- o -

• o : basic::options::OptionKeys::out::file
• o2prime_legacy_mode : basic::options::OptionKeys::stepwise::rna
• obey_ENDMDL : basic::options::OptionKeys::in::file
• objective_cut_increment : basic::options::OptionKeys::lh
• objective_dominate_cut : basic::options::OptionKeys::lh
• objective_function : basic::options::OptionKeys::lh
• obligate_pair : basic::options::OptionKeys::rna::farna
• obligate_pair_explicit : basic::options::OptionKeys::rna::farna
• observer : test::T150_PyMOL_Integration
• occupancy : basic::options::OptionKeys::mh::filter
• ocd_cutoff : basic::options::OptionKeys::antibody
• off_rotamer_pack : basic::options::OptionKeys
• offset : basic::options::OptionKeys::rna::farna
• offset_bump_dsq : basic::options::OptionKeys::sewing
• ofs : assign_charges
• ok : clean_pdb_keep_ligand
• old_estat : basic::options::OptionKeys::docking::ligand
• old_phi : test::T850_SubClassing
• old_sym_min : basic::options::OptionKeys::optimization
• oldresnum : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• omega : basic::options::OptionKeys::AnchoredDesign::filters
• omega_start_val : mrlo
• one : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• one_body : basic::options::OptionKeys::rotamerdump
• one_letter_names : amino_acids
• oneloop : basic::options::OptionKeys::mh::filter
• only_enumerate_non_match_redundant_ligand_rotamers : basic::options::OptionKeys::match
• only_repack : basic::options::OptionKeys::dna::specificity
• only_stage1 : basic::options::OptionKeys::abinitio
• oop_design_positions : oop_design
• operate : basic::options::OptionKeys::packing::ex1 , basic::options::OptionKeys::packing::ex2 , basic::options::OptionKeys::packing::ex3 , basic::options::OptionKeys::packing::ex4
• opt_input_structure : basic::options::OptionKeys::ddg
• opt_radius : basic::options::OptionKeys::casp , basic::options::OptionKeys::ddg
• optE : basic::options::OptionKeys::optE
• optE_no_protein_fa_elec : basic::options::OptionKeys::optE
• optE_soft_rep : basic::options::OptionKeys::optE
• optH_MCA : basic::options::OptionKeys::packing
• optH_patch : basic::options::OptionKeys::score
• optH_weights : basic::options::OptionKeys::score
• optimization : basic::options::OptionKeys::optimization
• optimize1 : basic::options::OptionKeys::mp::setup
• optimize2 : basic::options::OptionKeys::mp::setup
• optimize_cutpoints_margin : basic::options::OptionKeys::abinitio
• optimize_cutpoints_using_kic : basic::options::OptionKeys::abinitio
• optimize_cyclic_threshold : basic::options::OptionKeys::peptide_deriver
• optimize_ddG_bind_correlation : basic::options::OptionKeys::optE
• optimize_ddGmutation : basic::options::OptionKeys::optE
• optimize_ddGmutation_boltzman_average : basic::options::OptionKeys::optE
• optimize_ddGmutation_straight_mean : basic::options::OptionKeys::optE
• optimize_decoy_discrimination : basic::options::OptionKeys::optE
• optimize_dGbinding : basic::options::OptionKeys::optE
• optimize_embedding : basic::options::OptionKeys::mp::transform
• optimize_ligand_discrimination : basic::options::OptionKeys::optE
• optimize_ligand_rot : basic::options::OptionKeys::optE
• optimize_loops : basic::options::OptionKeys::DenovoProteinDesign
• optimize_nat_aa : basic::options::OptionKeys::optE
• optimize_nat_rot : basic::options::OptionKeys::optE
• optimize_only_kic_region_sidechains_after_move : basic::options::OptionKeys::loops
• optimize_pssm : basic::options::OptionKeys::optE
• optimize_starting_free_weights : basic::options::OptionKeys::optE
• option : basic::options
• option_file : basic::options::OptionKeys::docking::ligand
• Options : options
• options : setup_pyrosetta , toolbox::adjust_library_path , utility::options::OptionKeys::options
• options_file : basic::options::OptionKeys::make_rot_lib
• opts : app::surface_docking::surface_docking
• orbitals : basic::options::OptionKeys::orbitals
• orientation_atoms : basic::options::OptionKeys::match
• origin_res_num : basic::options::OptionKeys::fingerprint
• ot : test::T850_SubClassing
• other_pose_scorefile : basic::options::OptionKeys::run
• other_pose_to_scorefile : basic::options::OptionKeys::run
• other_poses : basic::options::OptionKeys::full_model
• out : basic::options::OptionKeys::canonical_sampling::out , basic::options::OptionKeys::ddg , basic::options::OptionKeys::out
• out_path : basic::options::OptionKeys::lh::fragpdb
• out_pdb_prefix : basic::options::OptionKeys::ddg
• outDIR : app::pyrosetta_toolkit::modules::SQLPDB
• outdir : setup_pyrosetta , test::G203_Module_SQLPDB
• outer_cycle_rounds : basic::options::OptionKeys::antibody::design
• outer_cycles : loops , loops_kic , test::T650_LoopsKIC
• outer_cycles_high : demo::D080_Loop_modeling
• outer_cycles_low : demo::D080_Loop_modeling
• outer_iteration_scale : basic::options::OptionKeys::flexpack::annealer
• outer_kt : basic::options::OptionKeys::antibody::design
• outeriterations_scaling : basic::options::OptionKeys::packing
• outfile : clean_pdb_keep_ligand , make_static_database , pyrosetta::toolbox::make_rna_rosetta_ready
• OUTFILE : setup_pyrosetta
• outfile : toolbox::make_rna_rosetta_ready
• outfile_path : setup_pyrosetta
• outid : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• outlog : basic::options::OptionKeys::optE::rescore
• output : basic::options::OptionKeys::cp , basic::options::OptionKeys::mp::benchmark::tilt_angle , basic::options::OptionKeys::mp::output , basic::options::OptionKeys::out , contacts , demo::D090_Ala_scan , make_static_database , test::Workshop7test , test::Workshop8test
• output_all : basic::options::OptionKeys::frags::contacts
• output_centroid : basic::options::OptionKeys::fold_from_loops
• output_clean_pdb : loadPDB
• output_cluster_size : basic::options::OptionKeys::stepwise
• output_dir : basic::options::OptionKeys::ddg
• output_etables : basic::options::OptionKeys::score
• output_extra_RMSDs : basic::options::OptionKeys::stepwise::rna
• output_feature_vector : basic::options::OptionKeys::ProQ
• output_fiber_spectra : basic::options::OptionKeys::score::fiber_diffraction
• output_file : basic::options::OptionKeys::motifs
• output_filters : basic::options::OptionKeys::rna::farna
• output_format : basic::options::OptionKeys::match
• output_frags_pdbs : basic::options::OptionKeys::frags::nonlocal
• output_hbond_info : basic::options::OptionKeys::run
• output_idealized : basic::options::OptionKeys::frags::nonlocal
• output_index : basic::options::OptionKeys::frags
• output_local_prediction : basic::options::OptionKeys::ProQ
• output_lores_silent_file : basic::options::OptionKeys::rna::farna
• output_matches_per_group : basic::options::OptionKeys::match
• output_matchres_only : basic::options::OptionKeys::match
• output_minimized_pose_list : basic::options::OptionKeys::stepwise
• output_mutant_structures : protocols::pmut_scan
• output_only_cluster_transitions : basic::options::OptionKeys::canonical_sampling::sampling
• output_orbitals : basic::options::OptionKeys::out::file
• output_pdb : basic::options::OptionKeys::loops
• output_per_glycan_data : basic::options::OptionKeys::carbohydrates::clash_check
• output_raw_scores : basic::options::OptionKeys::pH
• output_res_num : basic::options::OptionKeys::rna::farna
• output_residue_energies : basic::options::OptionKeys::score
• output_score_filter : basic::options::OptionKeys::cluster
• output_silent : basic::options::OptionKeys::ddg , basic::options::OptionKeys::frags::nonlocal , basic::options::OptionKeys::frags
• output_structures : basic::options::OptionKeys::dna::design::specificity
• output_tag : basic::options::OptionKeys::out
• output_top_n_new_decoys : basic::options::OptionKeys::optE
• output_torsions : basic::options::OptionKeys::out::file
• output_unbound_pdb : basic::options::OptionKeys::dna::design
• output_virtual : basic::options::OptionKeys::out::file
• output_virtual_zero_occ : basic::options::OptionKeys::out::file
• overlap_chainbreak : basic::options::OptionKeys::jumps
• overlap_chainbreak_weight : basic::options::OptionKeys::relax
• override_rot_lib_path : basic::options::OptionKeys::in::file
• override_rsd_type_limit : basic::options::OptionKeys::chemical
• override_vdw_all_stages : basic::options::OptionKeys::abinitio
• oversample : basic::options::OptionKeys::packstat
• overwrite : basic::options::OptionKeys::out
• overwrite_filter_scorefxn : basic::options::OptionKeys::fast_loops
• OZSTREAM_DEFAULT_BUFFER_SIZE : utility::io