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_ScoringInfo &	nonconst_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_EnergyMethodOptions > core::scoring::rna::RNA_EnergyMethodOptionsOP

typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate const > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCOP

typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateOP

typedef utility::pointer::shared_ptr< RNA_LowResolutionPotential const > core::scoring::rna::RNA_LowResolutionPotentialCOP

typedef utility::pointer::shared_ptr< RNA_LowResolutionPotential > core::scoring::rna::RNA_LowResolutionPotentialOP

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_LowResPairDistPotential > core::scoring::rna::RNP_LowResPairDistPotentialOP

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

enum core::scoring::rna::RNA_MotifType

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

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by get_rna_motifs().

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

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_unp, core::conformation::Residue::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and core::pose::Pose::residue().

Referenced by get_rna_motifs().

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

)

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 get_bin().

Size core::scoring::rna::get_bin

(

conformation::Residue const &

res_i

)

References core::chemical::aa_unp, core::chemical::rna::convert_acgu_to_1234(), convert_na_to_1234(), core::chemical::ResidueTypeBase::na_analogue(), core::conformation::Residue::name(), core::conformation::Residue::name1(), and core::conformation::Residue::type().

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().

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
	)

References protocols::match::upstream::b.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score().

template<class T >

Size core::scoring::rna::get_position_in_vector	(	utility::vector1< T > &	vec,
		T const &	element
	)

Referenced by core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters(), and core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW().

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

wrapper around get_rna_motifs – outputs score.

References core::scoring::rna::RNA_Motifs::get_motifs(), get_rna_motifs(), core::scoring::rna_motif, rna_motif_bonus, and protocols::hybridization::score.

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy().

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
	)

identify RNA motifs inside pose

this version allows user to supply preinstantiated potential and precalculated filtered_base_base_info for speed. Used to be inlined – since this function is long, this is probably to no one's advantage.

References A_MINOR, core::pose::Pose::aa(), core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::pose::rna::RNA_FilteredBaseBaseInfo::base_pair_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::base_stack_list(), BULGED_G, check_rna_loop(), check_stack(), check_watson_crick_sequence(), core::chemical::rna::CIS, DOUBLE_T_LOOP, GA_MINOR, core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::chemical::rna::get_rna_base_centroid(), GNRA_TETRALOOP, core::chemical::rna::HOOGSTEEN, INTERCALATED_T_LOOP, LOOP_E_SUBMOTIF, core::conformation::Residue::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::pose::Pose::pdb_info(), PLATFORM, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), SUGAR, T_LOOP, TANDEM_GA_SHEARED, TANDEM_GA_WATSON_CRICK, TETRALOOP_TL_RECEPTOR, TL_RECEPTOR, core::chemical::rna::TRANS, U_TURN, UA_HANDLE, core::chemical::rna::WATSON_CRICK, WC_STACKED_PAIR, core::conformation::Residue::xyz(), and Z_TURN.

Referenced by get_rna_motif_score().

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(), 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
	)

References core::conformation::membrane::out, and core::scoring::rna::RNA_EnergyMethodOptions::show().

std::ostream& core::scoring::rna::operator<< ( std::ostream &  out, RNA_Motif const &  s  )

inline

References core::conformation::membrane::out, core::scoring::rna::RNA_Motif::residues_, to_string(), and core::scoring::rna::RNA_Motif::type_.

std::ostream& core::scoring::rna::operator<< ( std::ostream &  out, RNA_Motifs const &  s  )

inline

References core::conformation::membrane::out.

bool core::scoring::rna::operator==	(	RNA_EnergyMethodOptions const &	a,
		RNA_EnergyMethodOptions const &	b
	)

References core::scoring::rna::RNA_EnergyMethodOptions::rna_base_pair_xy_filename_, core::scoring::rna::RNA_EnergyMethodOptions::suiteness_bonus_, core::scoring::rna::RNA_EnergyMethodOptions::syn_G_potential_bonus_, and core::scoring::rna::RNA_EnergyMethodOptions::torsion_potential_.

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

References core::conformation::Residue::annotated_name(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), rna_motif_bonus, to_string(), and core::scoring::rna::RNA_Motif::type().

Referenced by output_rna_motifs_detailed().

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

References core::scoring::rna::RNA_Motifs::get_motifs(), and output_rna_motif().

Size core::scoring::rna::protein_atom_name_to_num

(

std::string const &

name

)

Referenced by core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), and core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters().

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

)

References core::scoring::tr().

Referenced by core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters(), and core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW().

Size core::scoring::rna::rna_residue_type_to_num

(

chemical::ResidueType const &

rt

)

References core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), and core::scoring::tr().

Referenced by core::scoring::rna::RNA_AtomVDW::bump_parameter(), and core::scoring::rna::RNA_AtomVDW::bump_parameter_rnp().

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

References A_MINOR, BULGED_G, DOUBLE_T_LOOP, GA_MINOR, GNRA_TETRALOOP, INTERCALATED_T_LOOP, LOOP_E_SUBMOTIF, PLATFORM, STRICT_WC_STACKED_PAIR, T_LOOP, TANDEM_GA_SHEARED, TANDEM_GA_WATSON_CRICK, TETRALOOP_TL_RECEPTOR, TL_RECEPTOR, U_TURN, UA_HANDLE, WC_STACKED_PAIR, and Z_TURN.

Referenced by operator<<(), and output_rna_motif().

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" },
{ TANDEM_GA_WATSON_CRICK, "lime" },
{ GA_MINOR, "purple" },
{ DOUBLE_T_LOOP, "forest" }
}

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 },
{ INTERCALATED_T_LOOP, -1.0 },
{ LOOP_E_SUBMOTIF, -1.0 },
{ BULGED_G, -1.0 },
{ GNRA_TETRALOOP, -0.1 },  
{ STRICT_WC_STACKED_PAIR, 0.0 },
{ WC_STACKED_PAIR, 0.0 },
{ A_MINOR, -1.0 },
{ PLATFORM, -1.0 },
{ TL_RECEPTOR, -1.0 },
{ TETRALOOP_TL_RECEPTOR, -1.0 },
{ Z_TURN, -1.0 },
{ TANDEM_GA_SHEARED, -1.0 },
{ TANDEM_GA_WATSON_CRICK, -1.0 },
{ GA_MINOR, -1.0 },
{ DOUBLE_T_LOOP, -1.0 }
}

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