- u -

• U : docking
• u : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_common
• UBQ2_lys : basic::options::OptionKeys::chemically_conjugated_docking
• UBQ2_pdb : basic::options::OptionKeys::chemically_conjugated_docking
• ubq_cst_sd : basic::options::OptionKeys
• UBQ_tail_chain : basic::options::OptionKeys
• UBQ_tail_start_resnum : basic::options::OptionKeys
• UBQpdb : basic::options::OptionKeys::chemically_conjugated_docking
• ufv : basic::options::OptionKeys::ufv
• ufv_loops : basic::options::OptionKeys::ufv
• uint64_p : utility::json_spirit
• ulr_mulfactor : basic::options::OptionKeys::lh
• unbound_mode : basic::options::OptionKeys::AnchoredDesign
• unboundrot : basic::options::OptionKeys::packing
• unfolded_energies_file : basic::options::OptionKeys::unfolded_state
• unfolded_state : basic::options::OptionKeys::unfolded_state
• uniform_backrub : basic::options::OptionKeys::coupled_moves
• uniform_trans : basic::options::OptionKeys::docking
• uniformfrag : basic::options::OptionKeys::mh::filter
• unmask_bb : basic::options::OptionKeys::edensity
• unmodifypot : basic::options::OptionKeys::score
• unmute : basic::options::OptionKeys::out
• unset_acceptor_ether_oxygens : basic::options::OptionKeys::chemical
• update_pymol_on_conformation_changes_only : basic::options::OptionKeys::run
• update_pymol_on_energy_changes_only : basic::options::OptionKeys::run
• updown_collision_tolerance : basic::options::OptionKeys::match
• updown_residue_collision_score_cutoff : basic::options::OptionKeys::match
• updown_residue_collision_Wfa_atr : basic::options::OptionKeys::match
• updown_residue_collision_Wfa_rep : basic::options::OptionKeys::match
• updown_residue_collision_Wfa_sol : basic::options::OptionKeys::match
• upper : test_terpenes
• upper_chains : basic::options::OptionKeys::msd
• upstream_residue_collision_score_cutoff : basic::options::OptionKeys::match
• upstream_residue_collision_tolerance : basic::options::OptionKeys::match
• upstream_residue_collision_Wfa_atr : basic::options::OptionKeys::match
• upstream_residue_collision_Wfa_rep : basic::options::OptionKeys::match
• upstream_residue_collision_Wfa_sol : basic::options::OptionKeys::match
• upweight_interface : basic::options::OptionKeys::pepspec
• url : cache_trajectory
• URL : helpers
• urllib_urlretrieve : pyrosetta.toolbox.rcsb
• urls : job_manager
• use_1jj2_torsions : basic::options::OptionKeys::rna::denovo
• use_2prime_OH_potential : basic::options::OptionKeys::score::rna
• use_6D_potential : basic::options::OptionKeys::score::loop_close
• use_aa1 : basic::options::OptionKeys::mh::score
• use_aa2 : basic::options::OptionKeys::mh::score
• use_alpha_germline_templates : basic::options::OptionKeys::tcrmodel
• use_ambig_constraints : basic::options::OptionKeys::docking::ligand
• use_beta_germline_templates : basic::options::OptionKeys::tcrmodel
• use_bicubic_interpolation : basic::options::OptionKeys::corrections::score
• use_blueprint_sequence : basic::options::OptionKeys::remodel
• use_cart_relax : basic::options::OptionKeys::remodel
• use_CB : basic::options::OptionKeys::cluster::energy_based_clustering
• use_cen_score : basic::options::OptionKeys::flexPepDocking
• use_chainbreak_energy : basic::options::OptionKeys::cyclic_peptide
• use_classic_rama_for_sampling : basic::options::OptionKeys::cyclic_peptide
• use_clusters : basic::options::OptionKeys::remodel
• use_compact_residue_schema : basic::options::OptionKeys::inout::dbms
• use_cubic_interp : basic::options::OptionKeys::score::loop_close
• use_DARC_gpu : basic::options::OptionKeys::fingerprint
• use_database : basic::options::OptionKeys::in , basic::options::OptionKeys::out
• use_distance_constraints : basic::options::OptionKeys::trRosetta
• use_electrostatic_repulsion : basic::options::OptionKeys::packing
• use_ellipsoidal_randomization : basic::options::OptionKeys::docking
• use_empty_space_in_space_fill_pdb : basic::options::OptionKeys::motifs
• use_epitope_constraints : basic::options::OptionKeys::antibody::design
• use_explicit_water : basic::options::OptionKeys::relax
• use_filters : basic::options::OptionKeys::abinitio
• use_first_jump_for_submotif : basic::options::OptionKeys::stepwise::monte_carlo
• use_fraglib : basic::options::OptionKeys::loodo
• use_fraglibsc : basic::options::OptionKeys::loodo
• use_fullmer : basic::options::OptionKeys::ufv
• use_gaussian_sampling : basic::options::OptionKeys::carbohydrates::glycan_sampler
• use_gen_kirkwood : basic::options::OptionKeys::score
• use_general_protocol : basic::options::OptionKeys::loopfcst
• use_green_packer : basic::options::OptionKeys::stepwise
• use_gzip : basic::options::OptionKeys::ProQ
• use_H3_graft_outliers : basic::options::OptionKeys::antibody::design
• use_hb_env_dep : basic::options::OptionKeys::score
• use_hierarchical_clustering : basic::options::OptionKeys::canonical_sampling::probabilities
• use_input_bb : basic::options::OptionKeys::pepspec
• use_input_sc : basic::options::OptionKeys::packing
• use_legacy_protocol : basic::options::OptionKeys::docking
• use_legacy_setup : basic::options::OptionKeys::rna::denovo
• use_log : basic::options::OptionKeys::mh::score
• use_loop_hash : basic::options::OptionKeys::remodel::RemodelLoopMover
• use_loophash_filter : basic::options::OptionKeys::abinitio
• use_mean_cluster_cst_data : basic::options::OptionKeys::antibody
• use_name_as_custom_type : basic::options::OptionKeys::simple_metrics
• use_name_as_metric : basic::options::OptionKeys::simple_metrics
• use_occurrence_data : basic::options::OptionKeys::out::file
• use_octahedral_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_omega_constraints : basic::options::OptionKeys::trRosetta
• use_on_repack : basic::options::OptionKeys::patterson
• use_only_H3_kinked : basic::options::OptionKeys::antibody::design
• use_outliers : basic::options::OptionKeys::antibody::design
• use_packer_instead_of_rotamer_trials : basic::options::OptionKeys::stepwise::protein
• use_paraBBMB_filters : basic::options::OptionKeys::cyclic_peptide
• use_pdb_format_HETNAM_records : basic::options::OptionKeys::out::file
• use_pdb_numbering : local
• use_phi_constraints : basic::options::OptionKeys::trRosetta
• use_polarization : basic::options::OptionKeys::score
• use_pose_relax : basic::options::OptionKeys::remodel
• use_precomputed_library : basic::options::OptionKeys::stepwise::monte_carlo
• use_pybind_stl : make_bindings_via_cmake
• use_rama_filter : basic::options::OptionKeys::cyclic_peptide
• use_reweighted_score12_score_function : surface_app
• use_reweighted_score12_with_surfaceE_scorefunction : surface_app
• use_rna_chi_potential : basic::options::OptionKeys::score::rna
• use_rotamer_constraints_to_native : basic::options::OptionKeys::ddg
• use_same_length_fragments : basic::options::OptionKeys::remodel
• use_soft_rep : a3b_hddm , oddm , tddm
• use_spline_interpolation : basic::options::OptionKeys::patterson
• use_square_planar_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_square_pyramidal_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_ss1 : basic::options::OptionKeys::mh::score
• use_ss2 : basic::options::OptionKeys::mh::score
• use_symmetry_calc : basic::options::OptionKeys::nmr::pcs , basic::options::OptionKeys::nmr::pre , basic::options::OptionKeys::nmr::rdc
• use_TBMB_filters : basic::options::OptionKeys::cyclic_peptide
• use_template_sequence : basic::options::OptionKeys::DenovoProteinDesign
• use_template_topology : basic::options::OptionKeys::DenovoProteinDesign
• use_terminal_residues : basic::options::OptionKeys::make_rot_lib
• use_tetrahedral_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_theta_constraints : basic::options::OptionKeys::trRosetta
• use_time_as_seed : basic::options::OptionKeys::run
• use_TMA_filters : basic::options::OptionKeys::cyclic_peptide
• use_trigonal_planar_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_trigonal_pyramidal_metal_filters : basic::options::OptionKeys::cyclic_peptide
• use_trRosetta_constraints : basic::options::OptionKeys::abinitio
• use_truncated_termini : basic::options::OptionKeys::in
• use_unrelaxed_starting_points : basic::options::OptionKeys::cp
• use_user_templates : basic::options::OptionKeys::tcrmodel
• use_whole_matrix_in_space_fill_pdb : basic::options::OptionKeys::motifs
• user : basic::options::OptionKeys::inout::dbms , utility::options::OptionKeys::options
• user_set_alpha_dihedral_perturbation : basic::options::OptionKeys::cyclic_peptide
• user_set_alpha_dihedrals : basic::options::OptionKeys::cyclic_peptide
• USER_SITE : ez_setup
• user_tag : basic::options::OptionKeys::out
• user_tags : basic::options::OptionKeys::in::file
• useZ : basic::options::OptionKeys::csa , basic::options::OptionKeys::dc