core::pose::rna::BasePair Class Reference

#include <BasePair.hh>

Inheritance diagram for core::pose::rna::BasePair:

Public Member Functions
	BasePair (Size const res1=0, Size const res2=0, core::chemical::rna::BaseEdge const edge1=core::chemical::rna::ANY_BASE_EDGE, core::chemical::rna::BaseEdge const edge2=core::chemical::rna::ANY_BASE_EDGE, core::chemical::rna::BaseDoubletOrientation const orientation=core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION)
	~BasePair () override
BasePair	flipped () const
void	print_info (std::ostream &out=std::cout) const
void	set_res1 (core::Size const &setting)
core::Size	res1 () const
void	set_res2 (core::Size const &setting)
core::Size	res2 () const
void	set_edge1 (core::chemical::rna::BaseEdge const &setting)
core::chemical::rna::BaseEdge	edge1 () const
void	set_edge2 (core::chemical::rna::BaseEdge const &setting)
core::chemical::rna::BaseEdge	edge2 () const
void	set_orientation (core::chemical::rna::BaseDoubletOrientation const &setting)
core::chemical::rna::BaseDoubletOrientation	orientation () const
core::chemical::rna::LW_BaseDoubletOrientation	LW_orientation () const

Private Member Functions
void	derive_LW_orientation ()

Private Attributes
Size	res1_
Size	res2_
core::chemical::rna::BaseEdge	edge1_
core::chemical::rna::BaseEdge	edge2_
core::chemical::rna::BaseDoubletOrientation	orientation_
core::chemical::rna::LW_BaseDoubletOrientation	LW_orientation_

Friends
bool	operator< (BasePair const &lhs, BasePair const &rhs)
bool	operator== (BasePair const &lhs, BasePair const &rhs)
std::ostream &	operator<< (std::ostream &out, BasePair const &s)

Constructor & Destructor Documentation

core::pose::rna::BasePair::BasePair	(	Size const	res1 = 0,
		Size const	res2 = 0,
		core::chemical::rna::BaseEdge const	edge1 = core::chemical::rna::ANY_BASE_EDGE,
		core::chemical::rna::BaseEdge const	edge2 = core::chemical::rna::ANY_BASE_EDGE,
		core::chemical::rna::BaseDoubletOrientation const	orientation = core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION
	)

References derive_LW_orientation().

Referenced by flipped().

core::pose::rna::BasePair::~BasePair ( )

inlineoverride

Member Function Documentation

void core::pose::rna::BasePair::derive_LW_orientation ( )

private

References core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_LW_BASE_DOUBLET_ORIENTATION, edge1_, edge2_, core::pose::rna::get_LW_orientation(), core::chemical::rna::HOOGSTEEN, LW_orientation_, orientation_, core::chemical::rna::PARALLEL, SUGAR, and core::chemical::rna::WATSON_CRICK.

Referenced by BasePair(), set_edge1(), set_edge2(), and set_orientation().

core::chemical::rna::BaseEdge core::pose::rna::BasePair::edge1 ( ) const

inline

References edge1_.

Referenced by protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score(), core::pose::rna::get_number_base_pairs(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

core::chemical::rna::BaseEdge core::pose::rna::BasePair::edge2 ( ) const

inline

References edge2_.

Referenced by protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score(), core::pose::rna::get_number_base_pairs(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

BasePair core::pose::rna::BasePair::flipped

(

)

const

References BasePair(), edge1_, edge2_, orientation_, res1_, and res2_.

Referenced by core::pose::rna::check_in_base_pair_list().

core::chemical::rna::LW_BaseDoubletOrientation core::pose::rna::BasePair::LW_orientation ( ) const

inline

References LW_orientation_.

core::chemical::rna::BaseDoubletOrientation core::pose::rna::BasePair::orientation ( ) const

inline

References orientation_.

Referenced by protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), and core::pose::rna::get_number_base_pairs().

void core::pose::rna::BasePair::print_info

(

std::ostream &

out = std::cout

)

const

References edge1_, edge2_, core::chemical::rna::get_full_edge_from_num(), core::chemical::rna::get_full_LW_orientation_from_num(), core::chemical::rna::get_full_orientation_from_num(), LW_orientation_, orientation_, res1_, and res2_.

core::Size core::pose::rna::BasePair::res1 ( ) const

inline

References res1_.

Referenced by core::pose::rna::base_pair_moving(), protocols::rna::denovo::check_base_pair(), core::import_pose::RNA_DeNovoParameters::check_in_pairing_sets(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score(), core::pose::rna::get_number_base_pairs(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

core::Size core::pose::rna::BasePair::res2 ( ) const

inline

References res2_.

Referenced by core::pose::rna::base_pair_moving(), protocols::rna::denovo::check_base_pair(), core::import_pose::RNA_DeNovoParameters::check_in_pairing_sets(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score(), core::pose::rna::get_number_base_pairs(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

void core::pose::rna::BasePair::set_edge1

(

core::chemical::rna::BaseEdge const &

setting

)

References derive_LW_orientation(), and edge1_.

Referenced by core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::import_pose::RNA_DeNovoParameters::get_pairings_from_line().

void core::pose::rna::BasePair::set_edge2

(

core::chemical::rna::BaseEdge const &

setting

)

References derive_LW_orientation(), and edge2_.

Referenced by core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::import_pose::RNA_DeNovoParameters::get_pairings_from_line().

void core::pose::rna::BasePair::set_orientation

(

core::chemical::rna::BaseDoubletOrientation const &

setting

)

References derive_LW_orientation(), and orientation_.

Referenced by core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::import_pose::RNA_DeNovoParameters::get_pairings_from_line().

void core::pose::rna::BasePair::set_res1 ( core::Size const &  setting )

inline

References res1_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_inf_base_pairs(), and core::import_pose::RNA_DeNovoParameters::get_pairings_from_line().

void core::pose::rna::BasePair::set_res2 ( core::Size const &  setting )

inline

References res2_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_inf_base_pairs(), and core::import_pose::RNA_DeNovoParameters::get_pairings_from_line().

Friends And Related Function Documentation

bool operator< ( BasePair const &  lhs, BasePair const &  rhs  )

friend

std::ostream& operator<< ( std::ostream &  out, BasePair const &  s  )

friend

bool operator== ( BasePair const &  lhs, BasePair const &  rhs  )

friend

Member Data Documentation

core::chemical::rna::BaseEdge core::pose::rna::BasePair::edge1_

private

Referenced by derive_LW_orientation(), edge1(), flipped(), core::pose::rna::operator<(), core::pose::rna::operator<<(), core::pose::rna::operator==(), print_info(), and set_edge1().

core::chemical::rna::BaseEdge core::pose::rna::BasePair::edge2_

private

Referenced by derive_LW_orientation(), edge2(), flipped(), core::pose::rna::operator<(), core::pose::rna::operator<<(), core::pose::rna::operator==(), print_info(), and set_edge2().

core::chemical::rna::LW_BaseDoubletOrientation core::pose::rna::BasePair::LW_orientation_

private

Referenced by derive_LW_orientation(), LW_orientation(), and print_info().

core::chemical::rna::BaseDoubletOrientation core::pose::rna::BasePair::orientation_

private

Referenced by derive_LW_orientation(), flipped(), core::pose::rna::operator<(), core::pose::rna::operator<<(), core::pose::rna::operator==(), orientation(), print_info(), and set_orientation().

Size core::pose::rna::BasePair::res1_

private

Referenced by flipped(), core::pose::rna::operator<(), core::pose::rna::operator<<(), core::pose::rna::operator==(), print_info(), res1(), and set_res1().

Size core::pose::rna::BasePair::res2_

private

Referenced by flipped(), core::pose::rna::operator<(), core::pose::rna::operator<<(), core::pose::rna::operator==(), print_info(), res2(), and set_res2().

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The documentation for this class was generated from the following files:

• src/core/pose/rna/BasePair.hh
• src/core/pose/rna/BasePair.cc