- r -

r1 : basic::options::OptionKeys::motifs
r2 : basic::options::OptionKeys::motifs
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::ddg
radius_cutoffs : basic::options::OptionKeys::patterson
rama : basic::options::OptionKeys::remodel
rama2b_map : basic::options::OptionKeys::in::file
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
rama_score_nonstandard_connections : basic::options::OptionKeys::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_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
randomize2 : basic::options::OptionKeys::docking
randomize_equivalent_fragments : basic::options::OptionKeys::remodel
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
rank_by_bsasa : basic::options::OptionKeys::remodel
raw : basic::options::OptionKeys::out::file
raw_stats : basic::options::OptionKeys::packstat
rb_file : basic::options::OptionKeys::ddg , basic::options::OptionKeys::RBSegmentRelax , basic::options::OptionKeys::SSrbrelax
rb_mag : basic::options::OptionKeys::smhybrid
rb_min_post_graft : basic::options::OptionKeys::antibody::design
rb_param_file : basic::options::OptionKeys::SSrbrelax
rb_restrict_to_mutsite_nbrs : basic::options::OptionKeys::ddg
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_select : basic::options::OptionKeys::evaluation
rdc_target : basic::options::OptionKeys::evaluation
rdc_weight : basic::options::OptionKeys::nonlocal
rdf : basic::options::OptionKeys::in::rdf
read_fragfile : basic::options::OptionKeys::remodel
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
rebuild_bulge_mode : basic::options::OptionKeys::stepwise::rna
rebuild_disulf : basic::options::OptionKeys::run
receptor_chain : basic::options::OptionKeys::flexPepDocking
recover_low_in_stages : basic::options::OptionKeys::abinitio
recover_nat_rot : basic::options::OptionKeys::optE
recover_side_chains : basic::options::OptionKeys::cm
recover_sidechains : basic::options::OptionKeys::docking
redesign_complete : basic::options::OptionKeys::DenovoProteinDesign
redesign_core : basic::options::OptionKeys::DenovoProteinDesign
redesign_loops : basic::options::OptionKeys::DenovoProteinDesign
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_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
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
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_repack_cycles : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
refine_res : basic::options::OptionKeys::casp
refine_temp : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
refstruct : basic::options::OptionKeys::lh
region_def : basic::options::OptionKeys::contactMap
regions : basic::options::OptionKeys::run
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
relax : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax
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_sfxn : basic::options::OptionKeys::cp
relax_with_foldtree : basic::options::OptionKeys::loops
relax_with_jumps : basic::options::OptionKeys::abinitio
RELERROR : numeric::kinematic_closure
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_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
rename : basic::options::OptionKeys::ms::checkpoint
render_sigma : basic::options::OptionKeys::edensity
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_never : basic::options::OptionKeys::loops
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_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
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_design_bs : basic::options::OptionKeys::fold_from_loops
resample : basic::options::OptionKeys::resample
resclass_by_sasa : basic::options::OptionKeys::remodel
rescore : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::hotspot , basic::options::OptionKeys::in::file , basic::options::OptionKeys::optE::rescore , basic::options::OptionKeys::rescore
rescore_only : basic::options::OptionKeys::stepwise::protein
resfile : basic::options::OptionKeys::packing
resi : basic::options::OptionKeys::cmiles::jumping
residue : basic::options::OptionKeys::hotspot
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::residues , basic::options::OptionKeys::willmatch
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
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_to_canonical : basic::options::OptionKeys::ms
restrict_to_wt : basic::options::OptionKeys::motifs
restype : basic::options::OptionKeys::mh::filter
restype_one : basic::options::OptionKeys::mh::filter
resume_batch : basic::options::OptionKeys::out
retry_failed_reads : basic::options::OptionKeys::inout::dbms
return_full_atom : basic::options::OptionKeys::abinitio
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 : basic::options::OptionKeys::cm::hybridize
revert_scan : basic::options::OptionKeys::matdes::mutalyze
reweight_symm_interactions : basic::options::OptionKeys::symmetry
RG : basic::database
rg : basic::options::OptionKeys::remodel
RG : numeric::random
rg_local : basic::options::OptionKeys::remodel
rg_local_span : basic::options::OptionKeys::score
rg_reweight : basic::options::OptionKeys::abinitio
right : basic::options::OptionKeys::ufv
right_tail : basic::options::OptionKeys::krassk
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
rm_virt_phosphate : basic::options::OptionKeys::stepwise::rna
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::protein
rmsd_select : basic::options::OptionKeys::evaluation
rmsd_target : basic::options::OptionKeys::evaluation
rmsd_tol : basic::options::OptionKeys::loops , basic::options::OptionKeys::rot_anl
rna : basic::options::OptionKeys::rna , basic::options::OptionKeys::stepwise::rna
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_prot_erraser : basic::options::OptionKeys::rna
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
root_res : basic::options::OptionKeys::full_model
rot_anl : basic::options::OptionKeys::rot_anl
rot_cst_enrg_cutoff : basic::options::OptionKeys::ddg
rot_mag_smooth : basic::options::OptionKeys::fold_and_dock
rot_magnitude : basic::options::OptionKeys::enzdes
rotamer_prot_stats : basic::options::OptionKeys::pH::calc_pka
rotamerdump : basic::options::OptionKeys::rotamerdump
rotate_anchor_to_x : basic::options::OptionKeys::fold_and_dock
rotation : basic::options::OptionKeys::rigid
rotlevel : basic::options::OptionKeys::motifs
rots : basic::options::OptionKeys::casp
rots2add : basic::options::OptionKeys::motifs
rotsub_movebb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer
rounds : basic::options::OptionKeys::lh
row_format : basic::options::OptionKeys::contactMap
rpf : basic::options::OptionKeys::evaluation
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
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_flxbb : basic::options::OptionKeys::fldsgn
run_fullatom : basic::options::OptionKeys::DomainAssembly
run_level : basic::options::OptionKeys::run
run_ligand_motifs : basic::options::OptionKeys::enzdes
run_motifs : basic::options::OptionKeys::motifs
run_sequential : basic::options::OptionKeys::pepspec
run_test : basic::options::OptionKeys::dna::specificity