Referenced by PoseWrap::add_apcs_local(), TorsionVectorMover::apply(), SetupMover::apply(), MPFindInterfaceTestMover::apply(), TestQuickRelaxMover::apply(), benzene_pair_score_test(), calc_scores(), compare_frags_pose(), copy_residues(), correct_dunbrack(), cyclic_perm(), define_cut_points(), delete_protein_from_pose(), delete_RNA_from_pose(), doit(), ChallengeMover::downstream_residues_from_jump(), apps::pilot::downstream_residues_from_jump(), utility::graph::Node::find_edge(), utility::graph::DirectedNode::find_edge_from(), utility::graph::DirectedNode::find_edge_to(), basic_printf_context< OutputIt, Char >::format(), formatter< std::tm, Char >::format(), detail::format_uint(), get_ABGEO_string(), apps::pilot::MultiTemplateAlignChunkMover::get_alignment_from_chunk_mapping(), get_all_1helix_docks(), get_all_2helix_docks(), get_hb_info(), get_helix_axis(), get_helix_center(), get_helixCAInContact(), get_neighbor_subs(), SVC_Q::get_Q(), ONE_CLASS_Q::get_Q(), get_sasa(), get_sc(), basic::gpu::Timer::GetTime(), good_geometry(), MatchBase::init(), ChallengeMover::initialize_pose(), numeric::IntervalSet< T >::IntervalSet(), is_loop(), is_loop_neighbor(), kinclose(), numeric::linear_interpolate(), main(), make_frag_set(), make_frags(), HECTMover::make_frags(), new_sc(), newer_sc(), SleepForATenthOfASecond::operator()(), SequenceCoords::operator=(), apps::public1::scenarios::chemically_conjugated_docking::pack_extra_bodies(), utility::io::TarParser::parseFileSize(), Prepare(), prepare_full_length_start_model(), print_internal_coord_test(), basic::prof_stop_function_body(), numeric::IntervalSet< T >::push_back(), utility::quoted_split(), refold_second(), utility::replace_environment_variables(), basic::gpu::Timer::Reset(), apps::pilot::SampleSecondaryStructureAlignmentMover::revert_loops_to_original(), rot_pose(), numeric::IntervalSet< T >::set(), set_all_loop_dihedrals_to_180(), apps::pilot::SampleSecondaryStructureAlignmentMover::set_loops_to_virt_ala(), protocols::abinitio::JumpSpecificAbrelax::setup(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), setup_rhiju_fold_tree(), DomainDescription::sheet_match(), sigmoid(), utility::split(), utility::split_by_newlines(), utility::split_to_list(), utility::split_to_set(), svm_cross_validation(), svm_group_classes(), svm_predict_values(), svm_train(), myspace::GraftTester::test_rb_min_graft(), numeric::interpolation::spline::TricubicSpline::train(), numeric::interpolation::spline::PolycubicSpline< N >::train(), trans_pose(), and basic::DynamicProfileThis::~DynamicProfileThis().
