCOP : basic::resource_manager
• ResourceLoaderCreatorCOP : basic::resource_manager
• ResourceLoaderCreatorOP : basic::resource_manager
• ResourceLoaderOP : basic::resource_manager
• ResourceLocatorCOP : basic::resource_manager
• ResourceLocatorCreatorCOP : basic::resource_manager
• ResourceLocatorCreatorOP : basic::resource_manager
• ResourceLocatorOP : basic::resource_manager
• ResourceManagerCOP : basic::resource_manager
• ResourceManagerCreatorCOP : basic::resource_manager
• ResourceManagerCreatorOP : basic::resource_manager
• ResourceManagerOP : basic::resource_manager
• ResourceOP : basic::resource_manager
• ResourceOptionsCOP : basic::resource_manager
• ResourceOptionsCreatorCOP : basic::resource_manager
• ResourceOptionsCreatorOP : basic::resource_manager
• ResourceOptionsOP : basic::resource_manager
• ResourceOptionsTag : basic::resource_manager
• ResourceStreamCOP : basic::resource_manager
• ResourceStreamOP : basic::resource_manager
• ResourceTag : basic::resource_manager
• respect_resfile : basic::options::OptionKeys::relax , relax
• restore_pre_talaris_2013_behavior : basic::options::OptionKeys::mistakes , mistakes
• restrict_design_to_interface : basic::options::OptionKeys::smhybrid , smhybrid
• restrict_design_to_subsub_interface : basic::options::OptionKeys::smhybrid , smhybrid
• restrict_kic_sampling_to_torsion_string : basic::options::OptionKeys::loops , loops
• restrict_non_nbrs_from_repacking() : pyrosetta::toolbox , toolbox
• restrict_partners_to_chains : basic::options::OptionKeys::peptide_deriver , peptide_deriver
• restrict_receptors_to_chains : basic::options::OptionKeys::peptide_deriver , peptide_deriver
• restrict_to_wt : basic::options::OptionKeys::motifs , motifs
• restriction_type_name() : utility::tag
• restype : basic::options::OptionKeys::mh::filter , mh::filter
• restype1 : basic::options::OptionKeys::mh::filter , mh::filter
• restype2 : basic::options::OptionKeys::mh::filter , mh::filter
• restype_one : basic::options::OptionKeys::mh::filter , mh::filter
• restypedict : loadPDB
• resume_batch : basic::options::OptionKeys::out , out
• retry_failed_reads : basic::options::OptionKeys::inout::dbms , inout::dbms
• return_energy() : app::pyrosetta_toolkit::modules::tools::analysis
• return_full_atom() : abinitio , basic::options::OptionKeys::abinitio
• return_probability() : app::pyrosetta_toolkit::modules::tools::analysis
• return_residue_array() : app::pyrosetta_toolkit::modules::tools::loops
• return_rosetta_Loop() : app::pyrosetta_toolkit::modules::tools::loops
• return_zero_darc_score : basic::options::OptionKeys::fingerprint , fingerprint
• revamp_near_chain : basic::options::OptionKeys::pb_potential , pb_potential
• reversion : basic::options::OptionKeys::dna::design::reversion , dna::design::reversion
• reversion_scan : basic::options::OptionKeys::dna::design , dna::design
• revert_scan : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• reweight_symm_interactions : basic::options::OptionKeys::symmetry , symmetry
• rfactor_refinement : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• rg : basic::options::OptionKeys::remodel
• RG : basic
• rg() : numeric::random , remodel
• rg_local : basic::options::OptionKeys::remodel
• RG_LOCAL : basic
• rg_local() : remodel
• rg_local_span : basic::options::OptionKeys::score , score
• rg_reweight() : abinitio , basic::options::OptionKeys::abinitio
• rgb_to_hsv() : numeric
• rgg() : numeric::linear_algebra
• right : basic::options::OptionKeys::ufv , ufv
• right_Fstring_of() : ObjexxFCL
• right_justified() : ObjexxFCL
• right_justify() : ObjexxFCL
• RIGHT_PAREN : numeric::expression_parser
• right_string_of() : ObjexxFCL
• rigid : basic::options::OptionKeys::rigid , rigid
• rigid_body_cycles : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rigid_body_disable_mc : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rigid_body_frequency : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• ring_atm_dist_cutoff : basic::options::OptionKeys::gen_pharmacophore , gen_pharmacophore
• ring_close_shadow_constraint : basic::options::OptionKeys::score , score
• ring_ring_dist_cutoff : basic::options::OptionKeys::gen_pharmacophore , gen_pharmacophore
• ring_sasa_cutoff : basic::options::OptionKeys::gen_pharmacophore , gen_pharmacophore
• rings : basic::options::OptionKeys::rings , rings
• RJ() : ObjexxFCL::format
• rjust() : ObjexxFCL
• rm_virt_phosphate : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• rms : loops_kic , test::T650_LoopsKIC
• rms_hotspot : basic::options::OptionKeys::hotspot , hotspot
• rms_hotspot_res : basic::options::OptionKeys::hotspot , hotspot
• rms_limit : basic::options::OptionKeys::lh , lh
• rms_target : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::score , hotspot , score
• rms_threshold : basic::options::OptionKeys::evolution , evolution
• rms_topmargin : basic::options::OptionKeys::evolution , evolution
• rms_wrapper() : numeric::model_quality
• rms_wrapper_slow_and_correct() : numeric::model_quality
• rmsd() : AnchoredDesign , app::pyrosetta_toolkit::modules::tools::analysis , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::evaluation , basic::options::OptionKeys::patterson , evaluation , patterson
• rmsd_analysis : basic::options::OptionKeys::pepspec , pepspec
• rmsd_column : basic::options::OptionKeys::evaluation , evaluation
• RMSD_only_this() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• rmsd_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• rmsd_residues() : abinitio , basic::options::OptionKeys::abinitio
• rmsd_screen : basic::options::OptionKeys::stepwise , stepwise
• rmsd_select : basic::options::OptionKeys::evaluation , evaluation
• rmsd_target : basic::options::OptionKeys::evaluation , evaluation
• rmsd_tol : basic::options::OptionKeys::loops , loops
• rmsfitca2() : numeric::model_quality
• rmsfitca3() : numeric::model_quality
• rna : basic::options::OptionKeys::full_model::rna , basic::options::OptionKeys::rna , basic::options::OptionKeys::stepwise::rna , full_model::rna , rna , stepwise::rna
• rna_bulge_bonus_once_per_loop : basic::options::OptionKeys::score , score
• rna_chem_map_lores_weight : basic::options::OptionKeys::score , score
• rna_chemical_shift_exp_data : basic::options::OptionKeys::score , score
• rna_chemical_shift_H5_prime_mode : basic::options::OptionKeys::score , score
• rna_chemical_shift_include_res : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_beta : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_cut : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_nei : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_par : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_ref : basic::options::OptionKeys::score , score
• rna_chemical_shift_larmord_wt : basic::options::OptionKeys::score , score
• rna_chemical_shift_verbose : basic::options::OptionKeys::score , score
• rna_lores_chainbreak_weight : basic::options::OptionKeys::rna::farna , rna::farna
• rna_lores_linear_chainbreak_weight : basic::options::OptionKeys::rna::farna , rna::farna
• rna_prot_erraser : basic::options::OptionKeys::rna , rna
• rna_suite_potential : basic::options::OptionKeys::score , score
• rna_torsion_potential : basic::options::OptionKeys::score , score
• rna_torsion_skip_chainbreak : basic::options::OptionKeys::score , score
• rng : basic::options::OptionKeys::run , run
• rng_seed_device : basic::options::OptionKeys::run , run
• robert : basic::options::OptionKeys::robert , robert
• RocCurveOP : numeric
• RocPointOP : numeric
• RocStatus : numeric
• roll : test::Workshop4test
• root : app::pyrosetta_toolkit::window_modules::interactive_terminal::interactive_terminal
• root_at_first_rigid_body : basic::options::OptionKeys::rna::farna , rna::farna
• root_dir : toolbox::adjust_library_path
• root_res : basic::options::OptionKeys::full_model , full_model
• rosetta_bool_string() : utility::tag
• rosetta_database_from_env() : pyrosetta , src::initialization , src
• rosetta_svn_url() : devel
• rosetta_svn_version() : devel
• rosetta_version : pyrosetta
• rot_anl : basic::options::OptionKeys::rot_anl , rot_anl
• rot_lib_options_file : mrlo
• rot_mag_smooth : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rot_magnitude : basic::options::OptionKeys::enzdes , enzdes
• rot_z1 : make_symmdef_file_denovo
• rot_z2 : make_symmdef_file_denovo
• rotamer_prot_stats : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• rotamer_recovery : sequence_recovery
• ROTAMER_TRIALS : basic
• rotamer_trials : test::T500_Packing
• rotamerdump : basic::options::OptionKeys::rotamerdump , rotamerdump
• rotate_anchor_to_x : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rotate_vector() : PyMOLPyRosettaServer
• rotateX() : numeric::kinematic_closure::radians , numeric::kinematic_closure
• rotateY() : numeric::kinematic_closure::radians , numeric::kinematic_closure
• rotateZ() : numeric::kinematic_closure::radians , numeric::kinematic_closure
• rotation : basic::options::OptionKeys::rigid , demo::D100_Docking , rigid
• rotation_angle() : numeric
• rotation_axis() : numeric
• rotation_axis_angle() : numeric
• rotation_matrix() : numeric
• rotation_matrix_degrees() : numeric
• rotation_matrix_radians() : numeric , PyMOLPyRosettaServer
• rotation_z : make_symmdef_file_denovo
• rotation_z2 : make_symmdef_file_denovo
• rotlevel : basic::options::OptionKeys::motifs , motifs
• rots2add : basic::options::OptionKeys::motifs , motifs
• rotsub_movebb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• round() : utility
• round_pocketGrid_center : basic::options::OptionKeys::pocket_grid , pocket_grid
• rounds : basic::options::OptionKeys::lh , lh
• row_format : basic::options::OptionKeys::contactMap , contactMap
• RowDataBaseOP : basic::database::insert_statement_generator
• rpad() : ObjexxFCL
• rpadded() : ObjexxFCL
• rsd1 : test::T200_Scoring , test::Workshop3test
• rsd1_num : test::Workshop3test
• rsd2 : test::T200_Scoring , test::Workshop3test
• rsd2_num : test::Workshop3test
• rsd_wt_helix() : abinitio , basic::options::OptionKeys::abinitio
• rsd_wt_loop() : abinitio , basic::options::OptionKeys::abinitio
• rsd_wt_strand() : abinitio , basic::options::OptionKeys::abinitio
• rsigma : basic::options::OptionKeys::remodel , remodel
• rss() : coordlib
• rstrip() : ObjexxFCL
• rstrip_whitespace() : ObjexxFCL
• rstripped() : ObjexxFCL
• rstripped_whitespace() : ObjexxFCL
• rsym_eigenval() : numeric::model_quality
• rsym_evector() : numeric::model_quality
• rsym_rotation() : numeric::model_quality
• rt_min() : antibody , basic::options::OptionKeys::antibody
• rtmin : basic::options::OptionKeys::rot_anl , rot_anl
• rts : test::T100_Basic
• run() : app::surface_docking::surface_docking , basic::options::OptionKeys::run , run
• run_centroid : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_centroid_abinitio : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_confirmation : basic::options::OptionKeys::remodel , remodel
• run_fullatom : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_interface_analyzer() : antibody::design , basic::options::OptionKeys::antibody::design
• run_ligand_motifs : basic::options::OptionKeys::enzdes , enzdes
• run_motifs : basic::options::OptionKeys::motifs , motifs
• run_relax() : antibody::design , basic::options::OptionKeys::antibody::design
• run_sequential : basic::options::OptionKeys::pepspec , pepspec
• run_snugdock() : antibody::design , basic::options::OptionKeys::antibody::design
• run_test() : self-test , TestBindings
• rvalue_cast() : ObjexxFCL