- u -

• UBQ2_lys() : chemically_conjugated_docking
• UBQ2_pdb() : chemically_conjugated_docking
• ubq_ras_distance() : apps::public1::scenarios::chemically_conjugated_docking
• ubq_ras_rotation_angle() : apps::public1::scenarios::chemically_conjugated_docking
• UBQpdb() : chemically_conjugated_docking
• ufv() : ufv
• ufv_loops() : ufv
• uint_of() : ObjexxFCL
• ulong_of() : ObjexxFCL
• ulr_mulfactor() : lh
• unbound_mode() : AnchoredDesign
• unboundrot() : packing
• unfolded_energies_file() : unfolded_state
• unfolded_state() : unfolded_state
• unicode_str_to_char() : utility::json_spirit
• uniform() : numeric::random
• uniform_backrub() : coupled_moves
• uniform_trans() : docking
• uniform_vector_sphere() : numeric::random
• uniformfrag() : mh::filter
• unique() : ObjexxFCL
• uniqued() : ObjexxFCL
• unmask_bb() : edensity
• unmodifypot() : score
• unmute() : out
• unset_acceptor_ether_oxygens() : chemical
• unsigned_periodic_range() : basic
• upcase() : ObjexxFCL
• update_5way_operation() : numeric
• update_operation() : numeric
• update_pymol_on_conformation_changes_only() : run
• update_pymol_on_energy_changes_only() : run
• update_source_file() : binder , build
• updown_collision_tolerance() : match
• updown_residue_collision_score_cutoff() : match
• updown_residue_collision_Wfa_atr() : match
• updown_residue_collision_Wfa_rep() : match
• updown_residue_collision_Wfa_sol() : match
• upper() : utility
• uppercase() : ObjexxFCL
• UPPERCASE_ALPHANUMERICS() : utility
• UPPERCASE_LETTERS() : utility
• uppercased() : ObjexxFCL
• upstream_residue_collision_score_cutoff() : match
• upstream_residue_collision_tolerance() : match
• upstream_residue_collision_Wfa_atr() : match
• upstream_residue_collision_Wfa_rep() : match
• upstream_residue_collision_Wfa_sol() : match
• upweight_interface() : pepspec
• urs_norm4() : numeric
• urs_R2ang() : numeric
• use_1jj2_torsions() : rna::denovo
• use_2prime_OH_potential() : score::rna
• use_6D_potential() : score::loop_close
• use_aa1() : mh::score
• use_aa2() : mh::score
• use_alpha_germline_templates() : tcrmodel
• use_ambig_constraints() : docking::ligand
• use_beta_germline_templates() : tcrmodel
• use_bicubic_interpolation() : corrections::score
• use_blueprint_sequence() : remodel
• use_cart_relax() : remodel
• use_CB() : cluster::energy_based_clustering
• use_cen_score() : flexPepDocking
• use_chainbreak_energy() : cyclic_peptide
• use_classic_rama_for_sampling() : cyclic_peptide
• use_clusters() : remodel
• use_compact_residue_schema() : inout::dbms
• use_cubic_interp() : score::loop_close
• use_DARC_gpu() : fingerprint
• use_database() : in , out
• use_electrostatic_repulsion() : packing
• use_ellipsoidal_randomization() : docking
• use_epitope_constraints() : antibody::design
• use_explicit_water() : relax
• use_filters() : abinitio
• use_first_jump_for_submotif() : stepwise::monte_carlo
• use_fraglib() : loodo
• use_fraglibsc() : loodo
• use_fullmer() : ufv
• use_gaussian_sampling() : carbohydrates::glycan_sampler
• use_gen_kirkwood() : score
• use_general_protocol() : loopfcst
• use_green_packer() : stepwise
• use_gzip() : ProQ
• use_H3_graft_outliers() : antibody::design
• use_hb_env_dep() : score
• use_hierarchical_clustering() : canonical_sampling::probabilities
• use_input_bb() : pepspec
• use_input_sc() : packing
• use_legacy_protocol() : docking
• use_legacy_setup() : rna::denovo
• use_log() : mh::score
• use_loop_hash() : remodel::RemodelLoopMover
• use_loophash_filter() : abinitio
• use_mean_cluster_cst_data() : antibody
• use_occurrence_data() : out::file
• use_octahedral_metal_filters() : cyclic_peptide
• use_on_repack() : patterson
• use_only_H3_kinked() : antibody::design
• use_outliers() : antibody::design
• use_packer_instead_of_rotamer_trials() : stepwise::protein
• use_pdb_format_HETNAM_records() : out::file
• use_polarization() : score
• use_pose_relax() : remodel
• use_precomputed_library() : stepwise::monte_carlo
• use_rama_filter() : cyclic_peptide
• use_rna_chi_potential() : score::rna
• use_rotamer_constraints_to_native() : ddg
• use_same_length_fragments() : remodel
• use_setuptools() : ez_setup
• use_spline_interpolation() : patterson
• use_square_planar_metal_filters() : cyclic_peptide
• use_square_pyramidal_metal_filters() : cyclic_peptide
• use_ss1() : mh::score
• use_ss2() : mh::score
• use_symmetry_calc() : nmr::pcs , nmr::pre , nmr::rdc
• use_TBMB_filters() : cyclic_peptide
• use_template_sequence() : DenovoProteinDesign
• use_template_topology() : DenovoProteinDesign
• use_terminal_residues() : make_rot_lib
• use_tetrahedral_metal_filters() : cyclic_peptide
• use_time_as_seed() : run
• use_TMA_filters() : cyclic_peptide
• use_trigonal_planar_metal_filters() : cyclic_peptide
• use_trigonal_pyramidal_metal_filters() : cyclic_peptide
• use_truncated_termini() : in
• use_unrelaxed_starting_points() : cp
• use_user_templates() : tcrmodel
• user() : inout::dbms
• user_set_alpha_dihedral_perturbation() : cyclic_peptide
• user_set_alpha_dihedrals() : cyclic_peptide
• user_tag() : out
• user_tags() : in::file
• useZ() : csa , dc
• ushort_of() : ObjexxFCL