#include <RDAT.hh>

Inheritance diagram for core::io::rna::RDAT:

Public Member Functions
	RDAT ()

	RDAT (std::string const &filename)

	RDAT (std::string const &name, std::string const &sequence, core::Size const offset, utility::vector1< Size > const &seqpos, std::string const &structure, utility::vector1< Annotation > const &annotations, utility::vector1< utility::vector1< Annotation > > const &data_annotations, utility::vector1< utility::vector1< core::Real > > const &reactivity, utility::vector1< utility::vector1< core::Real > > const &reactivity_error, utility::vector1< std::string > const &comments)

	~RDAT () override

void	output_rdat_to_file (std::string const &filename) const

void	read_rdat_file (std::string const &filename)

void	fill_header_information (pose::Pose &pose)

void	fill_data_from_features (utility::vector1< char > const &seqchars, utility::vector1< core::Size > const &resnums, utility::vector1< std::string > const &feature_names, utility::vector1< utility::vector1< core::Real > > const &all_feature_vals)

void	output_data (utility::io::ozstream &out) const

bool	check_rdat () const

std::string const &	version () const

std::string const &	name () const

std::string const &	sequence () const

std::string const &	structure () const

utility::vector1< std::string > const &	sequences () const

utility::vector1< std::string > const &	structures () const

int const &	offset () const

utility::vector1< int > const &	seqpos () const

utility::vector1< Annotation > const &	annotations () const

utility::vector1< utility::vector1< Annotation > > const &	data_annotations () const

utility::vector1< utility::vector1< core::Real > > const &	reactivity () const

utility::vector1< utility::vector1< core::Real > > const &	reactivity_error () const

utility::vector1< std::string > const &	comments () const

utility::vector1< core::Real > const &	xsel () const

utility::vector1< utility::vector1< core::Real > > const &	xsel_refine () const

utility::vector1< utility::vector1< core::Real > > const &	trace () const

void	set_version (std::string const &setting)

void	set_name (std::string const &setting)

void	set_sequence (std::string const &setting)

void	set_structure (std::string const &setting)

void	set_sequences (utility::vector1< std::string > const &setting)

void	set_structures (utility::vector1< std::string > const &setting)

void	set_offset (int const &setting)

void	set_seqpos (utility::vector1< int > const &setting)

void	set_annotations (utility::vector1< Annotation > const &setting)

void	set_data_annotations (utility::vector1< utility::vector1< Annotation > > const &setting)

void	set_reactivity (utility::vector1< utility::vector1< core::Real > > const &setting)

void	set_reactivity_error (utility::vector1< utility::vector1< core::Real > > const &setting)

void	set_comments (utility::vector1< std::string > const &setting)

void	set_xsel (utility::vector1< core::Real > const &setting)

void	set_xsel_refine (utility::vector1< utility::vector1< core::Real > > const &setting)

void	set_trace (utility::vector1< utility::vector1< core::Real > > const &setting)

Private Member Functions
void	output_rdat_header (utility::io::ozstream &out) const

void	fill_sequences_and_structures ()

void	fill_sequences_if_empty ()

void	fill_structures_if_empty ()

void	fill_if_empty (std::string &data_string, utility::vector1< std::string > &data_strings, std::string const &tag) const

void	save_data (std::string const &line, utility::vector1< utility::vector1< Real > > &var) const

void	save_data (std::string const &line, utility::vector1< Real > &var) const

void	save_data_with_idx (utility::vector1< std::string > &var, Size const &idx, std::string const &value) const

void	save_data_with_idx (utility::vector1< utility::vector1< Annotation > > &var, Size const &idx, Annotation &value) const

Annotation	get_annotation (std::string const &tag) const

utility::vector1< std::string >	str2cell (std::string const &s) const

std::string	remove_tag (std::string &line, std::string const &tag) const

void	fill_data_annotations_if_empty ()

void	fill_seqpos (std::string const &seqpos_info, std::string &sequence_seqpos)

bool	check_sequence_seqpos (std::string const &sequence_seqpos) const

bool	check_annotations (utility::vector1< Annotation > const &annotations) const

bool	check_annotation (Annotation const &annotation) const

Private Attributes
std::string	version_

std::string	name_

std::string	sequence_

std::string	structure_

utility::vector1< std::string >	sequences_

utility::vector1< std::string >	structures_

int	offset_

utility::vector1< int >	seqpos_

utility::vector1< Annotation >	annotations_

utility::vector1< utility::vector1< Annotation > >	data_annotations_

utility::vector1< utility::vector1< core::Real > >	reactivity_

utility::vector1< utility::vector1< core::Real > >	reactivity_error_

utility::vector1< std::string >	comments_

utility::vector1< core::Real >	xsel_

utility::vector1< utility::vector1< core::Real > >	xsel_refine_

utility::vector1< utility::vector1< core::Real > >	trace_

Constructor & Destructor Documentation

◆ RDAT() [1/3]

core::io::rna::RDAT::RDAT ( )

◆ RDAT() [2/3]

core::io::rna::RDAT::RDAT ( std::string const & filename )

References protocols::abinitio::filename(), and read_rdat_file().

◆ RDAT() [3/3]

core::io::rna::RDAT::RDAT	(	std::string const &	name,
		std::string const &	sequence,
		core::Size const	offset,
		utility::vector1< Size > const &	seqpos,
		std::string const &	structure,
		utility::vector1< Annotation > const &	annotations,
		utility::vector1< utility::vector1< Annotation > > const &	data_annotations,
		utility::vector1< utility::vector1< core::Real > > const &	reactivity,
		utility::vector1< utility::vector1< core::Real > > const &	reactivity_error,
		utility::vector1< std::string > const &	comments
	)

References check_rdat(), and fill_sequences_and_structures().

◆ ~RDAT()

core::io::rna::RDAT::~RDAT ( )

overridedefault

Member Function Documentation

◆ annotations()

utility::vector1< Annotation > const& core::io::rna::RDAT::annotations ( ) const

inline

References annotations_.

Referenced by check_annotations(), and core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

◆ check_annotation()

bool core::io::rna::RDAT::check_annotation ( Annotation const & annotation ) const

private

References core::io::rna::ok_annotations.

Referenced by check_annotations().

◆ check_annotations()

bool core::io::rna::RDAT::check_annotations ( utility::vector1< Annotation > const & annotations ) const

private

References annotations(), check_annotation(), and core::io::rna::TR().

Referenced by check_rdat().

◆ check_rdat()

bool core::io::rna::RDAT::check_rdat ( ) const

References annotations_, check_annotations(), data_annotations_, name_, offset_, reactivity_, seqpos_, sequence_, core::io::rna::TR(), xsel_, and xsel_refine_.

Referenced by RDAT(), and read_rdat_file().

◆ check_sequence_seqpos()

bool core::io::rna::RDAT::check_sequence_seqpos ( std::string const & sequence_seqpos ) const

private

References offset_, seqpos_, sequence_, and core::io::rna::TR().

Referenced by read_rdat_file().

◆ comments()

utility::vector1< std::string > const& core::io::rna::RDAT::comments ( ) const

inline

References comments_.

◆ data_annotations()

utility::vector1< utility::vector1< Annotation > > const& core::io::rna::RDAT::data_annotations ( ) const

inline

References data_annotations_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

◆ fill_data_annotations_if_empty()

void core::io::rna::RDAT::fill_data_annotations_if_empty ( )

private

References data_annotations_, and reactivity_.

Referenced by read_rdat_file().

◆ fill_data_from_features()

void core::io::rna::RDAT::fill_data_from_features	(	utility::vector1< char > const &	seqchars,
		utility::vector1< core::Size > const &	resnums,
		utility::vector1< std::string > const &	feature_names,
		utility::vector1< utility::vector1< core::Real > > const &	all_feature_vals
	)

References data_annotations_, offset_, reactivity_, seqpos_, and sequence_.

◆ fill_header_information()

void core::io::rna::RDAT::fill_header_information ( pose::Pose & pose )

References annotations_, comments_, core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), name_, offset_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), sequence_, core::pose::Pose::size(), and structure_.

◆ fill_if_empty()

void core::io::rna::RDAT::fill_if_empty	(	std::string &	data_string,
		utility::vector1< std::string > &	data_strings,
		std::string const &	tag
	)		const

private

References core::io::rna::TR().

Referenced by read_rdat_file().

◆ fill_seqpos()

void core::io::rna::RDAT::fill_seqpos	(	std::string const &	seqpos_info,
		std::string &	sequence_seqpos
	)

private

References core::io::rna::numbers, seqpos_, and str2cell().

Referenced by read_rdat_file().

◆ fill_sequences_and_structures()

void core::io::rna::RDAT::fill_sequences_and_structures ( )

private

References fill_sequences_if_empty(), and fill_structures_if_empty().

Referenced by RDAT(), and read_rdat_file().

◆ fill_sequences_if_empty()

void core::io::rna::RDAT::fill_sequences_if_empty ( )

private

References data_annotations_, core::io::rna::numbers, offset_, core::chemical::rings::q, reactivity_, save_data_with_idx(), sequence_, sequences_, and core::io::rna::TR().

Referenced by fill_sequences_and_structures().

◆ fill_structures_if_empty()

void core::io::rna::RDAT::fill_structures_if_empty ( )

private

References data_annotations_, reactivity_, save_data_with_idx(), structure_, and structures_.

Referenced by fill_sequences_and_structures().

◆ get_annotation()

Annotation core::io::rna::RDAT::get_annotation ( std::string const & tag ) const

private

Referenced by read_rdat_file().

◆ name()

std::string const& core::io::rna::RDAT::name ( ) const

inline

References name_.

◆ offset()

int const& core::io::rna::RDAT::offset ( ) const

inline

References offset_.

◆ output_data()

void core::io::rna::RDAT::output_data ( utility::io::ozstream & out ) const

References data_annotations_, offset_, core::conformation::membrane::out, reactivity_, reactivity_error_, seqpos_, and sequence_.

Referenced by output_rdat_to_file().

◆ output_rdat_header()

void core::io::rna::RDAT::output_rdat_header ( utility::io::ozstream & out ) const

private

References annotations_, comments_, name_, offset_, core::conformation::membrane::out, sequence_, structure_, and version_.

Referenced by output_rdat_to_file().

◆ output_rdat_to_file()

void core::io::rna::RDAT::output_rdat_to_file ( std::string const & filename ) const

References core::conformation::membrane::out, output_data(), output_rdat_header(), and core::io::rna::TR().

◆ reactivity()

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::reactivity ( ) const

inline

References reactivity_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

◆ reactivity_error()

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::reactivity_error ( ) const

inline

References reactivity_error_.

◆ read_rdat_file()

void core::io::rna::RDAT::read_rdat_file ( std::string const & filename )

◆ remove_tag()

std::string core::io::rna::RDAT::remove_tag	(	std::string &	line,
		std::string const &	tag
	)		const

private

Referenced by read_rdat_file().

◆ save_data() [1/2]

void core::io::rna::RDAT::save_data	(	std::string const &	line,
		utility::vector1< Real > &	var
	)		const

private

References str2cell().

◆ save_data() [2/2]

void core::io::rna::RDAT::save_data	(	std::string const &	line,
		utility::vector1< utility::vector1< Real > > &	var
	)		const

private

References str2cell().

Referenced by read_rdat_file().

◆ save_data_with_idx() [1/2]

void core::io::rna::RDAT::save_data_with_idx	(	utility::vector1< std::string > &	var,
		Size const &	idx,
		std::string const &	value
	)		const

private

Referenced by fill_sequences_if_empty(), fill_structures_if_empty(), and read_rdat_file().

◆ save_data_with_idx() [2/2]

void core::io::rna::RDAT::save_data_with_idx	(	utility::vector1< utility::vector1< Annotation > > &	var,
		Size const &	idx,
		Annotation &	value
	)		const

private

◆ seqpos()

utility::vector1< int > const& core::io::rna::RDAT::seqpos ( ) const

inline

References seqpos_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

◆ sequence()

std::string const& core::io::rna::RDAT::sequence ( ) const

inline

References sequence_.

◆ sequences()

utility::vector1< std::string > const& core::io::rna::RDAT::sequences ( ) const

inline

References sequences_.

◆ set_annotations()

void core::io::rna::RDAT::set_annotations ( utility::vector1< Annotation > const & setting )

inline

References annotations_.

◆ set_comments()

void core::io::rna::RDAT::set_comments ( utility::vector1< std::string > const & setting )

inline

References comments_.

◆ set_data_annotations()

void core::io::rna::RDAT::set_data_annotations ( utility::vector1< utility::vector1< Annotation > > const & setting )

inline

References data_annotations_.

◆ set_name()

void core::io::rna::RDAT::set_name ( std::string const & setting )

inline

References name_.

◆ set_offset()

void core::io::rna::RDAT::set_offset ( int const & setting )

inline

References offset_.

◆ set_reactivity()

void core::io::rna::RDAT::set_reactivity ( utility::vector1< utility::vector1< core::Real > > const & setting )

inline

References reactivity_.

◆ set_reactivity_error()

void core::io::rna::RDAT::set_reactivity_error ( utility::vector1< utility::vector1< core::Real > > const & setting )

inline

References reactivity_error_.

◆ set_seqpos()

void core::io::rna::RDAT::set_seqpos ( utility::vector1< int > const & setting )

inline

References seqpos_.

◆ set_sequence()

void core::io::rna::RDAT::set_sequence ( std::string const & setting )

inline

References sequence_.

◆ set_sequences()

void core::io::rna::RDAT::set_sequences ( utility::vector1< std::string > const & setting )

inline

References sequences_.

◆ set_structure()

void core::io::rna::RDAT::set_structure ( std::string const & setting )

inline

References structure_.

◆ set_structures()

void core::io::rna::RDAT::set_structures ( utility::vector1< std::string > const & setting )

inline

References structures_.

◆ set_trace()

void core::io::rna::RDAT::set_trace ( utility::vector1< utility::vector1< core::Real > > const & setting )

inline

References trace_.

◆ set_version()

void core::io::rna::RDAT::set_version ( std::string const & setting )

inline

References version_.

◆ set_xsel()

void core::io::rna::RDAT::set_xsel ( utility::vector1< core::Real > const & setting )

inline

References xsel_.

◆ set_xsel_refine()

void core::io::rna::RDAT::set_xsel_refine ( utility::vector1< utility::vector1< core::Real > > const & setting )

inline

References xsel_refine_.

◆ str2cell()

utility::vector1< std::string > core::io::rna::RDAT::str2cell ( std::string const & s ) const

private

Referenced by fill_seqpos(), read_rdat_file(), and save_data().

◆ structure()

std::string const& core::io::rna::RDAT::structure ( ) const

inline

References structure_.

◆ structures()

utility::vector1< std::string > const& core::io::rna::RDAT::structures ( ) const

inline

References structures_.

◆ trace()

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::trace ( ) const

inline

References trace_.

◆ version()

std::string const& core::io::rna::RDAT::version ( ) const

inline

References version_.

◆ xsel()

utility::vector1< core::Real > const& core::io::rna::RDAT::xsel ( ) const

inline

References xsel_.

◆ xsel_refine()

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::xsel_refine ( ) const

inline

References xsel_refine_.

Member Data Documentation

◆ annotations_

utility::vector1< Annotation > core::io::rna::RDAT::annotations_

private

Referenced by annotations(), check_rdat(), fill_header_information(), output_rdat_header(), read_rdat_file(), and set_annotations().

◆ comments_

utility::vector1< std::string > core::io::rna::RDAT::comments_

private

Referenced by comments(), fill_header_information(), output_rdat_header(), read_rdat_file(), and set_comments().

◆ data_annotations_

utility::vector1< utility::vector1< Annotation > > core::io::rna::RDAT::data_annotations_

private

Referenced by check_rdat(), data_annotations(), fill_data_annotations_if_empty(), fill_data_from_features(), fill_sequences_if_empty(), fill_structures_if_empty(), output_data(), read_rdat_file(), and set_data_annotations().

◆ name_

std::string core::io::rna::RDAT::name_

private

Referenced by check_rdat(), fill_header_information(), name(), output_rdat_header(), read_rdat_file(), and set_name().

◆ offset_

int core::io::rna::RDAT::offset_

private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_header_information(), fill_sequences_if_empty(), offset(), output_data(), output_rdat_header(), read_rdat_file(), and set_offset().

◆ reactivity_

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::reactivity_

private

Referenced by check_rdat(), fill_data_annotations_if_empty(), fill_data_from_features(), fill_sequences_if_empty(), fill_structures_if_empty(), output_data(), reactivity(), read_rdat_file(), and set_reactivity().

◆ reactivity_error_

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::reactivity_error_

private

Referenced by output_data(), reactivity_error(), read_rdat_file(), and set_reactivity_error().

◆ seqpos_

utility::vector1< int > core::io::rna::RDAT::seqpos_

private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_seqpos(), output_data(), seqpos(), and set_seqpos().

◆ sequence_

std::string core::io::rna::RDAT::sequence_

private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_header_information(), fill_sequences_if_empty(), output_data(), output_rdat_header(), read_rdat_file(), sequence(), and set_sequence().

◆ sequences_

utility::vector1< std::string > core::io::rna::RDAT::sequences_

private

Referenced by fill_sequences_if_empty(), read_rdat_file(), sequences(), and set_sequences().

◆ structure_

std::string core::io::rna::RDAT::structure_

private

Referenced by fill_header_information(), fill_structures_if_empty(), output_rdat_header(), read_rdat_file(), set_structure(), and structure().

◆ structures_

utility::vector1< std::string > core::io::rna::RDAT::structures_

private

Referenced by fill_structures_if_empty(), read_rdat_file(), set_structures(), and structures().

◆ trace_

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::trace_

private

Referenced by read_rdat_file(), set_trace(), and trace().

◆ version_

std::string core::io::rna::RDAT::version_

private

Referenced by output_rdat_header(), read_rdat_file(), set_version(), and version().

◆ xsel_

utility::vector1< core::Real > core::io::rna::RDAT::xsel_

private

Referenced by check_rdat(), read_rdat_file(), set_xsel(), and xsel().

◆ xsel_refine_

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::xsel_refine_

private

Referenced by check_rdat(), set_xsel_refine(), and xsel_refine().

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

src/core/io/rna/RDAT.hh
src/core/io/rna/RDAT.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ RDAT() [1/3]

◆ RDAT() [2/3]

◆ RDAT() [3/3]

◆ ~RDAT()

Member Function Documentation

◆ annotations()

◆ check_annotation()

◆ check_annotations()

◆ check_rdat()

◆ check_sequence_seqpos()

◆ comments()

◆ data_annotations()

◆ fill_data_annotations_if_empty()

◆ fill_data_from_features()

◆ fill_header_information()

◆ fill_if_empty()

◆ fill_seqpos()

◆ fill_sequences_and_structures()

◆ fill_sequences_if_empty()

◆ fill_structures_if_empty()

◆ get_annotation()

◆ name()

◆ offset()

◆ output_data()

◆ output_rdat_header()

◆ output_rdat_to_file()

◆ reactivity()

◆ reactivity_error()

◆ read_rdat_file()

◆ remove_tag()

◆ save_data() [1/2]

◆ save_data() [2/2]

◆ save_data_with_idx() [1/2]

◆ save_data_with_idx() [2/2]

◆ seqpos()

◆ sequence()

◆ sequences()

◆ set_annotations()

◆ set_comments()

◆ set_data_annotations()

◆ set_name()

◆ set_offset()

◆ set_reactivity()

◆ set_reactivity_error()

◆ set_seqpos()

◆ set_sequence()

◆ set_sequences()

◆ set_structure()

◆ set_structures()

◆ set_trace()

◆ set_version()

◆ set_xsel()

◆ set_xsel_refine()

◆ str2cell()

◆ structure()

◆ structures()

◆ trace()

◆ version()

◆ xsel()

◆ xsel_refine()

Member Data Documentation

◆ annotations_

◆ comments_

◆ data_annotations_

◆ name_

◆ offset_

◆ reactivity_

◆ reactivity_error_

◆ seqpos_

◆ sequence_

◆ sequences_

◆ structure_

◆ structures_

◆ trace_

◆ version_

◆ xsel_