- r -

• r1 : basic::options::OptionKeys::motifs , test::Workshop3test
• r2 : basic::options::OptionKeys::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
• 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
• radius_cutoffs : basic::options::OptionKeys::patterson
• radius_size : basic::options::OptionKeys::lh
• rama : basic::options::OptionKeys::remodel
• rama2b_map : basic::options::OptionKeys::in::file
• rama_2b : basic::options::OptionKeys::loops::ccd
• rama_B : basic::options::OptionKeys::frags
• rama_C : basic::options::OptionKeys::frags
• rama_map : basic::options::OptionKeys::corrections::score
• rama_norm : basic::options::OptionKeys::frags
• rama_not_squared : basic::options::OptionKeys::corrections::score
• ramady : basic::options::OptionKeys::relax
• ramady_cutoff : basic::options::OptionKeys::relax
• ramady_force : basic::options::OptionKeys::relax
• ramady_max_rebuild : basic::options::OptionKeys::relax
• ramady_rms_limit : basic::options::OptionKeys::relax
• ramaneighbors : basic::options::OptionKeys::score
• ramp_chainbreaks : basic::options::OptionKeys::jumps
• ramp_constraints : basic::options::OptionKeys::relax
• ramp_coord_cst : basic::options::OptionKeys::fold_cst
• ramp_fa_rep : basic::options::OptionKeys::flexPepDocking , basic::options::OptionKeys::loops
• ramp_nativeness : basic::options::OptionKeys::optE
• ramp_rama : basic::options::OptionKeys::flexPepDocking , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax::centroid
• ramp_repulsive : basic::options::OptionKeys::ddg
• ramp_vdw : basic::options::OptionKeys::relax::centroid
• RANDOM : app::pyrosetta_toolkit::modules::prettytable::prettytable
• random_conformer : basic::options::OptionKeys::docking::ligand
• random_delay : basic::options::OptionKeys::run
• random_grow_loops_by : basic::options::OptionKeys::loops
• random_limit_cluster_size_percent : basic::options::OptionKeys::cluster
• random_loop : basic::options::OptionKeys::loops
• random_order : basic::options::OptionKeys::loops
• random_phi_psi_preturbation : basic::options::OptionKeys::flexPepDocking
• random_rot_start : basic::options::OptionKeys::flexPepDocking
• random_sheets : basic::options::OptionKeys::jumps
• random_trans_start : basic::options::OptionKeys::flexPepDocking
• randomize1 : basic::options::OptionKeys::docking , docking , test::Workshop7test
• randomize2 : basic::options::OptionKeys::docking , docking , test::Workshop7test
• randomize_input_sequence : basic::options::OptionKeys::AnchoredDesign::testing
• randomize_loops : basic::options::OptionKeys::remodel::RemodelLoopMover
• randomize_missing : basic::options::OptionKeys::nonlocal
• randomize_missing_coords : basic::options::OptionKeys::run
• randomize_motif : basic::options::OptionKeys::dna::specificity
• randomly_perturb_starting_free_weights : basic::options::OptionKeys::optE
• Rargs : app::surface_docking::surface_docking
• ras : test::Workshop3test , test::Workshop4test
• raw : basic::options::OptionKeys::out::file
• raw_stats : basic::options::OptionKeys::packstat
• rb_file : basic::options::OptionKeys::RBSegmentRelax , basic::options::OptionKeys::SSrbrelax
• rb_mag : basic::options::OptionKeys::smhybrid
• rb_mover_stage1_weight : basic::options::OptionKeys::broker
• rb_param_file : basic::options::OptionKeys::SSrbrelax
• rb_rot_magnitude : basic::options::OptionKeys::fold_and_dock
• rb_scorefxn : basic::options::OptionKeys::RBSegmentRelax
• rb_trans_magnitude : basic::options::OptionKeys::fold_and_dock
• rbe : basic::options::OptionKeys::rbe
• rbMCM : basic::options::OptionKeys::flexPepDocking
• RBSegmentRelax : basic::options::OptionKeys::RBSegmentRelax
• rdc : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::in::file , basic::options::OptionKeys::rdc
• rdc_column : basic::options::OptionKeys::evaluation
• rdc_target : basic::options::OptionKeys::evaluation
• rdf : basic::options::OptionKeys::in::rdf
• read_pdb_link_records : basic::options::OptionKeys::in::file
• read_structures_into_pool : basic::options::OptionKeys::mc
• readonly : basic::options::OptionKeys::inout::dbms
• real : basic::options::OptionKeys::james
• realign : basic::options::OptionKeys::edensity
• realign_domains : basic::options::OptionKeys::cm::hybridize
• realign_domains_stage2 : basic::options::OptionKeys::cm::hybridize
• reassign_atom_types : basic::options::OptionKeys::chemical
• reassign_icoor : basic::options::OptionKeys::chemical
• rebuild_bulge_mode : basic::options::OptionKeys::stepwise::rna
• rebuild_disulf : basic::options::OptionKeys::run
• recalculate_foldtree : basic::options::OptionKeys::flexPepDocking
• receptor_chain : basic::options::OptionKeys::flexPepDocking
• recover_low : basic::options::OptionKeys::stepwise::monte_carlo
• recover_low_in_stages : basic::options::OptionKeys::abinitio
• recover_nat_rot : basic::options::OptionKeys::optE
• recover_side_chain_mover : test::T600_Docking
• recover_side_chains : basic::options::OptionKeys::cm
• recover_sidechains : basic::options::OptionKeys::docking , docking , loops , loops_kic , test::T650_LoopsKIC , test::Workshop7test
• redesign_complete : basic::options::OptionKeys::DenovoProteinDesign
• redesign_core : basic::options::OptionKeys::DenovoProteinDesign
• redesign_loops : basic::options::OptionKeys::DenovoProteinDesign
• redesign_pdb_list : sequence_recovery
• redesign_surface : basic::options::OptionKeys::DenovoProteinDesign
• reduce_rays : basic::options::OptionKeys::pocket_grid
• reduced_couplings : basic::options::OptionKeys::rdc
• ref_cen_spectrum : basic::options::OptionKeys::score::saxs
• ref_fa_spectrum : basic::options::OptionKeys::score::saxs
• ref_lig : basic::options::OptionKeys::fingerprint
• ref_offset : basic::options::OptionKeys::score
• ref_offsets : basic::options::OptionKeys::score
• ref_pdb_list : basic::options::OptionKeys::pepspec
• ref_pddf : basic::options::OptionKeys::score::saxs
• ref_spectrum : basic::options::OptionKeys::score::saxs
• ref_startstruct : basic::options::OptionKeys::flexPepDocking
• refChain : calccontacts
• reference_pose : test::Workshop8test
• refine : basic::options::OptionKeys::antibody , basic::options::OptionKeys::loops , basic::options::OptionKeys::smhybrid
• refine_CCD_off : basic::options::OptionKeys::AnchoredDesign
• refine_cycles : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::TailSegment
• refine_design_iterations : basic::options::OptionKeys::loops
• refine_final_temp : basic::options::OptionKeys::loops
• refine_h3 : basic::options::OptionKeys::antibody
• refine_init_temp : basic::options::OptionKeys::loops
• refine_KIC_off : basic::options::OptionKeys::AnchoredDesign
• refine_only : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::loops
• refine_outer_cycles : basic::options::OptionKeys::loops
• refine_repack_cycles : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::TailSegment
• refine_res : basic::options::OptionKeys::casp
• refine_temp : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
• refstruct : basic::options::OptionKeys::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
• regions : test::G101_Functions_Output , test::G102_Functions_General
• regs : test::G200_Module_Region
• reinitialize_CCD_torsions : basic::options::OptionKeys::stepwise::rna
• reinitialize_mover_for_each_job : basic::options::OptionKeys::run
• reinitialize_mover_for_new_input : basic::options::OptionKeys::run
• rel : test::G200_Module_Region
• relax : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax , test::T800_ClassicRelax , test::Workshop5test
• relax_failures : basic::options::OptionKeys::abinitio
• relax_frags_repeats : basic::options::OptionKeys::frags::nonlocal
• relax_input : basic::options::OptionKeys::frags::nonlocal
• relax_input_with_coordinate_constraints : basic::options::OptionKeys::frags::nonlocal
• relax_mover : basic::options::OptionKeys::cp
• relax_p : test::T800_ClassicRelax
• relax_sfxn : basic::options::OptionKeys::cp
• relax_with_foldtree : basic::options::OptionKeys::loops
• relax_with_jumps : basic::options::OptionKeys::abinitio
• RELERROR : numeric::kinematic_closure
• remap_pdb_atom_names_for : basic::options::OptionKeys::in::file
• remember_unrecognized_res : basic::options::OptionKeys::in
• remember_unrecognized_water : basic::options::OptionKeys::in
• remodel : basic::options::OptionKeys::antibody , basic::options::OptionKeys::loops , basic::options::OptionKeys::remodel
• remodel_aggressiveness : basic::options::OptionKeys::enzdes
• remodel_final_temp : basic::options::OptionKeys::loops
• remodel_init_temp : basic::options::OptionKeys::loops
• remodel_kic_attempts : basic::options::OptionKeys::loops
• remodel_protocol : basic::options::OptionKeys::enzdes
• remodel_secmatch : basic::options::OptionKeys::enzdes
• remodel_trials : basic::options::OptionKeys::enzdes
• RemodelLoopMover : basic::options::OptionKeys::remodel::RemodelLoopMover
• remove_antigen : basic::options::OptionKeys::antibody::design
• remove_duplicates : basic::options::OptionKeys::mh
• remove_extended_loops : basic::options::OptionKeys::loops
• remove_highest_energy_member : basic::options::OptionKeys::cluster
• remove_input_bb : basic::options::OptionKeys::pepspec
• remove_singletons : basic::options::OptionKeys::cluster
• remove_ss_length_screen : basic::options::OptionKeys::run
• removechain : clean_pdb_keep_ligand , toolbox::make_rna_rosetta_ready
• rename : basic::options::OptionKeys::ms::checkpoint
• renumber_pdb : basic::options::OptionKeys::out::file
• rep_edge_files : basic::options::OptionKeys::smhybrid
• rep_ramp_cycles : basic::options::OptionKeys::flexPepDocking
• repack : basic::options::OptionKeys::casp , basic::options::OptionKeys::rot_anl
• repack_and_minimize_decoys : basic::options::OptionKeys::optE
• repack_and_minimize_input_structures : basic::options::OptionKeys::optE
• repack_fragments : usec
• repack_only : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::packing
• repack_period : basic::options::OptionKeys::docking , basic::options::OptionKeys::loops
• repack_rate : basic::options::OptionKeys::run
• repair_sidechains : basic::options::OptionKeys::in::file
• repeat : basic::options::OptionKeys::run
• repeat_mover : test::Workshop5test
• repeat_structure : basic::options::OptionKeys::remodel
• repeat_swarm_optimization_until_fitness_improves : basic::options::OptionKeys::optE
• replonly_loops : basic::options::OptionKeys::in
• replonly_residues : basic::options::OptionKeys::in
• report_format : basic::options::OptionKeys::peptide_deriver
• report_gzip : basic::options::OptionKeys::peptide_deriver
• require_frags_match_blueprint : basic::options::OptionKeys::remodel::staged_sampling
• required_active_site_atom_names : basic::options::OptionKeys::match
• reramp_cst_cycles : basic::options::OptionKeys::fold_cst
• reramp_iterations : basic::options::OptionKeys::fold_cst
• reramp_start_cstweight : basic::options::OptionKeys::fold_cst
• reread_all_structures : basic::options::OptionKeys::archive
• rerun : basic::options::OptionKeys::abinitio
• rerun_motifsearch : basic::options::OptionKeys::motifs
• res : app::delta_score_per_mutation
• res5 : test::T100_Basic
• res_design_bs : basic::options::OptionKeys::fold_from_loops
• res_set : test::T880_Other
• resample : basic::options::OptionKeys::resample
• resclass_by_sasa : basic::options::OptionKeys::remodel
• rescore : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::in::file , basic::options::OptionKeys::optE::rescore , basic::options::OptionKeys::rescore
• resfile : basic::options::OptionKeys::packing
• resfile_dump : basic::options::OptionKeys::mh::dump
• resfile_min_pair_score : basic::options::OptionKeys::mh::dump
• resfile_min_tot_score : basic::options::OptionKeys::mh::dump
• resi : basic::options::OptionKeys::cmiles::jumping
• residue : basic::options::OptionKeys::hotspot
• residue_1 : test::T220_AtomAtomPairEnergies
• residue_2 : test::T220_AtomAtomPairEnergies
• residue_buffer : clean_pdb_keep_ligand
• residue_invalid : clean_pdb_keep_ligand
• residue_letter : clean_pdb_keep_ligand
• residue_name : usec
• residue_pair_jump_file : basic::options::OptionKeys::jumps
• residue_scores : basic::options::OptionKeys::holes , basic::options::OptionKeys::packstat
• residue_trim_file : basic::options::OptionKeys::motifs
• residue_type_set : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• residues : basic::options::OptionKeys::willmatch , demo::D010_Pose_structure , demo::D020_Pose_scoring
• residues_backbone_move : basic::options::OptionKeys::rigid
• residues_repack_only : basic::options::OptionKeys::DomainAssembly
• residues_to_sample : basic::options::OptionKeys::remodel::staged_sampling
• resj : basic::options::OptionKeys::cmiles::jumping
• resnum : clean_pdb_keep_ligand , toolbox::make_rna_rosetta_ready
• resolution_cutoff_high : basic::options::OptionKeys::score::fiber_diffraction
• resolution_cutoff_low : basic::options::OptionKeys::score::fiber_diffraction
• resolution_cutoffs : basic::options::OptionKeys::patterson
• resource_definition_files : basic::options::OptionKeys::jd2
• respect_resfile : basic::options::OptionKeys::relax
• restore_pre_talaris_2013_behavior : basic::options::OptionKeys::mistakes
• restrict_design_to_interface : basic::options::OptionKeys::smhybrid
• restrict_design_to_subsub_interface : basic::options::OptionKeys::smhybrid
• restrict_kic_sampling_to_torsion_string : basic::options::OptionKeys::loops
• restrict_partners_to_chains : basic::options::OptionKeys::peptide_deriver
• restrict_receptors_to_chains : basic::options::OptionKeys::peptide_deriver
• restrict_to_wt : basic::options::OptionKeys::motifs
• restype : basic::options::OptionKeys::mh::filter
• restype1 : basic::options::OptionKeys::mh::filter
• restype2 : basic::options::OptionKeys::mh::filter
• restype_one : basic::options::OptionKeys::mh::filter
• restypedict : loadPDB
• resume_batch : basic::options::OptionKeys::out
• retry_failed_reads : basic::options::OptionKeys::inout::dbms
• return_full_atom : basic::options::OptionKeys::abinitio
• return_zero_darc_score : basic::options::OptionKeys::fingerprint
• revamp_near_chain : basic::options::OptionKeys::pb_potential
• reversion : basic::options::OptionKeys::dna::design::reversion
• reversion_scan : basic::options::OptionKeys::dna::design
• revert_scan : basic::options::OptionKeys::matdes::mutalyze
• reweight_symm_interactions : basic::options::OptionKeys::symmetry
• rfactor_refinement : basic::options::OptionKeys::score::fiber_diffraction
• rg : basic::options::OptionKeys::remodel
• rg_local : basic::options::OptionKeys::remodel
• rg_local_span : basic::options::OptionKeys::score
• rg_reweight : basic::options::OptionKeys::abinitio
• right : basic::options::OptionKeys::ufv
• rigid : basic::options::OptionKeys::rigid
• rigid_body_cycles : basic::options::OptionKeys::fold_and_dock
• rigid_body_disable_mc : basic::options::OptionKeys::fold_and_dock
• rigid_body_frequency : basic::options::OptionKeys::fold_and_dock
• ring_atm_dist_cutoff : basic::options::OptionKeys::gen_pharmacophore
• ring_close_shadow_constraint : basic::options::OptionKeys::score
• ring_ring_dist_cutoff : basic::options::OptionKeys::gen_pharmacophore
• ring_sasa_cutoff : basic::options::OptionKeys::gen_pharmacophore
• rings : basic::options::OptionKeys::rings
• rm_virt_phosphate : basic::options::OptionKeys::stepwise::rna
• rms : loops_kic , test::T650_LoopsKIC
• rms_hotspot : basic::options::OptionKeys::hotspot
• rms_hotspot_res : basic::options::OptionKeys::hotspot
• rms_limit : basic::options::OptionKeys::lh
• rms_target : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::score
• rms_threshold : basic::options::OptionKeys::evolution
• rms_topmargin : basic::options::OptionKeys::evolution
• rmsd : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::evaluation , basic::options::OptionKeys::patterson
• rmsd_analysis : basic::options::OptionKeys::pepspec
• rmsd_column : basic::options::OptionKeys::evaluation
• RMSD_only_this : basic::options::OptionKeys::AnchoredDesign::testing
• rmsd_res : basic::options::OptionKeys::stepwise::rna
• rmsd_residues : basic::options::OptionKeys::abinitio
• rmsd_screen : basic::options::OptionKeys::stepwise
• rmsd_select : basic::options::OptionKeys::evaluation
• rmsd_target : basic::options::OptionKeys::evaluation
• rmsd_tol : basic::options::OptionKeys::loops
• rna : basic::options::OptionKeys::full_model::rna , basic::options::OptionKeys::rna , basic::options::OptionKeys::stepwise::rna
• rna_bulge_bonus_once_per_loop : basic::options::OptionKeys::score
• rna_chem_map_lores_weight : basic::options::OptionKeys::score
• rna_chemical_shift_exp_data : basic::options::OptionKeys::score
• rna_chemical_shift_H5_prime_mode : basic::options::OptionKeys::score
• rna_chemical_shift_include_res : basic::options::OptionKeys::score
• rna_chemical_shift_larmord : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_beta : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_cut : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_nei : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_par : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_ref : basic::options::OptionKeys::score
• rna_chemical_shift_larmord_wt : basic::options::OptionKeys::score
• rna_chemical_shift_verbose : basic::options::OptionKeys::score
• rna_prot_erraser : basic::options::OptionKeys::rna
• rna_suite_potential : basic::options::OptionKeys::score
• rna_torsion_potential : basic::options::OptionKeys::score
• rna_torsion_skip_chainbreak : basic::options::OptionKeys::score
• rng : basic::options::OptionKeys::run
• rng_seed_device : basic::options::OptionKeys::run
• robert : basic::options::OptionKeys::robert
• roll : test::Workshop4test
• root : app::pyrosetta_toolkit::window_modules::interactive_terminal::interactive_terminal
• root_res : basic::options::OptionKeys::full_model
• rot_anl : basic::options::OptionKeys::rot_anl
• rot_lib_options_file : mrlo
• rot_mag_smooth : basic::options::OptionKeys::fold_and_dock
• rot_magnitude : basic::options::OptionKeys::enzdes
• rot_z1 : make_symmdef_file_denovo
• rot_z2 : make_symmdef_file_denovo
• rotamer_prot_stats : basic::options::OptionKeys::pH::calc_pka
• rotamer_recovery : sequence_recovery
• rotamer_trials : test::T500_Packing
• rotamerdump : basic::options::OptionKeys::rotamerdump
• rotate_anchor_to_x : basic::options::OptionKeys::fold_and_dock
• rotation : basic::options::OptionKeys::rigid , demo::D100_Docking
• rotation_z : make_symmdef_file_denovo
• rotation_z2 : make_symmdef_file_denovo
• rotlevel : basic::options::OptionKeys::motifs
• rots2add : basic::options::OptionKeys::motifs
• rotsub_movebb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer
• round_pocketGrid_center : basic::options::OptionKeys::pocket_grid
• rounds : basic::options::OptionKeys::lh
• row_format : basic::options::OptionKeys::contactMap
• rsd1 : test::T200_Scoring , test::Workshop3test
• rsd1_num : test::Workshop3test
• rsd2 : test::T200_Scoring , test::Workshop3test
• rsd2_num : test::Workshop3test
• rsd_wt_helix : basic::options::OptionKeys::abinitio
• rsd_wt_loop : basic::options::OptionKeys::abinitio
• rsd_wt_strand : basic::options::OptionKeys::abinitio
• rsigma : basic::options::OptionKeys::remodel
• rt_min : basic::options::OptionKeys::antibody
• rtmin : basic::options::OptionKeys::rot_anl
• rts : test::T100_Basic
• run : basic::options::OptionKeys::run
• run_centroid : basic::options::OptionKeys::DomainAssembly
• run_centroid_abinitio : basic::options::OptionKeys::DomainAssembly
• run_confirmation : basic::options::OptionKeys::remodel
• run_fullatom : basic::options::OptionKeys::DomainAssembly
• run_ligand_motifs : basic::options::OptionKeys::enzdes
• run_motifs : basic::options::OptionKeys::motifs
• run_relax : basic::options::OptionKeys::antibody::design
• run_sequential : basic::options::OptionKeys::pepspec
• run_snugdock : basic::options::OptionKeys::antibody::design