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core::scoring::rna Namespace Reference

Namespaces

 chemical_shift
 
 data
 

Classes

class  RG_Energy_RNA
 
class  RG_Energy_RNACreator
 
class  RNA_AtomVDW
 
class  RNA_BulgeEnergy
 
class  RNA_BulgeEnergyCreator
 
class  RNA_CentroidInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
 
class  RNA_EnergyMethodOptions
 
class  RNA_FullAtomStackingEnergy
 
class  RNA_FullAtomStackingEnergyCreator
 
class  RNA_FullAtomVDW_BasePhosphate
 
class  RNA_FullAtomVDW_BasePhosphateCreator
 
class  RNA_JR_SuiteEnergy
 
class  RNA_JR_SuiteEnergyCreator
 
class  RNA_LJ_BaseEnergy
 
class  RNA_LJ_BaseEnergyCreator
 
class  RNA_LowResolutionPotential
 
class  RNA_LowResolutionPotentialCreator
 
class  RNA_Motif
 
class  RNA_Motifs
 
class  RNA_PairwiseLowResolutionEnergy
 
class  RNA_PairwiseLowResolutionEnergyCreator
 
class  RNA_PartitionEnergy
 
class  RNA_PartitionEnergyCreator
 
class  RNA_ScoringInfo
 Keep track of RNA centroid, useful atom, base-base info inside the pose. More...
 
class  RNA_StubCoordinateEnergy
 
class  RNA_StubCoordinateEnergyCreator
 
class  RNA_SugarCloseEnergy
 
class  RNA_SugarCloseEnergyCreator
 
class  RNA_SuiteEnergy
 
class  RNA_SuiteEnergyCreator
 
class  RNA_SuitePotential
 
class  RNA_TorsionEnergy
 
class  RNA_TorsionEnergyCreator
 
class  RNA_TorsionPotential
 
class  RNA_VDW_Energy
 
class  RNA_VDW_EnergyCreator
 
class  RNP_LowResEnergy
 
class  RNP_LowResEnergyCreator
 
class  RNP_LowResPairDistEnergy
 
class  RNP_LowResPairDistEnergyCreator
 
class  RNP_LowResPairDistPotential
 
class  RNP_LowResPotential
 
class  RNP_LowResStackData
 
class  RNP_LowResStackEnergy
 
class  RNP_LowResStackEnergyCreator
 
class  StackElecEnergy
 
class  StackElecEnergyCreator
 
class  TNA_SuiteEnergy
 
class  TNA_SuiteEnergyCreator
 
class  TNA_SuitePotential
 

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 
typedef
utility::pointer::shared_ptr
< RNA_FullAtomVDW_BasePhosphate
RNA_FullAtomVDW_BasePhosphateOP
 
typedef
utility::pointer::shared_ptr
< RNA_FullAtomVDW_BasePhosphate
const > 
RNA_FullAtomVDW_BasePhosphateCOP
 
typedef
utility::pointer::shared_ptr
< RNA_SugarCloseEnergy
RNA_SugarCloseEnergyOP
 
typedef
utility::pointer::shared_ptr
< RNA_SugarCloseEnergy const > 
RNA_SugarCloseEnergyCOP
 
typedef
utility::pointer::shared_ptr
< RNA_TorsionEnergy
RNA_TorsionEnergyOP
 
typedef
utility::pointer::shared_ptr
< RNA_TorsionEnergy const > 
RNA_TorsionEnergyCOP
 
typedef
utility::pointer::shared_ptr
< RNA_AtomVDW
RNA_AtomVDWOP
 
typedef
utility::pointer::shared_ptr
< RNA_AtomVDW const > 
RNA_AtomVDWCOP
 
typedef
utility::pointer::shared_ptr
< RNA_CentroidInfo
RNA_CentroidInfoOP
 
typedef
utility::pointer::shared_ptr
< RNA_EnergyMethodOptions
RNA_EnergyMethodOptionsOP
 
typedef
utility::pointer::shared_ptr
< RNA_EnergyMethodOptions
const > 
RNA_EnergyMethodOptionsCOP
 
typedef
utility::pointer::shared_ptr
< RNA_LowResolutionPotential
RNA_LowResolutionPotentialOP
 
typedef
utility::pointer::shared_ptr
< RNA_LowResolutionPotential
const > 
RNA_LowResolutionPotentialCOP
 
typedef
utility::pointer::shared_ptr
< RNA_Motif
RNA_MotifOP
 
typedef
utility::pointer::shared_ptr
< RNA_Motif const > 
RNA_MotifCOP
 
typedef
utility::pointer::shared_ptr
< RNA_Motifs
RNA_MotifsOP
 
typedef
utility::pointer::shared_ptr
< RNA_Motifs const > 
RNA_MotifsCOP
 
typedef
utility::pointer::shared_ptr
< RNA_ScoringInfo
RNA_ScoringInfoOP
 
typedef
utility::pointer::shared_ptr
< RNA_SuitePotential
RNA_SuitePotentialOP
 
typedef
utility::pointer::shared_ptr
< RNA_SuitePotential const > 
RNA_SuitePotentialCOP
 
typedef
utility::pointer::shared_ptr
< RNA_TorsionPotential
RNA_TorsionPotentialOP
 
typedef
utility::pointer::shared_ptr
< RNA_TorsionPotential const > 
RNA_TorsionPotentialCOP
 
typedef
utility::pointer::shared_ptr
< RNP_LowResPairDistPotential
RNP_LowResPairDistPotentialOP
 
typedef
utility::pointer::shared_ptr
< RNP_LowResPotential
RNP_LowResPotentialOP
 
typedef
utility::pointer::shared_ptr
< RNP_LowResStackData
RNP_LowResStackDataOP
 
typedef
utility::pointer::shared_ptr
< TNA_SuitePotential
TNA_SuitePotentialOP
 
typedef
utility::pointer::shared_ptr
< TNA_SuitePotential const > 
TNA_SuitePotentialCOP
 

Enumerations

enum  RNA_MotifType {
  U_TURN, UA_HANDLE, T_LOOP, INTERCALATED_T_LOOP,
  LOOP_E_SUBMOTIF, BULGED_G, GNRA_TETRALOOP, STRICT_WC_STACKED_PAIR,
  WC_STACKED_PAIR, A_MINOR, PLATFORM, TL_RECEPTOR,
  TETRALOOP_TL_RECEPTOR, Z_TURN, TANDEM_GA_SHEARED, TANDEM_GA_WATSON_CRICK,
  GA_MINOR, DOUBLE_T_LOOP
}
 

Functions

template<class T >
Size get_position_in_vector (utility::vector1< T > &vec, T const &element)
 
Size rna_residue_type_to_num (chemical::ResidueType const &rt)
 
bool operator== (RNA_EnergyMethodOptions const &a, RNA_EnergyMethodOptions const &b)
 
std::ostream & operator<< (std::ostream &out, const RNA_EnergyMethodOptions &options)
 
Size convert_na_to_1234 (core::chemical::AA const foo)
 
Size get_bin (conformation::Residue const &res_i)
 
RNA_Motifs get_rna_motifs (pose::Pose const &pose, core::scoring::rna::RNA_LowResolutionPotential const &potential, core::pose::rna::RNA_FilteredBaseBaseInfo const &filtered_base_base_info)
 identify RNA motifs inside pose More...
 
void output_rna_motifs (std::ostream &out, core::pose::Pose const &pose, RNA_Motifs const &rna_motifs, bool const output_WC_stacked_pair)
 
void output_motifs_to_pymol (std::ostream &out, core::pose::Pose const &pose, RNA_Motifs const &rna_motifs)
 sets up .pml file that will color motifs. More...
 
std::string to_string (RNA_MotifType type)
 
std::ostream & operator<< (std::ostream &out, RNA_Motif const &s)
 
bool operator< (RNA_Motif const &lhs, RNA_Motif const &rhs)
 
std::ostream & operator<< (std::ostream &out, RNA_Motifs const &s)
 
bool check_rna_loop (core::pose::Pose const &pose, core::Size const n, core::Size const nloop)
 
bool check_stack (Size const i, Size const j, core::pose::rna::RNA_BaseStackList const &base_stack_list)
 
void output_rna_motif (pose::Pose const &pose, RNA_Motif const &motif)
 
void output_rna_motifs_detailed (pose::Pose const &pose, RNA_Motifs const &motifs)
 
bool check_watson_crick_sequence (pose::Pose const &pose, Size const res1, Size const res2, bool const strict=false)
 
Real get_rna_motif_score (pose::Pose const &pose, core::scoring::rna::RNA_LowResolutionPotential const &potential, core::pose::rna::RNA_FilteredBaseBaseInfo const &filtered_base_base_info)
 wrapper around get_rna_motifs – outputs score. More...
 
RNA_ScoringInfo const & rna_scoring_info_from_pose (pose::Pose const &pose)
 
RNA_ScoringInfononconst_rna_scoring_info_from_pose (pose::Pose &pose)
 
void clear_rna_scoring_info (pose::Pose &pose)
 
void get_fade_correction (Real const z, Real const cutoff_lower, Real const cutoff_upper, Real const fade_zone, Real &fade_value, Real &fade_deriv)
 
Size rna_residue_name_to_num (char const c)
 
Size protein_atom_name_to_num (std::string const &name)
 
Size protein_atom_name_to_num (std::string const &name, std::string const &resname)
 

Variables

std::map< RNA_MotifType,
core::Real > const 
rna_motif_bonus
 
std::map< RNA_MotifType,
std::string > const 
motif_color
 

Typedef Documentation

typedef numeric::xyzMatrix< Real > core::scoring::rna::Matrix
typedef utility::pointer::shared_ptr< RNA_AtomVDW const > core::scoring::rna::RNA_AtomVDWCOP
typedef utility::pointer::shared_ptr< RNA_AtomVDW > core::scoring::rna::RNA_AtomVDWOP
typedef utility::pointer::shared_ptr< RNA_CentroidInfo > core::scoring::rna::RNA_CentroidInfoOP
typedef utility::pointer::shared_ptr< RNA_EnergyMethodOptions const > core::scoring::rna::RNA_EnergyMethodOptionsCOP
typedef utility::pointer::shared_ptr< RNA_Motif const > core::scoring::rna::RNA_MotifCOP
typedef utility::pointer::shared_ptr< RNA_Motif > core::scoring::rna::RNA_MotifOP
typedef utility::pointer::shared_ptr< RNA_Motifs const > core::scoring::rna::RNA_MotifsCOP
typedef utility::pointer::shared_ptr< RNA_Motifs > core::scoring::rna::RNA_MotifsOP
typedef utility::pointer::shared_ptr< RNA_ScoringInfo > core::scoring::rna::RNA_ScoringInfoOP
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy const > core::scoring::rna::RNA_SugarCloseEnergyCOP
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy > core::scoring::rna::RNA_SugarCloseEnergyOP
typedef utility::pointer::shared_ptr< RNA_SuitePotential const > core::scoring::rna::RNA_SuitePotentialCOP
typedef utility::pointer::shared_ptr< RNA_SuitePotential > core::scoring::rna::RNA_SuitePotentialOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy const > core::scoring::rna::RNA_TorsionEnergyCOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy > core::scoring::rna::RNA_TorsionEnergyOP
typedef utility::pointer::shared_ptr< RNA_TorsionPotential const > core::scoring::rna::RNA_TorsionPotentialCOP
typedef utility::pointer::shared_ptr< RNA_TorsionPotential > core::scoring::rna::RNA_TorsionPotentialOP
typedef utility::pointer::shared_ptr< RNP_LowResPotential > core::scoring::rna::RNP_LowResPotentialOP
typedef utility::pointer::shared_ptr< RNP_LowResStackData > core::scoring::rna::RNP_LowResStackDataOP
typedef utility::pointer::shared_ptr< TNA_SuitePotential const > core::scoring::rna::TNA_SuitePotentialCOP
typedef utility::pointer::shared_ptr< TNA_SuitePotential > core::scoring::rna::TNA_SuitePotentialOP

Enumeration Type Documentation

Enumerator
U_TURN 
UA_HANDLE 
T_LOOP 
INTERCALATED_T_LOOP 
LOOP_E_SUBMOTIF 
BULGED_G 
GNRA_TETRALOOP 
STRICT_WC_STACKED_PAIR 
WC_STACKED_PAIR 
A_MINOR 
PLATFORM 
TL_RECEPTOR 
TETRALOOP_TL_RECEPTOR 
Z_TURN 
TANDEM_GA_SHEARED 
TANDEM_GA_WATSON_CRICK 
GA_MINOR 
DOUBLE_T_LOOP 

Function Documentation

bool core::scoring::rna::check_rna_loop ( core::pose::Pose const &  pose,
core::Size const  n,
core::Size const  nloop 
)
inline
bool core::scoring::rna::check_stack ( Size const  i,
Size const  j,
core::pose::rna::RNA_BaseStackList const &  base_stack_list 
)
inline

Referenced by get_rna_motifs().

bool core::scoring::rna::check_watson_crick_sequence ( pose::Pose const &  pose,
Size const  res1,
Size const  res2,
bool const  strict = false 
)
inline
void core::scoring::rna::clear_rna_scoring_info ( pose::Pose pose)

remove RNA scoring info object so that it will be re-initialized if necessary

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RNA_SCORING_INFO.

Referenced by protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants().

Size core::scoring::rna::convert_na_to_1234 ( core::chemical::AA const  foo)
Size core::scoring::rna::get_bin ( conformation::Residue const &  res_i)
void core::scoring::rna::get_fade_correction ( Real const  z,
Real const  cutoff_lower,
Real const  cutoff_upper,
Real const  fade_zone,
Real &  fade_value,
Real &  fade_deriv 
)
template<class T >
Size core::scoring::rna::get_position_in_vector ( utility::vector1< T > &  vec,
T const &  element 
)
Real core::scoring::rna::get_rna_motif_score ( pose::Pose const &  pose,
core::scoring::rna::RNA_LowResolutionPotential const &  potential,
core::pose::rna::RNA_FilteredBaseBaseInfo const &  filtered_base_base_info 
)
inline
RNA_Motifs core::scoring::rna::get_rna_motifs ( pose::Pose const &  pose,
core::scoring::rna::RNA_LowResolutionPotential const &  potential,
core::pose::rna::RNA_FilteredBaseBaseInfo const &  filtered_base_base_info 
)
RNA_ScoringInfo & core::scoring::rna::nonconst_rna_scoring_info_from_pose ( pose::Pose pose)

Either returns a non-const reference to the rna_scoring object already stored in the pose, or creates a new rna scoring info object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::RNA_SCORING_INFO, and core::pose::Pose::size().

Referenced by core::pose::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::classify_base_pairs(), core::pose::rna::figure_out_base_pair_orientation(), core::io::rna::RNA_DataReader::fill_rna_data_info(), protocols::rna::denovo::RNA_FragmentMonteCarlo::final_score(), core::scoring::rna::RG_Energy_RNA::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::io::rna::get_rna_data_info(), protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_scorefxn(), core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::scoring::rna::StackElecEnergy::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), core::scoring::rna::StackElecEnergy::setup_for_packing(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::setup_for_scoring(), core::scoring::rna::StackElecEnergy::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), core::scoring::rna::data::RNA_DataBackboneEnergy::setup_for_scoring(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info().

bool core::scoring::rna::operator< ( RNA_Motif const &  lhs,
RNA_Motif const &  rhs 
)
inline
std::ostream& core::scoring::rna::operator<< ( std::ostream &  out,
const RNA_EnergyMethodOptions &  options 
)
std::ostream& core::scoring::rna::operator<< ( std::ostream &  out,
RNA_Motif const &  s 
)
inline
std::ostream& core::scoring::rna::operator<< ( std::ostream &  out,
RNA_Motifs const &  s 
)
inline
bool core::scoring::rna::operator== ( RNA_EnergyMethodOptions const &  a,
RNA_EnergyMethodOptions const &  b 
)
void core::scoring::rna::output_motifs_to_pymol ( std::ostream &  out,
pose::Pose const &  pose,
RNA_Motifs const &  rna_motifs 
)

sets up .pml file that will color motifs.

References motif_color, core::pose::Pose::pdb_info(), and core::pose::tag_from_pose().

void core::scoring::rna::output_rna_motif ( pose::Pose const &  pose,
RNA_Motif const &  motif 
)
inline
void core::scoring::rna::output_rna_motifs ( std::ostream &  out,
core::pose::Pose const &  pose,
RNA_Motifs const &  rna_motifs,
bool const  output_WC_stacked_pair 
)

used in RiboDraw (which takes output from rna_motif app)

References core::pose::Pose::pdb_info(), rna_motif_bonus, and core::id::to_string().

void core::scoring::rna::output_rna_motifs_detailed ( pose::Pose const &  pose,
RNA_Motifs const &  motifs 
)
inline
Size core::scoring::rna::protein_atom_name_to_num ( std::string const &  name)
Size core::scoring::rna::protein_atom_name_to_num ( std::string const &  name,
std::string const &  resname 
)
Size core::scoring::rna::rna_residue_name_to_num ( char const  c)
Size core::scoring::rna::rna_residue_type_to_num ( chemical::ResidueType const &  rt)
RNA_ScoringInfo const & core::scoring::rna::rna_scoring_info_from_pose ( pose::Pose const &  pose)

Pose must already contain a rna_scoring_info object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RNA_SCORING_INFO.

Referenced by core::scoring::rna::data::RNA_ChemicalMappingEnergy::calculate_energy(), protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::classify_base_pairs_lores(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::data::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), protocols::magnesium::SampleGrid::get_mg_positions(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status(), core::io::rna::get_rna_data_info(), core::pose::rna::get_scored_base_stack_list(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::pose::rna::output_other_contacts(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), and core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way().

std::string core::scoring::rna::to_string ( RNA_MotifType  type)
inline

Variable Documentation

std::map< RNA_MotifType, std::string > const core::scoring::rna::motif_color
Initial value:
= {
{ U_TURN, "lightblue" },
{ UA_HANDLE, "marine" },
{ T_LOOP, "tv_blue" },
{ INTERCALATED_T_LOOP, "deepblue" },
{ LOOP_E_SUBMOTIF, "salmon" },
{ BULGED_G, "red" },
{ GNRA_TETRALOOP, "ruby" },
{ STRICT_WC_STACKED_PAIR, "gray20" },
{ WC_STACKED_PAIR, "gray50" },
{ A_MINOR, "gold" },
{ PLATFORM, "sand" },
{ TL_RECEPTOR, "limon" },
{ TETRALOOP_TL_RECEPTOR, "orange" },
{ Z_TURN, "violet" },
{ TANDEM_GA_SHEARED, "lime" },
{ GA_MINOR, "purple" },
{ DOUBLE_T_LOOP, "forest" }
}
Definition: RNA_Motif.hh:59
Definition: RNA_Motif.hh:61
Definition: RNA_Motif.hh:63
Definition: RNA_Motif.hh:57
Definition: RNA_Motif.hh:69
Definition: RNA_Motif.hh:71
Definition: RNA_Motif.hh:64
Definition: RNA_Motif.hh:66
Definition: RNA_Motif.hh:58
Definition: RNA_Motif.hh:55
Definition: RNA_Motif.hh:72
Definition: RNA_Motif.hh:56
Definition: RNA_Motif.hh:60
Definition: RNA_Motif.hh:68
Definition: RNA_Motif.hh:65

Referenced by output_motifs_to_pymol().

std::map< RNA_MotifType, core::Real > const core::scoring::rna::rna_motif_bonus
Initial value:
= {
{ U_TURN, -1.0 },
{ UA_HANDLE, -1.0 },
{ T_LOOP, -1.0 },
{ LOOP_E_SUBMOTIF, -1.0 },
{ BULGED_G, -1.0 },
{ GNRA_TETRALOOP, -0.1 },
{ WC_STACKED_PAIR, 0.0 },
{ A_MINOR, -1.0 },
{ PLATFORM, -1.0 },
{ TL_RECEPTOR, -1.0 },
{ Z_TURN, -1.0 },
{ GA_MINOR, -1.0 },
{ DOUBLE_T_LOOP, -1.0 }
}
Definition: RNA_Motif.hh:59
Definition: RNA_Motif.hh:61
Definition: RNA_Motif.hh:63
Definition: RNA_Motif.hh:57
Definition: RNA_Motif.hh:69
Definition: RNA_Motif.hh:71
Definition: RNA_Motif.hh:64
Definition: RNA_Motif.hh:66
Definition: RNA_Motif.hh:58
Definition: RNA_Motif.hh:55
Definition: RNA_Motif.hh:72
Definition: RNA_Motif.hh:56
Definition: RNA_Motif.hh:60
Definition: RNA_Motif.hh:68
Definition: RNA_Motif.hh:65

Referenced by get_rna_motif_score(), output_rna_motif(), and output_rna_motifs().