- u -

• UBQ2_lys() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• UBQ2_pdb() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• UBQpdb() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• ufv() : ufv
• ufv_loops() : ufv
• unbound_mode() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• unboundrot() : packing
• unicode_str_to_char() : utility::json_spirit
• unified_framework() : stepwise::rna
• uniform() : numeric::random
• uniform_trans() : basic::options::OptionKeys::docking , docking
• unmask_bb() : basic::options::OptionKeys::edensity , edensity
• unmodifypot() : score
• unmute() : out
• unsigned_periodic_range() : basic
• updown_collision_tolerance() : basic::options::OptionKeys::match , match
• updown_residue_collision_score_cutoff() : basic::options::OptionKeys::match , match
• updown_residue_collision_Wfa_atr() : basic::options::OptionKeys::match , match
• updown_residue_collision_Wfa_rep() : basic::options::OptionKeys::match , match
• updown_residue_collision_Wfa_sol() : basic::options::OptionKeys::match , match
• upstream_residue_collision_score_cutoff() : basic::options::OptionKeys::match , match
• upstream_residue_collision_tolerance() : basic::options::OptionKeys::match , match
• upstream_residue_collision_Wfa_atr() : basic::options::OptionKeys::match , match
• upstream_residue_collision_Wfa_rep() : basic::options::OptionKeys::match , match
• upstream_residue_collision_Wfa_sol() : basic::options::OptionKeys::match , match
• upweight_interface() : pepspec
• use_2prime_OH_potential() : score
• use_ambig_constraints() : basic::options::OptionKeys::docking::ligand , docking::ligand
• use_bicubic_interpolation() : basic::options::OptionKeys::corrections::score , corrections::score
• use_blueprint_sequence() : remodel
• use_bound_cst() : basic::options::OptionKeys::ddg , ddg
• use_cart_relax() : remodel
• use_ccd_refine() : remodel
• use_cen_score() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• use_clusters() : remodel
• use_compact_residue_schema() : basic::options::OptionKeys::inout::dbms , inout::dbms
• use_DARC_gpu() : basic::options::OptionKeys::fingerprint , fingerprint
• use_database() : basic::options::OptionKeys::in , in , out
• use_deterministic() : antibody::design , basic::options::OptionKeys::antibody::design
• use_dssp_assignment() : remodel
• use_electrostatic_repulsion() : packing
• use_ellipsoidal_randomization() : basic::options::OptionKeys::docking , docking
• use_filters() : abinitio , antibody::design , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::antibody::design
• use_fullmer() : ufv
• use_general_protocol() : basic::options::OptionKeys::loopfcst , loopfcst
• use_green_packer() : stepwise
• use_gzip() : ProQ
• use_hierarchical_clustering() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• use_incorrect_hbond_deriv() : basic::options::OptionKeys::corrections::score , corrections::score
• use_input_bb() : pepspec
• use_input_sc() : packing
• use_legacy_protocol() : basic::options::OptionKeys::docking , docking
• use_loop_hash() : remodel::RemodelLoopMover
• use_occurrence_data() : out::file
• use_on_repack() : patterson
• use_packer_instead_of_rotamer_trials() : stepwise::protein
• use_pose_relax() : remodel
• use_rotamer_constraints_to_native() : basic::options::OptionKeys::ddg , ddg
• use_same_length_fragments() : remodel
• use_spline_interpolation() : patterson
• use_template_sequence() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• use_template_topology() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• use_time_as_seed() : run
• use_truncated_termini() : basic::options::OptionKeys::in , in
• use_unrelaxed_starting_points() : basic::options::OptionKeys::cp , cp
• usecache() : willmatch
• user() : basic::options::OptionKeys::inout::dbms , inout::dbms
• user_tag() : out
• user_tags() : basic::options::OptionKeys::in::file , in::file
• useZ() : basic::options::OptionKeys::csa , basic::options::OptionKeys::dc , csa , dc