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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::pose::rna::RNA_SecStruct Class Reference

#include <RNA_SecStruct.hh>

Inheritance diagram for core::pose::rna::RNA_SecStruct:
Inheritance graph
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Public Member Functions

 RNA_SecStruct (std::string const &secstruct, std::string const &secstruct_file="", std::string const &sequence="")
 
 RNA_SecStruct (pose::Pose const &pose)
 
 RNA_SecStruct ()
 
 ~RNA_SecStruct () override
 
utility::vector1< std::pair
< core::Size, core::Size > > 		base_pairs () const
 
utility::vector1
< utility::vector1< std::pair
< core::Size, core::Size > > > 		stems () const
 
void check_compatible_with_sequence (std::string const &sequence_in, bool const check_complementarity=true) const
 
core::Size size () const
 
std::string secstruct () const
 
void remove_pair (std::pair< core::Size, core::Size > pair)
 
bool blank () const
 
bool in_helix (core::Size const &i) const
 
bool in_same_helix (core::Size const &i, core::Size const &j) const
 
void remove_singlet_base_pairs ()
 

Private Member Functions

void set_secstruct (std::string const &secstruct)
 
void set_basepairs_from_secstruct ()
 
bool check_balanced_secstruct () const
 
void blank_secstruct (std::string const &sequence_in)
 
void read_secstruct_from_file (std::string const &filename)
 
void figure_out_stems ()
 

Private Attributes

std::string secstruct_
 
utility::vector1< std::pair
< core::Size, core::Size > > 		base_pairs_
 
utility::vector1
< utility::vector1< std::pair
< core::Size, core::Size > > > 		stems_
 
utility::vector1< Size > spacer_positions_
 
std::map< char,
utility::vector1< char > > 		rna_complement_
 

Constructor & Destructor Documentation

core::pose::rna::RNA_SecStruct::RNA_SecStruct ( std::string const &  secstruct,
std::string const &  secstruct_file = "",
std::string const &  sequence = "" 
)

References blank_secstruct(), check_balanced_secstruct(), figure_out_stems(), read_secstruct_from_file(), rna_complement_, secstruct_, set_basepairs_from_secstruct(), set_secstruct(), and core::pose::TR().

core::pose::rna::RNA_SecStruct::RNA_SecStruct ( pose::Pose const &  pose)
core::pose::rna::RNA_SecStruct::RNA_SecStruct ( )
inline
core::pose::rna::RNA_SecStruct::~RNA_SecStruct ( )
overridedefault

Member Function Documentation

utility::vector1< std::pair< core::Size, core::Size > > core::pose::rna::RNA_SecStruct::base_pairs ( ) const
inline

References base_pairs_.

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::recces::recces_pose_setup(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_obligate_pair().

bool core::pose::rna::RNA_SecStruct::blank ( ) const

References secstruct_.

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::check_secstructs(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag(), protocols::recces::sampler::get_recces_turner_sampler(), and protocols::recces::set_gaussian_stdevs_recces_turner().

void core::pose::rna::RNA_SecStruct::blank_secstruct ( std::string const &  sequence_in)
private

References secstruct_, spacer_positions_, and core::sequence::strip_spacers().

Referenced by RNA_SecStruct().

bool core::pose::rna::RNA_SecStruct::check_balanced_secstruct ( ) const
private

References secstruct_.

Referenced by RNA_SecStruct().

void core::pose::rna::RNA_SecStruct::check_compatible_with_sequence ( std::string const &  sequence_in,
bool const  check_complementarity = true 
) const

References protocols::comparative_modeling::features::A, base_pairs_, core::chemical::element::I, core::scoring::pair, rna_complement_, secstruct_, core::sequence::strip_spacers(), and core::pose::TR().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::check_secstructs(), and core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options().

void core::pose::rna::RNA_SecStruct::figure_out_stems ( )
private

References base_pairs_, spacer_positions_, stems(), and stems_.

Referenced by RNA_SecStruct().

bool core::pose::rna::RNA_SecStruct::in_helix ( core::Size const &  i) const

References base_pairs_, and core::scoring::pair.

Referenced by protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), and protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct().

bool core::pose::rna::RNA_SecStruct::in_same_helix ( core::Size const &  i,
core::Size const &  j 
) const

References core::scoring::pair, and stems_.

Referenced by protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), and protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct().

void core::pose::rna::RNA_SecStruct::read_secstruct_from_file ( std::string const &  filename)
private

References secstruct(), set_secstruct(), and core::pose::TR().

Referenced by RNA_SecStruct().

void core::pose::rna::RNA_SecStruct::remove_pair ( std::pair< core::Size, core::Size >  pair)

References base_pairs_, core::scoring::pair, and secstruct_.

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag().

void core::pose::rna::RNA_SecStruct::remove_singlet_base_pairs ( )
std::string core::pose::rna::RNA_SecStruct::secstruct ( ) const
inline

References secstruct_.

Referenced by read_secstruct_from_file(), set_secstruct(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map().

void core::pose::rna::RNA_SecStruct::set_basepairs_from_secstruct ( )
private

References base_pairs_, secstruct_, and core::sequence::spacers.

Referenced by RNA_SecStruct().

void core::pose::rna::RNA_SecStruct::set_secstruct ( std::string const &  secstruct)
private

References secstruct(), secstruct_, spacer_positions_, and core::sequence::strip_spacers().

Referenced by read_secstruct_from_file(), and RNA_SecStruct().

core::Size core::pose::rna::RNA_SecStruct::size ( ) const
inline

References secstruct_.

Referenced by protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct().

utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > core::pose::rna::RNA_SecStruct::stems ( ) const
inline

References stems_.

Referenced by core::import_pose::dump_stems(), and figure_out_stems().

Member Data Documentation

utility::vector1< std::pair< core::Size, core::Size > > core::pose::rna::RNA_SecStruct::base_pairs_
private

Referenced by base_pairs(), check_compatible_with_sequence(), figure_out_stems(), in_helix(), remove_pair(), and set_basepairs_from_secstruct().

std::map< char, utility::vector1< char > > core::pose::rna::RNA_SecStruct::rna_complement_
private

Referenced by check_compatible_with_sequence(), and RNA_SecStruct().

std::string core::pose::rna::RNA_SecStruct::secstruct_
private

Referenced by blank(), blank_secstruct(), check_balanced_secstruct(), check_compatible_with_sequence(), remove_pair(), RNA_SecStruct(), secstruct(), set_basepairs_from_secstruct(), set_secstruct(), and size().

utility::vector1< Size > core::pose::rna::RNA_SecStruct::spacer_positions_
private

Referenced by blank_secstruct(), figure_out_stems(), and set_secstruct().

utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > core::pose::rna::RNA_SecStruct::stems_
private

Referenced by figure_out_stems(), in_same_helix(), and stems().

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