- u -

• unbound_protein_minimization() : rnp_ddg.cc
• unsatisfied_buried_polars() : cryst_reporters.hh
• unvirtualize_phosphates() : rna_graft.cc
• up_jump_tree() : smhybrid.cc
• update_atom_positions() : make_retroinverso.cc
• update_backbone() : turner_two_chain.cc
• update_bicelle_radius() : mp_optimize_geometry_params.cc
• update_constraints() : minimization_test.cc , msd.cc
• update_double_vesicle() : mp_optimize_geometry_params.cc
• update_nucleoside() : turner_two_chain.cc
• update_system() : turner_test_double_helix.cc
• update_torsion_set() : lariat_modeling.cc
• update_vesicle_radius() : mp_optimize_geometry_params.cc
• updateSSAtoms() : CycDsulf.cc
• usage() : conserve_disulfides.cc , rotamerize_disulfides.cc , disulfide_scorer.cc , disulfide_handoff.cc , disulfide_finder.cc , disulfide_filter.cc , create_disulf_file.cc , convert.cc
• use_backrub() : call_mover.cc
• use_in_rmsd() : make_a3b_bundle.cc , bettercluster.cc , design_cycpeptide_MPI.cc , make_betahelicalbundle.cc , make_helicalbundle.cc , cluster_cyc_disulf.cc
• use_in_rmsd_offset() : bettercluster.cc
• user_overwrites_options() : mp_parameters.cc