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core::import_pose::RNA_BasePairHandler Class Reference

#include <RNA_BasePairHandler.hh>

Inheritance diagram for core::import_pose::RNA_BasePairHandler:
Inheritance graph
[legend]

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, Sizeconnections () 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< Sizeget_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< Sizecutpoints_open_
 
utility::vector1< std::pair
< utility::vector1< core::Size >
, utility::vector1< core::Size > > > 
chain_connections_
 

Constructor & Destructor Documentation

core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler ( core::pose::Pose const &  pose)
core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler ( core::import_pose::RNA_DeNovoParameters const &  rna_params)
core::import_pose::RNA_BasePairHandler::~RNA_BasePairHandler ( )
overridedefault

Member Function Documentation

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_.

bool core::import_pose::RNA_BasePairHandler::check_base_pairs ( core::pose::Pose pose,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map 
) const
std::map< Size, Size > core::import_pose::RNA_BasePairHandler::connections ( ) const
void core::import_pose::RNA_BasePairHandler::figure_out_partner ( std::map< Size, Size > &  partner,
bool const  force_canonical 
) const
private
utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_base_pair_steps ( bool const  just_canonical) const
utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_canonical_base_pair_steps ( ) const
utility::vector1< BasePairStep > core::import_pose::RNA_BasePairHandler::get_noncanonical_base_pair_steps ( ) const
utility::vector1< Size > core::import_pose::RNA_BasePairHandler::get_stem_residues ( core::pose::Pose const &  pose) const
core::pose::rna::RNA_BasePairList core::import_pose::RNA_BasePairHandler::rna_pairing_list ( ) const
inline

References rna_pairing_list_.

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

Member Data Documentation

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

Referenced by chain_connections().

utility::vector1< Size > core::import_pose::RNA_BasePairHandler::cutpoints_open_
private
core::pose::rna::RNA_BasePairList core::import_pose::RNA_BasePairHandler::rna_pairing_list_
private

Referenced by rna_pairing_list().


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