core::import_pose::RNA_BasePairHandler Class Reference

#include <RNA_BasePairHandler.hh>

Inheritance diagram for core::import_pose::RNA_BasePairHandler:

Public Member Functions
	RNA_BasePairHandler (core::pose::Pose const &pose)
	RNA_BasePairHandler (core::import_pose::RNA_DeNovoParameters const &rna_params)
	~RNA_BasePairHandler () override
bool	check_base_pairs (core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map) const
std::map< Size, Size >	connections () const
void	setup_base_pair_constraints (core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::Real const suppress_bp_constraint=1.0) const
core::pose::rna::RNA_BasePairList	rna_pairing_list () const
utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const &	chain_connections () const
utility::vector1< Size >	get_stem_residues (core::pose::Pose const &pose) const
utility::vector1< core::pose::rna::BasePairStep >	get_canonical_base_pair_steps () const
utility::vector1< core::pose::rna::BasePairStep >	get_noncanonical_base_pair_steps () const
utility::vector1< core::pose::rna::BasePairStep >	get_base_pair_steps (bool const just_canonical) const

Private Member Functions
void	figure_out_partner (std::map< Size, Size > &partner, bool const force_canonical) const

Private Attributes
core::pose::rna::RNA_BasePairList	rna_pairing_list_
utility::vector1< Size >	cutpoints_open_
utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > >	chain_connections_

Constructor & Destructor Documentation

RNA_BasePairHandler() [1/2]

core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler

(

core::pose::Pose const &

pose

)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

RNA_BasePairHandler() [2/2]

core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler

(

core::import_pose::RNA_DeNovoParameters const &

rna_params

)

References core::import_pose::RNA_DeNovoParameters::chain_connections(), core::import_pose::RNA_DeNovoParameters::cutpoints_open(), and core::import_pose::RNA_DeNovoParameters::rna_pairing_list().

~RNA_BasePairHandler()

core::import_pose::RNA_BasePairHandler::~RNA_BasePairHandler ( )

overridedefault

Member Function Documentation

chain_connections()

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > const& core::import_pose::RNA_BasePairHandler::chain_connections ( ) const

inline

References chain_connections_.

check_base_pairs()

bool core::import_pose::RNA_BasePairHandler::check_base_pairs	(	core::pose::Pose &	pose,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map
	)		const

References core::chemical::rna::ANTIPARALLEL, core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::is_cutpoint_open(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), core::pose::TR(), and core::chemical::rna::WATSON_CRICK.

connections()

std::map< Size, Size > core::import_pose::RNA_BasePairHandler::connections

(

)

const

figure_out_partner()

void core::import_pose::RNA_BasePairHandler::figure_out_partner ( std::map< Size, Size > &  partner, bool const  force_canonical  ) const

private

References core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, core::pose::TR(), and core::chemical::rna::WATSON_CRICK.

get_base_pair_steps()

utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_base_pair_steps

(

bool const

just_canonical

)

const

References core::import_pose::MAX_BULGE_LENGTH(), and core::chemical::rings::q.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

get_canonical_base_pair_steps()

utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_canonical_base_pair_steps

(

)

const

get_noncanonical_base_pair_steps()

utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_noncanonical_base_pair_steps

(

)

const

get_stem_residues()

utility::vector1< Size > core::import_pose::RNA_BasePairHandler::get_stem_residues

(

core::pose::Pose const &

pose

)

const

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::possibly_canonical(), core::pose::Pose::residue(), and core::chemical::rna::WATSON_CRICK.

rna_pairing_list()

core::pose::rna::RNA_BasePairList core::import_pose::RNA_BasePairHandler::rna_pairing_list ( ) const

inline

References rna_pairing_list_.

setup_base_pair_constraints()

void core::import_pose::RNA_BasePairHandler::setup_base_pair_constraints	(	core::pose::Pose &	pose,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map,
		core::Real const	suppress_bp_constraint = 1.0
	)		const

References core::chemical::rna::ANTIPARALLEL, core::chemical::element::I, core::chemical::ResidueTypeBase::is_RNA(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), core::pose::rna::setup_base_pair_constraints(), core::pose::TR(), and core::chemical::rna::WATSON_CRICK.

Member Data Documentation

chain_connections_

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > core::import_pose::RNA_BasePairHandler::chain_connections_

private

Referenced by chain_connections().

cutpoints_open_

utility::vector1< Size > core::import_pose::RNA_BasePairHandler::cutpoints_open_

private

rna_pairing_list_

core::pose::rna::RNA_BasePairList core::import_pose::RNA_BasePairHandler::rna_pairing_list_

private

Referenced by rna_pairing_list().

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

• src/core/import_pose/RNA_BasePairHandler.hh
• src/core/import_pose/RNA_BasePairHandler.cc