Referenced by LoopHash_Analyze::apply(), FragmentBasedDesign::apply(), SwapElementsMover1::apply(), SwapElementsMover2::apply(), MPFoldingMover::apply(), MPDomainAssembly::apply(), complex_interface_optimize::apply(), bind_T60_pybind11(), build_helix_test(), build_template(), byres_analysis(), calc_blosum_scores(), calc_vm(), calculate_average_residue_scores(), calculate_disorder(), calculate_rmsd_variance(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), calculate_tm_variance(), check_all_poses_have_the_same_sequence(), cluster_rotamers(), myspace::collect_silent(), composite_sequences_from_cmd_line(), dinucleotide_test(), dna_test(), double_helix_test(), figure_out_icoord_test(), protocols::abinitio::JumpSpecificAbrelax::generate_extended_pose(), generate_extended_pose(), generate_sequence_binary_alphabet(), protocols::abinitio::ApplicationContext::generateExtendedPose(), get_bps_seq(), get_fragment_sets(), get_min_frag_rmsd(), get_n_mer_maltose(), get_n_mer_polyalanine(), SequenceProfileDB::get_next_profile(), get_radius_in_frag_set(), get_sequence_and_secstruct_from_dssp(), get_t033_ss(), graphics_main(), helix_ST(), homolog_finder(), AbInitio_MPI::init_on_new_input(), input_alignments(), journal_club_syn_chi(), main(), measure_sequence_recovery(), mutate_to_sequence(), my_main(), native_frag_CA_RMSD(), nucleobase_probe_score_test(), SequenceCoords::operator=(), output_pdb(), output_results(), PickSSE::PickSSE(), pose_from_scratch(), myspace::pose_from_scratch(), predict_disorder(), Prepare(), present_in_native(), SequenceCoords::print(), print_ddgs(), print_verbose_ddgs(), rb_entropy_test(), read_alignment_fasta_file(), read_fasta(), rebuild_test(), region_density_score(), region_rmsd_structures_aligned(), removeConstraintsNearGap(), apps::pilot::SampleSecondaryStructureAlignmentMover::revert_loops_to_original(), rna_build_helix_test(), rna_denovo(), rna_fullatom_minimize_test(), rna_motif_test(), rna_thread_test(), rotamerize_rna_test(), DockFragmentsMover::run(), run_pep_prep(), score12_plot_test(), score_folded_residues(), score_loop(), scoreall(), SequenceCoords::SequenceCoords(), sequences_from_cmd_line(), setup_dinucleotide_pose(), setup_double_helix_pose(), setup_fragment_mover(), setup_one_chain_pose(), TryScoreFilter::setup_pose(), setup_two_base_pair_pose_with_chainbreak(), simple_frag_test(), slice_sequence(), superimpose_pose_using_aln(), SymmAbRelaxTest(), and two_region_rmsd().
