Referenced by align_pdbs(), analyze_interface_test(), atom_tree_torsion_test(), atom_vdw_test(), build_next_nucleotide_test(), calculate_pairwise_RMSD(), ccd_test(), cluster_rotamers(), convert_to_native_test(), cs_rosetta_rna_pdb(), dinucleotide_test(), dna_deriv_test_old(), dump_hbond_pdb(), TCDock::dump_pdb(), Link::dump_pdb(), TCDock::dump_top_hits(), endo_test(), figure_out_icoord_test(), BuildFullModel::fill_and_sample_full_model(), find_dna_rotamers(), gen_pep_bb_sequential(), get_ddG(), hermann_phase_two(), hermann_phase_two_minimize(), idealize_tf_pose(), import_and_dump_pdb(), intra_dna_stats(), journal_club_syn_chi(), juke_sam_test(), TCDock::justone(), loop_modeling_test(), loop_rebuilding_test(), luxr_setup(), main(), minimize_pdb(), minimizer_test(), mm_pack_test(), multiple_variant_type_test(), mutate_residues_wrapper(), my_main(), o2prime_packer(), old_simple_conformation_test(), output_single_motif(), pack_rotamers_test(), place_waters_and_minimize(), post_rebuild_bulge_assembly(), print_pep_analysis(), Bola::random_nonclashing_move(), rb_test(), RBSegmentRelax_test(), refine_fa_pep_bb(), register_options(), repack_minimize_test(), repack_test(), rna_design_test(), rna_fullatom_minimize_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rotamer_trials_test(), rotamerize_rna_test(), protocols::abinitio::CustomAbinitio::run(), run(), TCDock::run(), run_mc(), run_pep_prep(), RunPepSpec(), sasa_test(), ui::widgets::PoseEditor::save_pose(), myspace::DataClass::set_dumppdb(), set_fullatom_flag_test(), shear_moves_test(), simple_centroid_test(), simple_copy_test(), simple_frag_test(), simple_hbond_test(), simple_loop_modeling_test(), simple_relax(), simple_rotamer_test(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), small_min_test(), small_moves_test(), spec_test(), test_gb(), test_suck_res(), tf_specificity_test(), wriggle_test(), MatchSet::write_to_file(), and zif268_test().
