- r -

• r1() : basic::options::OptionKeys::motifs , motifs
• r2() : basic::options::OptionKeys::motifs , motifs
• radial_disp() : basic::options::OptionKeys::matdes , matdes
• radians() : numeric::conversions
• radius() : basic::options::OptionKeys::cluster , basic::options::OptionKeys::ddg , cluster , ddg
• radius_cutoffs() : patterson
• rama() : remodel
• rama2b_map() : basic::options::OptionKeys::in::file , in::file
• rama_B() : basic::options::OptionKeys::frags , frags
• rama_C() : basic::options::OptionKeys::frags , frags
• rama_map() : 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_score_nonstandard_connections() : score
• ramady() : relax
• ramady_cutoff() : relax
• ramady_force() : relax
• ramady_max_rebuild() : relax
• ramady_rms_limit() : relax
• ramaneighbors() : score
• ramp_chainbreaks() : basic::options::OptionKeys::jumps , jumps
• ramp_constraints() : 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 , flexPepDocking , loops , relax::centroid
• ramp_repulsive() : basic::options::OptionKeys::ddg , ddg
• ramp_vdw() : relax::centroid
• rand_sleep() : utility::file
• random_conformer() : basic::options::OptionKeys::docking::ligand , docking::ligand
• random_delay() : run
• 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_order() : basic::options::OptionKeys::loops , loops
• random_permutation() : numeric::random
• random_phi_psi_preturbation() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• random_range() : numeric::random
• random_rot_start() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• random_sheets() : basic::options::OptionKeys::jumps , jumps
• random_trans_start() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• randomize1() : basic::options::OptionKeys::docking , docking
• randomize2() : basic::options::OptionKeys::docking , docking
• randomize_equivalent_fragments() : remodel
• randomize_input_sequence() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• randomize_loops() : remodel::RemodelLoopMover
• randomize_missing() : basic::options::OptionKeys::nonlocal , nonlocal
• randomize_missing_coords() : run
• randomize_motif() : basic::options::OptionKeys::dna::specificity , dna::specificity
• randomly_perturb_starting_free_weights() : basic::options::OptionKeys::optE , optE
• rank_by_bsasa() : remodel
• raw() : out::file
• raw_stats() : packstat
• rb_file() : basic::options::OptionKeys::ddg , ddg , RBSegmentRelax , SSrbrelax
• rb_mag() : smhybrid
• rb_min_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• rb_param_file() : SSrbrelax
• rb_restrict_to_mutsite_nbrs() : basic::options::OptionKeys::ddg , ddg
• rb_rot_magnitude() : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rb_scorefxn() : RBSegmentRelax
• rb_trans_magnitude() : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rbe() : rbe
• rbMCM() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• RBSegmentRelax() : RBSegmentRelax
• rdc() : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::in::file , evaluation , in::file , rdc
• rdc_column() : basic::options::OptionKeys::evaluation , evaluation
• rdc_select() : basic::options::OptionKeys::evaluation , evaluation
• rdc_target() : basic::options::OptionKeys::evaluation , evaluation
• rdc_weight() : basic::options::OptionKeys::nonlocal , nonlocal
• rdf() : basic::options::OptionKeys::in::rdf , in::rdf
• read() : utility::json_spirit
• read_fragfile() : remodel
• 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_pdb_link_records() : basic::options::OptionKeys::in::file , in::file
• read_probabilities_or_die() : numeric
• read_range() : utility::json_spirit
• read_range_or_throw() : utility::json_spirit
• 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_vector() : utility::io
• ReadFromFileOrDie() : utility
• readonly() : basic::options::OptionKeys::inout::dbms , inout::dbms
• real() : basic::options::OptionKeys::james , james
• real2afteroption() : basic::options
• real3afteroption() : basic::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
• rebuild_bulge_mode() : stepwise::rna
• rebuild_disulf() : run
• 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_string_from_node() : utility
• receptor_chain() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• recover_low_in_stages() : abinitio , basic::options::OptionKeys::abinitio
• recover_nat_rot() : basic::options::OptionKeys::optE , optE
• recover_side_chains() : basic::options::OptionKeys::cm , cm
• recover_sidechains() : basic::options::OptionKeys::docking , docking
• redesign_complete() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_core() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_loops() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• redesign_surface() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• reduce_rays() : pocket_grid
• reduced_couplings() : rdc
• ref_cen_spectrum() : score::saxs
• ref_fa_spectrum() : score::saxs
• ref_offset() : score
• ref_offsets() : score
• ref_pdb_list() : pepspec
• ref_pddf() : score::saxs
• ref_spectrum() : score::saxs
• ref_startstruct() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• refine() : antibody , basic::options::OptionKeys::antibody , basic::options::OptionKeys::loops , loops , smhybrid
• refine_CCD_off() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• refine_cycles() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• 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_only() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::loops , loops
• refine_repack_cycles() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• refine_res() : basic::options::OptionKeys::casp , casp
• refine_temp() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• refstruct() : basic::options::OptionKeys::lh , lh
• region_def() : basic::options::OptionKeys::contactMap , contactMap
• regions() : run
• register_version_with_core() : devel
• reinitialize_CCD_torsions() : stepwise::rna
• reinitialize_mover_for_each_job() : run
• reinitialize_mover_for_new_input() : run
• relax() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize , basic::options::OptionKeys::loops , cm::hybridize , loops , relax
• 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_sfxn() : basic::options::OptionKeys::cp , cp
• relax_with_foldtree() : basic::options::OptionKeys::loops , loops
• relax_with_jumps() : abinitio , basic::options::OptionKeys::abinitio
• remainder() : numeric
• remainder_conversion() : numeric
• 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 , 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() : remodel::RemodelLoopMover
• remove_exit_callback() : utility
• remove_extended_loops() : basic::options::OptionKeys::loops , loops
• remove_highest_energy_member() : basic::options::OptionKeys::cluster , cluster
• remove_input_bb() : pepspec
• remove_singletons() : basic::options::OptionKeys::cluster , cluster
• remove_ss_length_screen() : run
• remove_trailing() : utility::json_spirit
• rename() : basic::options::OptionKeys::ms::checkpoint , ms::checkpoint
• render_sigma() : basic::options::OptionKeys::edensity , edensity
• renumber_pdb() : out::file
• rep_edge_files() : smhybrid
• rep_ramp_cycles() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• repack() : basic::options::OptionKeys::casp , casp , rot_anl
• repack_and_minimize_decoys() : basic::options::OptionKeys::optE , optE
• repack_and_minimize_input_structures() : basic::options::OptionKeys::optE , optE
• repack_never() : basic::options::OptionKeys::loops , loops
• repack_only() : basic::options::OptionKeys::dna::design , dna::design , packing
• repack_period() : basic::options::OptionKeys::docking , basic::options::OptionKeys::loops , docking , loops
• repack_rate() : run
• repair_sidechains() : basic::options::OptionKeys::in::file , in::file
• repeat() : run
• repeat_structure() : remodel
• repeat_swarm_optimization_until_fitness_improves() : basic::options::OptionKeys::optE , optE
• replace_environment_variables() : utility
• replace_in() : utility
• replonly_loops() : basic::options::OptionKeys::in , in
• replonly_residues() : basic::options::OptionKeys::in , in
• request_data_from_head_node() : basic::message_listening
• require_frags_match_blueprint() : remodel::staged_sampling
• required_active_site_atom_names() : basic::options::OptionKeys::match , match
• 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
• rerun() : abinitio , basic::options::OptionKeys::abinitio
• rerun_motifsearch() : basic::options::OptionKeys::motifs , motifs
• res_design_bs() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• resample() : resample
• resclass_by_sasa() : remodel
• rescore() : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::hotspot , basic::options::OptionKeys::in::file , basic::options::OptionKeys::optE::rescore , docking::ligand , hotspot , in::file , optE::rescore , rescore
• rescore_only() : stepwise::protein
• reservoir_sample() : numeric::random
• reservoir_sample_accept_prob() : numeric::random
• resfile() : packing
• resi() : basic::options::OptionKeys::cmiles::jumping , cmiles::jumping
• residue() : basic::options::OptionKeys::hotspot , hotspot
• residue_pair_jump_file() : basic::options::OptionKeys::jumps , jumps
• residue_scores() : basic::options::OptionKeys::holes , holes , packstat
• residue_trim_file() : basic::options::OptionKeys::motifs , motifs
• residue_type_set() : basic::options::OptionKeys::in::file , in::file , out::file
• residues() : residues , willmatch
• residues_backbone_move() : rigid
• residues_repack_only() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• residues_to_sample() : remodel::staged_sampling
• resj() : basic::options::OptionKeys::cmiles::jumping , cmiles::jumping
• resolution_cutoffs() : patterson
• resolve_db_partition() : basic::database
• resource_definition_files() : basic::options::OptionKeys::jd2 , jd2
• respect_resfile() : relax
• restore_pre_talaris_2013_behavior() : basic::options::OptionKeys::mistakes , mistakes
• restrict_design_to_interface() : smhybrid
• restrict_design_to_subsub_interface() : smhybrid
• restrict_kic_sampling_to_torsion_string() : basic::options::OptionKeys::loops , loops
• restrict_to_canonical() : basic::options::OptionKeys::ms , ms
• restrict_to_wt() : basic::options::OptionKeys::motifs , motifs
• restype() : basic::options::OptionKeys::mh::filter , mh::filter
• restype_one() : basic::options::OptionKeys::mh::filter , mh::filter
• resume_batch() : out
• retry_failed_reads() : basic::options::OptionKeys::inout::dbms , inout::dbms
• return_full_atom() : abinitio , basic::options::OptionKeys::abinitio
• revamp_near_chain() : pb_potential
• reversion() : basic::options::OptionKeys::dna::design::reversion , dna::design::reversion
• reversion_scan() : basic::options::OptionKeys::dna::design , dna::design
• revert_real_loops() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• revert_scan() : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• reweight_symm_interactions() : symmetry
• rg() : remodel
• rg_local() : remodel
• rg_local_span() : score
• rg_reweight() : abinitio , basic::options::OptionKeys::abinitio
• rgb_to_hsv() : numeric
• rgg() : numeric::linear_algebra
• right() : ufv
• right_tail() : basic::options::OptionKeys::krassk , krassk
• 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
• rm_virt_phosphate() : stepwise::rna
• 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 , 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 , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::evaluation , evaluation , patterson
• rmsd_analysis() : pepspec
• rmsd_column() : basic::options::OptionKeys::evaluation , evaluation
• RMSD_only_this() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• rmsd_res() : stepwise::rna
• rmsd_residues() : abinitio , basic::options::OptionKeys::abinitio
• rmsd_screen() : stepwise::protein
• rmsd_select() : basic::options::OptionKeys::evaluation , evaluation
• rmsd_target() : basic::options::OptionKeys::evaluation , evaluation
• rmsd_tol() : basic::options::OptionKeys::loops , loops , rot_anl
• rmsfitca2() : numeric::model_quality
• rmsfitca3() : numeric::model_quality
• rna() : rna , stepwise::rna
• rna_chemical_shift_exp_data() : score
• rna_chemical_shift_H5_prime_mode() : score
• rna_chemical_shift_include_res() : score
• rna_prot_erraser() : rna
• rna_torsion_potential() : score
• rna_torsion_skip_chainbreak() : score
• rng() : run
• rng_seed_device() : run
• robert() : robert
• root_res() : basic::options::OptionKeys::full_model , full_model
• rosetta_svn_url() : devel
• rosetta_svn_version() : devel
• rot_anl() : rot_anl
• rot_cst_enrg_cutoff() : basic::options::OptionKeys::ddg , ddg
• rot_mag_smooth() : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• rot_magnitude() : basic::options::OptionKeys::enzdes , enzdes
• rotamer_prot_stats() : pH::calc_pka
• rotamerdump() : rotamerdump
• rotate_anchor_to_x() : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• 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() : rigid
• rotation_angle() : numeric
• rotation_axis() : numeric
• rotation_axis_angle() : numeric
• rotation_matrix() : numeric
• rotation_matrix_degrees() : numeric
• rotation_matrix_radians() : numeric
• rotlevel() : basic::options::OptionKeys::motifs , motifs
• rots() : basic::options::OptionKeys::casp , casp
• rots2add() : basic::options::OptionKeys::motifs , motifs
• rotsub_movebb_substitutions_scale() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• rounds() : basic::options::OptionKeys::lh , lh
• row_format() : basic::options::OptionKeys::contactMap , contactMap
• rpf() : basic::options::OptionKeys::evaluation , evaluation
• 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() : remodel
• rsym_eigenval() : numeric::model_quality
• rsym_evector() : numeric::model_quality
• rsym_rotation() : numeric::model_quality
• rt_min() : antibody , basic::options::OptionKeys::antibody
• rtmin() : rot_anl
• run() : run
• run_centroid() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_centroid_abinitio() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_confirmation() : remodel
• run_flxbb() : basic::options::OptionKeys::fldsgn , fldsgn
• run_fullatom() : basic::options::OptionKeys::DomainAssembly , DomainAssembly
• run_level() : run
• run_ligand_motifs() : basic::options::OptionKeys::enzdes , enzdes
• run_motifs() : basic::options::OptionKeys::motifs , motifs
• run_sequential() : pepspec
• run_test() : basic::options::OptionKeys::dna::specificity , dna::specificity