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Rosetta
2016.11
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Classes | |
class | GaussianParameter |
class | RNA_FittedTorsionInfo |
class | RNA_ResidueType |
Typedefs | |
typedef utility::pointer::shared_ptr < RNA_FittedTorsionInfo > | RNA_FittedTorsionInfoOP |
typedef utility::pointer::weak_ptr < RNA_ResidueType > | RNA_ResidueTypeAP |
typedef utility::pointer::weak_ptr < RNA_ResidueType const > | RNA_ResidueTypeCAP |
typedef utility::pointer::shared_ptr < RNA_ResidueType > | RNA_ResidueTypeOP |
typedef utility::pointer::shared_ptr < RNA_ResidueType const > | RNA_ResidueTypeCOP |
Enumerations | |
enum | BaseEdge { ANY_BASE_EDGE, WATSON_CRICK, HOOGSTEEN, SUGAR, O2PRIME, PHOSPHATE } |
enum | RNA_Torsion { ANY_TORSION, ALPHA, BETA, GAMMA, DELTA, EPSILON, ZETA, CHI, NU2, NU1, O2H } |
enum | ChiState { ANY_CHI, ANTI, SYN, NO_CHI } |
enum | PuckerState { ANY_PUCKER, NORTH, SOUTH, NO_PUCKER } |
enum | BaseDoubletOrientation { ANY_BASE_DOUBLET_ORIENTATION, ANTIPARALLEL, PARALLEL } |
enum | LW_BaseDoubletOrientation { ANY_LW_BASE_DOUBLET_ORIENTATION, CIS, TRANS } |
enum | BaseStackWhichSide { ANY_BASE_STACK_SIDE, ABOVE, BELOW } |
Variables | |
utility::vector1< std::string > const | non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" ) |
utility::vector1< std::string > const | atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" ) |
utility::vector1< std::string > const | non_base_atoms |
utility::vector1< std::string > const | sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" ) |
typedef utility::pointer::shared_ptr< RNA_FittedTorsionInfo > core::chemical::rna::RNA_FittedTorsionInfoOP |
typedef utility::pointer::weak_ptr< RNA_ResidueType > core::chemical::rna::RNA_ResidueTypeAP |
typedef utility::pointer::weak_ptr< RNA_ResidueType const > core::chemical::rna::RNA_ResidueTypeCAP |
typedef utility::pointer::shared_ptr< RNA_ResidueType const > core::chemical::rna::RNA_ResidueTypeCOP |
typedef utility::pointer::shared_ptr< RNA_ResidueType > core::chemical::rna::RNA_ResidueTypeOP |
void core::chemical::rna::add_values_from_center | ( | utility::vector1< core::Real > & | torsions, |
Real const | center, | ||
Real const | max_range, | ||
Real const | bin_size | ||
) |
std::string const core::chemical::rna::chi1_torsion_atom | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::atom_name(), and chi1_torsion_atom_index().
Referenced by protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_init_pose(), default_jump_atom(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), core::pose::pdbslice(), and protocols::farna::movers::RNA_LoopCloser::rna_ccd_close().
Size core::chemical::rna::chi1_torsion_atom_index | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::chi_atoms().
Referenced by chi1_torsion_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), and core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone().
Size core::chemical::rna::convert_acgu_to_1234 | ( | char const | c | ) |
References rna_nts().
Referenced by core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff(), and core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs().
std::string const core::chemical::rna::default_jump_atom | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::atom_name(), chi1_torsion_atom(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), and core::conformation::Residue::name3().
Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::farna::fill_in_default_jump_atoms(), protocols::stepwise::monte_carlo::mover::filter_for_proximity(), protocols::stepwise::setup::get_tree(), protocols::stepwise::modeler::merge_two_poses(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::stepwise::setup::put_in_cutpoint(), protocols::farna::movers::RNA_JumpMover::random_jump_change(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::magnesium::update_mg_hoh_fold_tree().
std::string const core::chemical::rna::first_base_atom | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::atom_name(), and first_base_atom_index().
Size core::chemical::rna::first_base_atom_index | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::chi_atoms().
Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), first_base_atom(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), and core::pose::rna::initialize_atoms_for_which_we_need_new_dofs().
BaseEdge core::chemical::rna::get_edge_from_char | ( | char const | e | ) |
char core::chemical::rna::get_edge_from_num | ( | Size const | num | ) |
References HOOGSTEEN, O2PRIME, PHOSPHATE, SUGAR, and WATSON_CRICK.
Referenced by protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs(), core::pose::rna::classify_base_pairs(), core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and protocols::farna::libraries::BasePairType::tag().
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions | ( | Real const | delta, |
bool const | extra_epsilon, | ||
Real const | bin_size | ||
) |
References core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), and torsion_info.
Referenced by core::pack::rotamer_set::build_three_prime_phosphate_rotamers(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate().
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions | ( | bool const | north_pucker, |
bool const | extra_epsilon, | ||
Real | const | ||
) |
References add_values_from_center(), core::conformation::membrane::center, and torsion_info.
std::string core::chemical::rna::get_full_edge_from_num | ( | Size const | num | ) |
References HOOGSTEEN, O2PRIME, PHOSPHATE, SUGAR, and WATSON_CRICK.
Referenced by core::pose::rna::BasePair::print_info().
std::string core::chemical::rna::get_full_LW_orientation_from_num | ( | Size const | num | ) |
Referenced by core::pose::rna::BasePair::print_info().
std::string core::chemical::rna::get_full_orientation_from_num | ( | Size const | num | ) |
References ANTIPARALLEL, ANY_BASE_DOUBLET_ORIENTATION, and PARALLEL.
Referenced by core::pose::rna::operator<<(), and core::pose::rna::BasePair::print_info().
std::string core::chemical::rna::get_full_side_from_num | ( | Size const | num | ) |
for stacking
References ABOVE, ANY_BASE_STACK_SIDE, and BELOW.
Referenced by core::pose::rna::operator<<().
References add_values_from_center().
Referenced by core::pack::rotamer_set::build_five_prime_phosphate_rotamers(), core::pack::rotamer_set::build_three_prime_phosphate_rotamers(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate().
LW_BaseDoubletOrientation core::chemical::rna::get_LW_orientation_from_char | ( | char const | o | ) |
References ANY_LW_BASE_DOUBLET_ORIENTATION, CIS, and TRANS.
Referenced by protocols::farna::setup::RNA_DeNovoParameters::get_pairings_from_line().
BaseDoubletOrientation core::chemical::rna::get_orientation_from_char | ( | char const | o | ) |
char core::chemical::rna::get_orientation_from_num | ( | Size const | num | ) |
ChiState core::chemical::rna::get_residue_base_state | ( | conformation::Residue const & | rsd | ) |
References ANTI, CHI, core::conformation::Residue::chi(), NUM_RNA_MAINCHAIN_TORSIONS(), and SYN.
Referenced by core::pose::rna::get_residue_base_state().
PuckerState core::chemical::rna::get_residue_pucker_state | ( | conformation::Residue const & | rsd | ) |
numeric::xyzVector< core::Real > core::chemical::rna::get_rna_base_centroid | ( | conformation::Residue const & | rsd, |
bool | verbose | ||
) |
References core::chemical::rna::RNA_ResidueType::atom_is_virtual(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::first_sidechain_atom(), core::chemical::AtomType::is_repulsive(), core::conformation::Residue::is_RNA(), core::chemical::AtomType::name(), core::conformation::Residue::nheavyatoms(), core::chemical::rna::RNA_ResidueType::o2prime_index(), core::conformation::Residue::RNA_type(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::toolbox::sample_around::centroid_dist(), protocols::stepwise::screener::CentroidDistanceScreener::check_screen(), core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::toolbox::rigid_body::set_to_origin(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker().
numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system | ( | core::conformation::Residue const & | rsd, |
numeric::xyzVector< core::Real > const & | centroid | ||
) |
numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system | ( | conformation::Residue const & | rsd, |
Vector const & | centroid | ||
) |
References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_unp, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_RNA(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and core::conformation::Residue::xyz().
Referenced by core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::toolbox::rigid_body::set_to_origin(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker().
char core::chemical::rna::get_side_from_num | ( | Size const | num | ) |
References ABOVE, ANY_BASE_STACK_SIDE, and BELOW.
void core::chemical::rna::get_watson_crick_base_pair_atoms | ( | conformation::Residue const & | rsd_type1, |
conformation::Residue const & | rsd_type2, | ||
std::string & | atom1, | ||
std::string & | atom2 | ||
) |
void core::chemical::rna::get_watson_crick_base_pair_atoms | ( | conformation::Residue const & | rsd_type1, |
conformation::Residue const & | rsd_type2, | ||
utility::vector1< std::string > & | atom_ids1, | ||
utility::vector1< std::string > & | atom_ids2 | ||
) |
References core::conformation::Residue::aa(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and core::conformation::Residue::name3().
Referenced by protocols::farna::figure_out_base_pair_partner(), protocols::farna::get_base_pairing_info(), protocols::farna::get_base_pairing_list(), and protocols::farna::setup_base_pair_constraints().
std::string core::chemical::rna::get_WC_atom | ( | core::chemical::AA const & | res_type | ) |
References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.
bool core::chemical::rna::is_base_phosphate_atom_pair | ( | conformation::Residue const & | rsd_1, |
conformation::Residue const & | rsd_2, | ||
Size const | atomno_1, | ||
Size const | atomno_2 | ||
) |
References core::chemical::rna::RNA_ResidueType::atom_is_phosphate(), core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_ResidueType::is_RNA_base_atom(), core::conformation::Residue::path_distance(), core::conformation::Residue::RNA_type(), and core::conformation::Residue::seqpos().
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().
bool core::chemical::rna::is_purine | ( | conformation::Residue const & | rsd | ) |
References core::conformation::Residue::name1().
Referenced by protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::stepwise::monte_carlo::rna::RNA_TorsionMover::apply_random_nucleoside_torsion(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list(), and protocols::stepwise::sampler::rna::setup_sampler().
Size const core::chemical::rna::NUM_EDGES | ( | 3 | ) |
Referenced by core::scoring::rna::RNA_RawBaseBaseInfo::copy_values(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), protocols::farna::fragments::FullAtomRNA_Fragments::read_vall_torsions(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), and core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy().
Size const core::chemical::rna::NUM_RNA_CHI_TORSIONS | ( | NUM_RNA_TORSIONS- | NUM_RNA_MAINCHAIN_TORSIONS | ) |
Size const core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS | ( | 6 | ) |
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), core::pose::rna::apply_non_main_chain_sugar_coords(), protocols::farna::create_rna_vall_torsions(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::io::silent::RNA_SilentStruct::fill_pose(), get_residue_base_state(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::farna::fragments::FullAtomRNA_Fragments::insert_fragment(), core::io::silent::RNA_SilentStruct::print_conformation(), protocols::farna::movers::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::farna::movers::RNA_Minimizer::setup_movemap(), and protocols::farna::movers::RNA_LoopCloser::setup_variants_at_extra_cutpoints().
Size const core::chemical::rna::NUM_RNA_TORSIONS | ( | 10 | ) |
Referenced by core::pose::rna::apply_non_main_chain_sugar_coords(), protocols::farna::fragments::FullAtomRNA_Fragments::insert_fragment(), protocols::farna::fragments::TorsionSet::operator=(), protocols::farna::fragments::FullAtomRNA_Fragments::read_vall_torsions(), and protocols::farna::fragments::TorsionSet::TorsionSet().
bool core::chemical::rna::possibly_canonical | ( | chemical::AA const & | aa1, |
chemical::AA const & | aa2 | ||
) |
References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.
Referenced by protocols::farna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs(), protocols::farna::check_base_pair(), protocols::farna::figure_out_base_pair_partner(), protocols::farna::get_base_pairing_info(), protocols::farna::get_base_pairing_list(), protocols::farna::base_pairs::RNA_BasePairHandler::get_stem_residues(), and protocols::farna::setup::RNA_DeNovoPoseSetup::initialize_secstruct().
bool core::chemical::rna::possibly_canonical_strict | ( | chemical::AA const & | aa1, |
chemical::AA const & | aa2 | ||
) |
References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.
Referenced by protocols::farna::figure_out_base_pair_partner().
bool core::chemical::rna::rna_dna_match | ( | core::chemical::AA const & | aa1, |
core::chemical::AA const & | aa2 | ||
) |
References core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, and core::chemical::na_ura.
Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks().
std::string const core::chemical::rna::rna_nts | ( | "acgu" | ) |
|
static |
Referenced by protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::atom_square_deviation(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), protocols::stepwise::modeler::rna::freeze_sugar_torsions(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::stepwise::modeler::rna::get_num_side_chain_atom_from_res_name(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pose::rna::has_virtual_rna_residue_variant_type(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::o2prime_trials(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_rotamer(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::pass_FARFAR_no_auto_bulge_filter(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::stepwise::modeler::rna::print_individual_atom_info(), core::pose::rna::print_torsion_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::modeler::rna::rescale_scorefxn(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::stepwise::modeler::rna::show_scorefxn_weight_lines(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering(), and protocols::stepwise::modeler::rna::virtualize_free_rna_moieties().
utility::vector1< std::string > const core::chemical::rna::atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" ) |
utility::vector1< std::string > const core::chemical::rna::non_base_atoms |
Referenced by core::pose::rna::RNA_IdealCoord::apply_coords().
utility::vector1< std::string > const core::chemical::rna::non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" ) |
utility::vector1< std::string > const core::chemical::rna::sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" ) |