- r -

• r : create_a3b_hbs
• R : docking , kmeans_adaptive_kernel_density_bb_dependent_rotlib
• r : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib
• R : kmeans_common
• r : kmeans_common , PREcst
• r1 : basic::options::OptionKeys::motifs , test.Workshop3test
• r2 : basic::options::OptionKeys::motifs
• R2 : predPRE
• r2 : test.Workshop3test
• R5C : test.Workshop2test
• R5CA : test.Workshop2test
• R5N : test.Workshop2test
• r_1 : build_jacobian
• r_2 : build_jacobian
• r_c : build_jacobian
• r_ca : build_jacobian
• r_n : build_jacobian
• 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
• ralford : basic::options::OptionKeys::ralford
• 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_cutoff : basic::options::OptionKeys::cyclic_peptide
• rama_map : basic::options::OptionKeys::corrections::score
• rama_map_average_L_flat : basic::options::OptionKeys::corrections::score
• rama_map_average_L_flat_stringent : basic::options::OptionKeys::corrections::score
• rama_map_sym_average_L_flat : basic::options::OptionKeys::corrections::score
• rama_map_sym_average_L_flat_stringent : basic::options::OptionKeys::corrections::score
• rama_map_sym_gly_flat : basic::options::OptionKeys::corrections::score
• rama_map_sym_gly_flat_stringent : basic::options::OptionKeys::corrections::score
• rama_map_sym_pro_flat : basic::options::OptionKeys::corrections::score
• rama_map_sym_pro_flat_stringent : basic::options::OptionKeys::corrections::score
• rama_norm : basic::options::OptionKeys::frags
• rama_not_squared : basic::options::OptionKeys::corrections::score
• rama_power : basic::options::OptionKeys::score
• rama_pp_map : basic::options::OptionKeys::corrections::score
• rama_prepro_nobidentate : basic::options::OptionKeys::corrections::score
• rama_prepro_steep : basic::options::OptionKeys::corrections::score
• rama_sampling_table_by_res : basic::options::OptionKeys::cyclic_peptide
• 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 : basic::options::OptionKeys::msd
• 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_rnp_vdw : basic::options::OptionKeys::rna::denovo
• ramp_scorefxn : basic::options::OptionKeys::carbohydrates::glycan_dock
• ramp_vdw : basic::options::OptionKeys::relax::centroid
• rand_checkpoint_file : basic::options::OptionKeys::cyclic_peptide
• rand_glycan_jump_res : basic::options::OptionKeys::carbohydrates::glycan_dock
• 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_start : basic::options::OptionKeys::antibody::design
• random_trans_start : basic::options::OptionKeys::flexPepDocking
• randomize : basic::options::OptionKeys::recon
• randomize1 : basic::options::OptionKeys::docking , docking , test.Workshop7test
• randomize2 : basic::options::OptionKeys::docking , docking , test.Workshop7test
• randomize_init_rnp : basic::options::OptionKeys::rna::denovo
• 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
• randomize_substrate_torsions : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• randomly_perturb_starting_free_weights : basic::options::OptionKeys::optE
• range : basic::options::OptionKeys::relax::range , hist2d
• rank : basic::options::OptionKeys::legacy_sewing
• rank_by_bsasa : basic::options::OptionKeys::remodel
• ras : test.Workshop3test , test.Workshop4test
• ratio : PREcst , predPRE
• 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
• Rconst : PREcst , predPRE
• rdc : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::in::file , basic::options::OptionKeys::nmr::rdc , basic::options::OptionKeys::rdc
• rdc_column : basic::options::OptionKeys::evaluation
• rdc_target : basic::options::OptionKeys::evaluation
• rdf : basic::options::OptionKeys::in::rdf
• reaction_file : basic::options::OptionKeys::ligand_evolution
• read_only_ATOM_entries : basic::options::OptionKeys::in
• read_structures_into_pool : basic::options::OptionKeys::mc
• reading_only : basic::options::OptionKeys::PDB_diagnostic
• readonly : basic::options::OptionKeys::inout::dbms
• readout : internal_coordinates
• ready_set_only : basic::options::OptionKeys::rna::erraser
• reagent_file : basic::options::OptionKeys::ligand_evolution
• real : basic::options::OptionKeys::james
• real_phi : oop_conformations
• real_psi : oop_conformations
• 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_all_in_dihedral_mode : basic::options::OptionKeys::cluster::energy_based_clustering
• rebuild_bulge_mode : basic::options::OptionKeys::stepwise::rna
• rebuild_disulf : basic::options::OptionKeys::run
• rebuild_rmsds : average_rmsds
• rebuild_surrounding : setup_for_complex_scoring_general
• recalculate_foldtree : basic::options::OptionKeys::flexPepDocking
• recces : basic::options::OptionKeys::recces::base_pair
• receptor_chain : basic::options::OptionKeys::flexPepDocking
• recon : basic::options::OptionKeys::recon
• 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
• recursive_depth : basic::options::OptionKeys::sewing
• 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
• ref_zinc : local
• reference : closure_error , explosion_error
• reference_pose : test.Workshop8test
• reference_structure : find_position_matches_using_inverse_rotamers
• reference_structure_epitope_residue_range : find_position_matches_using_inverse_rotamers
• reference_structure_glycan_residues : find_position_matches_using_inverse_rotamers
• reference_structure_positions_to_match : find_position_matches_using_inverse_rotamers
• reference_zinc_site : local
• refinable_lattice : basic::options::OptionKeys::cryst
• refine : basic::options::OptionKeys::loops , basic::options::OptionKeys::smhybrid , kic_runner
• refine_all_tcr_cdr_loops : basic::options::OptionKeys::tcrmodel
• 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_native : basic::options::OptionKeys::rna::denovo
• refine_native_get_good_FT : basic::options::OptionKeys::rna::denovo
• refine_only : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::carbohydrates::glycan_dock , 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_silent_file : basic::options::OptionKeys::rna::denovo
• refine_silent_number_of_poses : basic::options::OptionKeys::rna::denovo
• refine_silent_tags : basic::options::OptionKeys::rna::denovo
• refine_tcr_cdr3_loops : basic::options::OptionKeys::tcrmodel
• refine_tcr_cdr3a_loop : basic::options::OptionKeys::tcrmodel
• refine_tcr_cdr3b_loop : basic::options::OptionKeys::tcrmodel
• refine_temp : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
• refsimilarity_cut : basic::options::OptionKeys::cm
• 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
• register_pandas_container_traversal : pyrosetta.distributed.packed_pose
• 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::mp::mutate_relax , basic::options::OptionKeys::relax , test.T800_ClassicRelax , test.Workshop5test
• relax_commands : relax_starting_structure
• relax_cycle_rounds : basic::options::OptionKeys::antibody::design
• 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_model : basic::options::OptionKeys::tcrmodel
• relax_mover : basic::options::OptionKeys::cp
• relax_p : test.T800_ClassicRelax
• relax_pdb : minimalCstRelax
• relax_rna : basic::options::OptionKeys::rna::denovo
• relax_rounds : basic::options::OptionKeys::cluster::energy_based_clustering
• relax_sfxn : basic::options::OptionKeys::cp
• relax_with_foldtree : basic::options::OptionKeys::loops
• relax_with_jumps : basic::options::OptionKeys::abinitio
• relaxed_native : unalignedEvaluate
• release : conf
• RELERROR : numeric::kinematic_closure
• remap_pdb_atom_names_for : basic::options::OptionKeys::in::file
• remapped_rosetta_modules : rosetta
• remember_unrecognized_res : basic::options::OptionKeys::in
• remember_unrecognized_water : basic::options::OptionKeys::in
• remodel : basic::options::OptionKeys::loops , basic::options::OptionKeys::remodel , kic_runner
• 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_loop_cdr3a : basic::options::OptionKeys::tcrmodel
• remodel_loop_cdr3b : basic::options::OptionKeys::tcrmodel
• remodel_protocol : basic::options::OptionKeys::enzdes
• remodel_secmatch : basic::options::OptionKeys::enzdes
• remodel_tcr_cdr3_loops : basic::options::OptionKeys::tcrmodel
• remodel_tcr_cdr3a_loop : basic::options::OptionKeys::tcrmodel
• remodel_tcr_cdr3b_loop : basic::options::OptionKeys::tcrmodel
• remodel_trials : basic::options::OptionKeys::enzdes
• RemodelLoopMover : basic::options::OptionKeys::remodel::RemodelLoopMover
• remove_all_dssp : basic::options::OptionKeys::legacy_sewing
• remove_antigen : basic::options::OptionKeys::antibody::design
• remove_any_dssp : basic::options::OptionKeys::legacy_sewing
• 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_obligate_pair : basic::options::OptionKeys::rna::denovo
• remove_pair : basic::options::OptionKeys::rna::denovo
• remove_singletons : basic::options::OptionKeys::cluster
• remove_ss_length_screen : basic::options::OptionKeys::run
• removechain : clean_pdb_keep_ligand
• rename : basic::options::OptionKeys::ms::checkpoint
• render_density : basic::options::OptionKeys::edensity
• renumber_pdb : basic::options::OptionKeys::out::file
• renumbering : rna_rosetta_ready_set
• rep : test.T220_AtomAtomPairEnergies
• rep1 : test_mm_lj
• rep2 : test_mm_lj
• rep_edge_files : basic::options::OptionKeys::smhybrid
• rep_ramp_cycles : basic::options::OptionKeys::flexPepDocking
• rep_total : test.T220_AtomAtomPairEnergies
• repack : basic::options::OptionKeys::casp , basic::options::OptionKeys::rot_anl
• repack_again : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range
• repack_and_minimize_decoys : basic::options::OptionKeys::optE
• repack_and_minimize_input_structures : basic::options::OptionKeys::optE
• repack_cycles : basic::options::OptionKeys
• repack_fragments : usec
• repack_mutant_position_only : surface_app
• repack_mutation_only : basic::options::OptionKeys::mp::mutate_relax
• repack_neighborhood : basic::options::OptionKeys::coupled_moves
• repack_only : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::packing
• repack_period : basic::options::OptionKeys::docking , basic::options::OptionKeys::loops
• repack_radius : basic::options::OptionKeys::mp::mutate_relax , chrisk
• repack_rate : basic::options::OptionKeys::run
• repacking_distance : local
• repair_sidechains : basic::options::OptionKeys::in::file
• repeat : basic::options::OptionKeys::legacy_sewing , basic::options::OptionKeys::run , byres_data , hbscan
• repeat_mover : test.Workshop5test
• repeat_prints : HelicalAssembly
• 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
• reporter : globals
• require_bordering_ss : local
• require_disulfides : basic::options::OptionKeys::cyclic_peptide
• require_frags_match_blueprint : basic::options::OptionKeys::remodel::staged_sampling
• require_symmetry_angle_threshold : basic::options::OptionKeys::cyclic_peptide
• require_symmetry_mirroring : basic::options::OptionKeys::cyclic_peptide
• require_symmetry_perturbation : basic::options::OptionKeys::cyclic_peptide
• require_symmetry_repeats : basic::options::OptionKeys::cyclic_peptide
• required : auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , drrafter_rna , finalize_models
• 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
• reroot_tree : basic::options::OptionKeys::remodel
• rerun : basic::options::OptionKeys::abinitio
• rerun_motifsearch : basic::options::OptionKeys::motifs
• res : erraser_analysis , erraser_single_res_analysis , val2thr
• res1 : erraser_analysis
• res2 : erraser_analysis
• res5 : test.T100_basic
• res_design_bs : basic::options::OptionKeys::fold_from_loops
• res_num : cal_NBR_radius
• res_pna : pna
• res_pna_cterm : pna
• res_pna_nterm : pna
• res_pnc : pna
• res_png : pna
• res_pnt : pna
• res_pnu : pna
• res_pnu_cterm : pna
• res_pnu_nterm : pna
• res_slice_list : rna_decompose
• 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 , pna , test_terpenes
• residue : 3d_histogram , basic::options::OptionKeys::hotspot , ss_finder
• 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 : basic::options::OptionKeys::make_mainchain_potential , dumper , torsion_scoring , usec
• residue_pair_jump_file : basic::options::OptionKeys::jumps
• residue_scores : basic::options::OptionKeys::holes , basic::options::OptionKeys::packstat
• residue_set_cap : lactamize
• residue_to_glycosylate : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• 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 , execute , run_sidechain
• residues_backbone_move : basic::options::OptionKeys::rigid
• residues_repack_only : basic::options::OptionKeys::DomainAssembly
• residues_to_ignore : basic::options::OptionKeys::cluster::energy_based_clustering
• residues_to_sample : basic::options::OptionKeys::remodel::staged_sampling
• resj : basic::options::OptionKeys::cmiles::jumping
• reslines : cal_NBR_radius
• resnum : clean_pdb_keep_ligand , predPRE
• resolution_cutoff_high : basic::options::OptionKeys::score::fiber_diffraction
• resolution_cutoff_low : basic::options::OptionKeys::score::fiber_diffraction
• resolution_cutoffs : basic::options::OptionKeys::patterson
• resolution_scale_factor : basic::options::OptionKeys::motifs
• resolution_scale_factor_float : basic::options::OptionKeys::motifs
• resource_definition_files : basic::options::OptionKeys::jd3
• resource_definition_schema : basic::options::OptionKeys::jd3
• respect_resfile : basic::options::OptionKeys::relax
• restore_from_checkpoint : basic::options::OptionKeys::jd3
• restore_lazaridis_imm_behavior : basic::options::OptionKeys::mp
• restore_pre_talaris_2013_behavior : basic::options::OptionKeys::mistakes
• restore_talaris_behavior : basic::options::OptionKeys::corrections
• restrict_design_to_interface : basic::options::OptionKeys::msd , basic::options::OptionKeys::smhybrid
• restrict_design_to_subsub_interface : basic::options::OptionKeys::smhybrid
• restrict_kic_sampling_to_torsion_string : basic::options::OptionKeys::loops
• restrict_min_to_interface : basic::options::OptionKeys::msd
• 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 , build_restypes , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib , test.T150_core
• restype1 : basic::options::OptionKeys::mh::filter
• restype2 : basic::options::OptionKeys::mh::filter
• restype_one : basic::options::OptionKeys::mh::filter
• restype_set : beta_sc_scan , create_a3b_hbs , evaluate_beta_mutants
• restype_set_cap : vancomycin
• restypes : hbscan
• result : build_jacobian , pyrosetta.tests.__main__
• 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_real_loops : challenge
• revert_scan : basic::options::OptionKeys::matdes::mutalyze
• reweight_symm_interactions : basic::options::OptionKeys::symmetry
• rf_peptide : basic::options::OptionKeys::mean_field
• 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
• rho : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• rho_dat : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• rhos : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• 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_conformer_dbpath : basic::options::OptionKeys::rings
• ring_ring_dist_cutoff : basic::options::OptionKeys::gen_pharmacophore
• ring_sasa_cutoff : basic::options::OptionKeys::gen_pharmacophore
• ring_set : test.C001_Carbohydrates_Demo01
• 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_mode : devel::metal_interface
• rms_target : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::score
• rms_threshold : basic::options::OptionKeys::evolution
• rms_topmargin : basic::options::OptionKeys::evolution
• rms_type : basic::options::OptionKeys::evaluation
• rmsd : average_rmsds , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::evaluation , basic::options::OptionKeys::patterson , legacy_score_vs_rmsd
• rmsd_analysis : basic::options::OptionKeys::pepspec
• rmsd_column : basic::options::OptionKeys::evaluation
• rmsd_cutoff : basic::options::OptionKeys::recces::base_pair
• 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 , chrisk
• rmsds : legacy_score_vs_rmsd , score_vs_rmsd
• rna : basic::options::OptionKeys::full_model::rna , basic::options::OptionKeys::rna , basic::options::OptionKeys::score::rna , basic::options::OptionKeys::stepwise::rna
• rna_all_prot_sc_min_only : basic::options::OptionKeys::ddg
• rna_base_pair_xy_filename : basic::options::OptionKeys::score::rna
• rna_bulge_bonus_once_per_loop : basic::options::OptionKeys::score::rna
• rna_chem_map_lores_weight : basic::options::OptionKeys::score::rna
• rna_chemical_shift_exp_data : basic::options::OptionKeys::score::rna
• rna_chemical_shift_H5_prime_mode : basic::options::OptionKeys::score::rna
• rna_chemical_shift_include_res : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_beta : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_cut : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_nei : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_par : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_ref : basic::options::OptionKeys::score::rna
• rna_chemical_shift_larmord_wt : basic::options::OptionKeys::score::rna
• rna_chemical_shift_verbose : basic::options::OptionKeys::score::rna
• rna_lores_chainbreak_weight : basic::options::OptionKeys::rna::denovo
• rna_lores_linear_chainbreak_weight : basic::options::OptionKeys::rna::denovo
• rna_P : basic::options::OptionKeys::cluster
• rna_prot_erraser : basic::options::OptionKeys::rna::erraser
• rna_protein_docking : basic::options::OptionKeys::rna::denovo
• rna_protein_docking_freq : basic::options::OptionKeys::rna::denovo
• rna_protein_docking_legacy : basic::options::OptionKeys::rna::denovo
• RNA_residues : mutant_modeler
• RNA_residues_1letter : mutant_modeler
• rna_suite_potential : basic::options::OptionKeys::score::rna
• rna_torsion_potential : basic::options::OptionKeys::score
• rna_torsion_skip_chainbreak : basic::options::OptionKeys::score::rna
• rng : basic::options::OptionKeys::run
• rng_seed_device : basic::options::OptionKeys::run
• rnp_high_res_cycles : basic::options::OptionKeys::rna::denovo
• rnp_high_res_relax : basic::options::OptionKeys::rna::denovo
• rnp_min_first : basic::options::OptionKeys::rna::denovo
• rnp_pack_first : basic::options::OptionKeys::rna::denovo
• rnp_ramp_rep : basic::options::OptionKeys::rna::denovo
• robert : basic::options::OptionKeys::robert
• roll : test.Workshop4test
• root_at_first_rigid_body : basic::options::OptionKeys::rna::denovo
• root_project_template : update_ui_project
• root_res : basic::options::OptionKeys::full_model
• rosetta_dir : drrafter_rna
• rosetta_path : execute , kic_runner , run_backbone , run_sidechain
• ROSETTA_SCAL_FACT : get_final_ddG_scores
• rosetta_subpath : execute , kic_runner , run_backbone , run_sidechain
• rot_anl : basic::options::OptionKeys::rot_anl
• rot_bb_data : kmeans_bb_dependent_rotlib
• rot_bb_data_lst : kmeans_bb_dependent_rotlib
• rot_mag_smooth : basic::options::OptionKeys::fold_and_dock
• rot_magnitude : basic::options::OptionKeys::enzdes
• rot_norm_weight : basic::options::OptionKeys::mean_field
• rot_z1 : make_symmdef_file_denovo
• rot_z2 : make_symmdef_file_denovo
• rotamer_info_prefix : basic::options::OptionKeys::ralford::dump_rotamers
• rotamer_prot_stats : basic::options::OptionKeys::pH::calc_pka
• rotamer_recovery : sequence_recovery
• rotamer_sets : test.T120_core
• rotamer_trials : test.T500_Packing
• rotamerdump : basic::options::OptionKeys::rotamerdump
• rotate_anchor_to_x : basic::options::OptionKeys::fold_and_dock
• rotation : 3d_histogram , basic::options::OptionKeys::rigid , demo.D100_Docking , subloop_histogram
• rotation_mag : basic::options::OptionKeys::recces::base_pair
• 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 , basic::options::OptionKeys::rna::denovo
• row : dummy-distribution
• row_format : basic::options::OptionKeys::contactMap
• rp : basic::options::OptionKeys::sc
• rr2dd : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• rsd1 : test.T200_Scoring , test.Workshop3test
• rsd1_num : test.Workshop3test
• rsd2 : test.T200_Scoring , test.Workshop3test
• rsd2_num : test.Workshop3test
• rsd_index : basic::options::OptionKeys::ralford::dump_rotamers
• 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
• rt_tol : chrisk
• rtmin : basic::options::OptionKeys::rot_anl
• rts : beta_nonlocal , orn_macrocycle , pna , test.T100_basic , test.T880_Other , test_terpenes
• 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_interface_analyzer : basic::options::OptionKeys::antibody::design
• 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
• runner : pyrosetta.tests.distributed.test_dask