Referenced by pyrosetta.bindings.pose.PoseResidueAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor::__reversed__(), PoseWrap::align_orig_pose(), DockGlycansProtocol::apply(), apply_nucleoside(), benchmark_contacts(), Bola::Bola(), ChiMover::ChiMover(), compute_windowed_rama(), compute_windowed_rmsd(), copy_each_residue(), dock(), get_nucleoside(), go_main(), MatchSet::init(), is_cut(), is_loop(), is_loop_neighbor(), ligand_centroid(), main(), apps::pilot::frankdt::main(), mutate_and_score_RNP(), new_pose_generator(), output_residue_struct(), peptide_plane_test_OLD(), refresh_cutpoints(), rna_sequence_recovery_metrics(), run(), run_pep_prep(), set_basic_dock_options(), set_up_pose(), ConstraintConfig::show_cst_grids(), TorsionList::torsion(), and transform_pose().