Referenced by analyze_poses_for_convergence(), apply_linked_constraints(), calculate_average_residue_scores(), calculate_disorder(), cl_score(), do_disorder_prediction(), myspace::evaluate_and_write(), fillPoseAndDataList(), filterAlignment(), filterAllAlignments(), filterNonCore(), MatchSet::init(), main(), apps::pilot::frankdt::main(), MatchSet::MatchSet(), morph_pdbs_test(), parse_resfiles(), poses_from_cmd_line(), poses_from_cmd_line_noPDBtag(), PoseWrap::PoseWrap(), posewrap_from_command_line(), read_in_pdbs(), MPDomainAssembly::register_options(), run(), RunPepSpec(), simple_rotamer_recovery(), myspace::test_bbgauss(), myspace::test_loophash(), myspace::test_MD(), myspace::test_NMrelaxer(), myspace::test_recombine(), myspace::test_relax(), and update_constraints().
