core::io::rna::RNA_DataReader Class Reference

#include <RNA_DataReader.hh>

Inheritance diagram for core::io::rna::RNA_DataReader:

Public Member Functions
	~RNA_DataReader () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	RNA_DataReader (std::string const &rna_data_file)
void	initialize (std::string const &rna_data_file)
void	fill_rna_data_info (core::pose::Pose &pose)
bool	has_reactivities ()

Private Member Functions
void	read_backbone_info (std::istringstream &line_stream, utility::vector1< Size > &backbone_res)
void	read_data_info (std::istringstream &line_stream)
void	read_data_from_file (std::string const &rna_data_file)
void	read_reactivity_info (std::istringstream &line_stream, pose::rna::RNA_ReactivityType const type)
void	get_reactivity_from_rdat (core::io::rna::RDAT const &rdat, pose::rna::RNA_ReactivityType const &type, std::string const &modifier_name)
void	read_data_from_rdat (std::string const &filename)
ObjexxFCL::FArray1D< bool >	fill_backbone_array (utility::vector1< Size > const &backbone_res, core::pose::Pose const &pose)

Private Attributes
pose::rna::RNA_DataInfoOP	rna_data_info_with_conventional_numbering_
utility::vector1< Size >	backbone_burial_res_
utility::vector1< Size >	backbone_exposed_res_

Constructor & Destructor Documentation

~RNA_DataReader()

core::io::rna::RNA_DataReader::~RNA_DataReader ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

RNA_DataReader()

core::io::rna::RNA_DataReader::RNA_DataReader

(

std::string const &

rna_data_file

)

Member Function Documentation

fill_backbone_array()

ObjexxFCL::FArray1D< bool > core::io::rna::RNA_DataReader::fill_backbone_array ( utility::vector1< Size > const &  backbone_res, core::pose::Pose const &  pose  )

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), and core::pose::Pose::size().

fill_rna_data_info()

void core::io::rna::RNA_DataReader::fill_rna_data_info

(

core::pose::Pose &

pose

)

References core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::nonconst_full_model_info(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::rna::RNA_Reactivity::position(), core::scoring::rna::RNA_ScoringInfo::rna_data_info(), and core::pose::rna::RNA_Reactivity::set_position().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), 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().

get_reactivity_from_rdat()

void core::io::rna::RNA_DataReader::get_reactivity_from_rdat ( core::io::rna::RDAT const &  rdat, pose::rna::RNA_ReactivityType const &  type, std::string const &  modifier_name  )

private

References core::io::rna::RDAT::annotations(), core::io::rna::RDAT::data_annotations(), core::io::rna::get_tag(), core::io::rna::get_tags(), core::io::rna::RDAT::reactivity(), and core::io::rna::RDAT::seqpos().

has_reactivities()

bool core::io::rna::RNA_DataReader::has_reactivities ( )

inline

References rna_data_info_with_conventional_numbering_.

initialize()

void core::io::rna::RNA_DataReader::initialize

(

std::string const &

rna_data_file

)

read_backbone_info()

void core::io::rna::RNA_DataReader::read_backbone_info ( std::istringstream &  line_stream, utility::vector1< Size > &  backbone_res  )

private

read_data_from_file()

void core::io::rna::RNA_DataReader::read_data_from_file ( std::string const &  rna_data_file )

private

References core::pose::rna::DMS, protocols::abinitio::filename(), and core::io::rna::TR().

read_data_from_rdat()

void core::io::rna::RNA_DataReader::read_data_from_rdat ( std::string const &  filename )

private

References core::pose::rna::DMS, and protocols::abinitio::filename().

read_data_info()

void core::io::rna::RNA_DataReader::read_data_info ( std::istringstream &  line_stream )

private

References core::chemical::rna::HOOGSTEEN, SUGAR, and core::chemical::rna::WATSON_CRICK.

read_reactivity_info()

void core::io::rna::RNA_DataReader::read_reactivity_info ( std::istringstream &  line_stream, pose::rna::RNA_ReactivityType const  type  )

private

Member Data Documentation

backbone_burial_res_

utility::vector1< Size > core::io::rna::RNA_DataReader::backbone_burial_res_

private

backbone_exposed_res_

utility::vector1< Size > core::io::rna::RNA_DataReader::backbone_exposed_res_

private

rna_data_info_with_conventional_numbering_

pose::rna::RNA_DataInfoOP core::io::rna::RNA_DataReader::rna_data_info_with_conventional_numbering_

private

Referenced by has_reactivities().

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

• src/core/io/rna/RNA_DataReader.hh
• src/core/io/rna/RNA_DataReader.cc