- o -

• o() : out::file
• o2prime_legacy_mode() : stepwise::rna
• Oaro_amp_scaling() : score::occ_sol_fitted
• obey_ENDMDL() : in::file
• obj_to_map() : utility::json_spirit
• objective_cut_increment() : lh
• objective_dominate_cut() : lh
• objective_function() : lh
• obligate_pair() : rna::denovo
• obligate_pair_explicit() : rna::denovo
• OC3_amp_scaling() : score::occ_sol_fitted
• OCbb_amp_scaling() : score::occ_sol_fitted
• occ_sol_fitted() : score::occ_sol_fitted
• occupancy() : mh::filter
• ocd_cutoff() : antibody
• oct() : fmt
• octahedral_metal_constraints_energy_filter_multiplier() : cyclic_peptide
• octahedral_metal_positions() : cyclic_peptide
• octahedral_metal_sidechain_distance_filter_multiplier() : cyclic_peptide
• Oet2_amp_scaling() : score::occ_sol_fitted
• Oet3_amp_scaling() : score::occ_sol_fitted
• offset() : rna::denovo
• offset_bump_dsq() : legacy_sewing
• OH_amp_scaling() : score::occ_sol_fitted
• OHha_amp_scaling() : score::occ_sol_fitted
• Oice_amp_scaling() : score::occ_sol_fitted
• old_estat() : docking::ligand
• old_sym_min() : optimization
• omega() : AnchoredDesign::filters
• one_body() : rotamerdump
• oneloop() : mh::filter
• ONH2_amp_scaling() : score::occ_sol_fitted
• only_enumerate_non_match_redundant_ligand_rotamers() : match
• only_remove_non_buried_waters() : hydrate
• only_repack() : dna::specificity
• only_stage1() : abinitio
• OOC_amp_scaling() : score::occ_sol_fitted
• open() : basic::database
• open_compressed() : pyrosetta::io::silent_file_map
• operate() : packing::ex1 , packing::ex2 , packing::ex3 , packing::ex4
• operator!=() : numeric , ObjexxFCL , utility::file , utility::keys , utility
• operator&() : ObjexxFCL
• operator*() : numeric::kinematic_closure , numeric , ObjexxFCL
• operator*=() : numeric
• operator+() : numeric::kinematic_closure , numeric , ObjexxFCL , utility , utility::options , utility::tag
• operator+=() : numeric
• operator-() : numeric::kinematic_closure , numeric , ObjexxFCL , utility
• operator-=() : numeric
• operator/() : numeric::kinematic_closure , numeric , ObjexxFCL
• operator/=() : numeric
• operator<() : numeric , ObjexxFCL , utility::file , utility::keys , utility , utility::options
• operator<<() : basic::resource_manager , basic::sampling::orientations , binder , numeric::geometry::hashing , numeric::kdtree , numeric::kinematic_closure , numeric , ObjexxFCL , rosetta_binders::has_insertion_operator_implementation , utility::CSI , utility::excn , utility::file , utility , utility::options , utility::py , utility::tag , utility::type_traits::has_insertion_operator_implementation
• operator<=() : numeric , ObjexxFCL , utility::file , utility::keys , utility
• operator==() : numeric , ObjexxFCL , utility::file , utility::json_spirit , utility::keys , utility
• operator>() : numeric , ObjexxFCL , utility::file , utility::keys , utility
• operator>=() : numeric , ObjexxFCL , utility::file , utility::keys , utility
• operator>>() : numeric , ObjexxFCL::format , ObjexxFCL , utility::file
• operator^() : numeric , ObjexxFCL
• operator|() : ObjexxFCL , utility
• OPha_amp_scaling() : score::occ_sol_fitted
• opt_input_structure() : ddg
• opt_radius() : casp , ddg
• optE() : optE
• optE_no_protein_fa_elec() : optE
• optE_soft_rep() : optE
• optH_MCA() : packing
• optH_patch() : score
• optH_weights() : score
• optimization() : optimization
• optimize1() : mp::setup
• optimize2() : mp::setup
• optimize_cutpoints_margin() : abinitio
• optimize_cutpoints_using_kic() : abinitio
• optimize_cyclic_threshold() : peptide_deriver
• optimize_ddG_bind_correlation() : optE
• optimize_ddGmutation() : optE
• optimize_ddGmutation_boltzman_average() : optE
• optimize_ddGmutation_straight_mean() : optE
• optimize_decoy_discrimination() : optE
• optimize_dGbinding() : optE
• optimize_embedding() : mp::transform
• optimize_ligand_discrimination() : optE
• optimize_ligand_rot() : optE
• optimize_loops() : DenovoProteinDesign
• optimize_nat_aa() : optE
• optimize_nat_rot() : optE
• optimize_only_kic_region_sidechains_after_move() : loops
• optimize_para_ion_position() : nmr::pre
• optimize_proline() : ddg
• optimize_pssm() : optE
• optimize_starting_free_weights() : optE
• optimize_tensor() : nmr::pcs
• option_file() : docking::ligand
• Option_Group() : options_class
• option_map_contains_key() : basic::resource_manager
• optional_name_attribute() : utility::tag
• optional_positive_intafteroption() : basic::options
• options_file() : make_rot_lib
• orbitals() : orbitals
• ordered_pt_wat_penalty() : corrections::water
• ordered_wat_penalty() : corrections::water
• orientation_atoms() : match
• origin_res_num() : fingerprint
• OSi_amp_scaling() : score::occ_sol_fitted
• other_pose_scorefile() : run
• other_pose_to_scorefile() : run
• other_poses() : full_model
• out() : canonical_sampling::out , ddg , out , rna::denovo::out
• out_path() : lh::fragpdb
• out_pdb_prefix() : ddg
• out_prefix() : recces
• out_torsions() : recces
• outer_cycle_rounds() : antibody::design
• outer_iteration_scale() : flexpack::annealer
• outer_kt() : antibody::design
• outer_product() : numeric
• outeriterations_scaling() : packing
• outlier_rebuild_if_necessary() : erraser_wrapper
• outlog() : optE::rescore
• output() : cp , mp::benchmark::tilt_angle , mp::output , out
• output_ab_scheme() : antibody
• output_alignments_to_file() : legacy_sewing
• output_all() : frags::contacts
• output_all_tag_options() : utility::xsd_util
• output_alternate_atomids() : inout
• output_centroid() : fold_from_loops
• output_cluster_size() : stepwise
• output_dir() : ddg
• output_etables() : score
• output_exp_calc() : nmr::score
• output_extra_RMSDs() : stepwise::rna
• output_fasta() : coupled_moves
• output_feature_vector() : ProQ
• output_fiber_spectra() : score::fiber_diffraction
• output_file() : motifs
• output_filename() : make_mainchain_potential
• output_filters() : rna::denovo
• output_format() : match
• output_frags_pdbs() : frags::nonlocal
• output_hbond_info() : run
• output_histogram_file() : rna::denovo::out
• output_idealized() : frags::nonlocal
• output_index() : frags
• output_jump_chainbreak() : rna::denovo::out
• output_jump_o3p_to_o5p() : rna::denovo::out
• output_jump_reference_RT() : rna::denovo::out
• output_jump_res() : rna::denovo::out
• output_ligands_as_separate_chains() : out::file
• output_local_prediction() : ProQ
• output_logging() : make_rot_lib
• output_lores_silent_file() : rna::denovo::out
• output_matches_per_group() : match
• output_matchres_only() : match
• output_min_pose() : recces
• output_minimized_pose_list() : stepwise
• output_only_asymmetric_unit() : out::file
• output_only_cluster_transitions() : canonical_sampling::sampling
• output_orbitals() : out::file
• output_pdb() : loops
• output_per_glycan_data() : carbohydrates::clash_check
• output_pose_cache_data() : out::file
• output_pose_energies_table() : out::file
• output_pose_fold_tree() : out::file
• output_prefix() : coupled_moves
• output_raw_scores() : pH
• output_res_num() : rna::denovo
• output_residue_energies() : score
• output_rotation_vector() : rna::denovo::out
• output_schema() : parser
• output_score_file() : rna::denovo::out
• output_score_filter() : cluster
• output_score_frequency() : rna::denovo::out
• output_scorefile() : pyrosetta::toolbox::py_jobdistributor
• output_secondary_structure() : out::file
• output_silent() : ddg , frags::nonlocal , frags
• output_stats() : coupled_moves
• output_structures() : dna::design::specificity
• output_tag() : out
• output_tensor_info() : nmr::score
• output_top_n_new_decoys() : optE
• output_torsions() : out::file
• output_unbound_pdb() : dna::design
• output_virtual() : out::file
• output_virtual_zero_occ() : out::file
• overlap_chainbreak() : jumps
• overlap_chainbreak_weight() : relax
• overlay() : ObjexxFCL
• override_refine_pose_rounds() : rna::denovo
• override_rot_lib_path() : in::file
• override_rsd_type_limit() : chemical
• override_vdw_all_stages() : abinitio
• oversample() : packstat
• overwrite() : out
• overwrite_filter_scorefxn() : fast_loops