core::io::rna::RDAT Class Reference

#include <RDAT.hh>

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 ()
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

core::io::rna::RDAT::RDAT

(

)

core::io::rna::RDAT::RDAT

(

std::string const

filename

)

References read_rdat_file().

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().

core::io::rna::RDAT::~RDAT

(

)

Member Function Documentation

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

inline

References annotations_.

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

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

private

References utility::vector1< T, class >::has_value(), and core::io::rna::ok_annotations.

Referenced by check_annotations().

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

private

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

Referenced by check_rdat().

bool core::io::rna::RDAT::check_rdat

(

)

const

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

Referenced by RDAT(), and read_rdat_file().

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

private

References offset_, s1, s2, seqpos_, sequence_, and core::io::rna::TR.

Referenced by read_rdat_file().

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

inline

References comments_.

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().

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

private

References data_annotations_, and reactivity_.

Referenced by read_rdat_file().

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_, utility::tools::make_vector1(), offset_, reactivity_, runtime_assert, seqpos_, sequence_, and core::io::serialization::size().

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_, structure_, and core::pose::Pose::total_residue().

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().

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

private

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

Referenced by read_rdat_file().

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().

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

private

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

Referenced by fill_sequences_and_structures().

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().

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

private

References runtime_assert.

Referenced by read_rdat_file().

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

inline

References name_.

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

inline

References offset_.

void core::io::rna::RDAT::output_data

(

utility::io::ozstream &

out

)

const

References data_annotations_, offset_, reactivity_, reactivity_error_, runtime_assert, seqpos_, sequence_, and core::io::serialization::size().

Referenced by output_rdat_to_file().

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

private

References annotations_, comments_, name_, offset_, sequence_, structure_, and version_.

Referenced by output_rdat_to_file().

void core::io::rna::RDAT::output_rdat_to_file

(

std::string const

filename

)

const

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

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().

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

inline

References reactivity_error_.

void core::io::rna::RDAT::read_rdat_file

(

std::string const

filename

)

References annotations_, check_rdat(), check_sequence_seqpos(), utility::io::izstream::close(), comments_, data_annotations_, fill_data_annotations_if_empty(), fill_if_empty(), fill_seqpos(), fill_sequences_and_structures(), get_annotation(), getline(), utility::io::izstream::good(), name_, offset_, reactivity_, reactivity_error_, remove_tag(), utility::replace_in(), runtime_assert, save_data(), save_data_with_idx(), sequence_, sequences_, core::io::serialization::size(), str2cell(), string_split_simple(), strip_whitespace(), structure_, structures_, tags, core::io::rna::TR, trace_, utility_exit_with_message, version_, and xsel_.

Referenced by RDAT().

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

private

References utility::replace_in().

Referenced by read_rdat_file().

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

private

References runtime_assert, and str2cell().

Referenced by read_rdat_file().

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

private

References str2cell().

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

private

References runtime_assert.

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

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

private

References runtime_assert.

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

inline

References seqpos_.

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

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

inline

References sequence_.

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

inline

References sequences_.

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

inline

References annotations_.

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

inline

References comments_.

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

inline

References data_annotations_.

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

inline

References name_.

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

inline

References offset_.

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

inline

References reactivity_.

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

inline

References reactivity_error_.

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

inline

References seqpos_.

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

inline

References sequence_.

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

inline

References sequences_.

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

inline

References structure_.

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

inline

References structures_.

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

inline

References trace_.

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

inline

References version_.

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

inline

References xsel_.

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

inline

References xsel_refine_.

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

private

References string_split_simple().

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

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

inline

References structure_.

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

inline

References structures_.

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

inline

References trace_.

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

inline

References version_.

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

inline

References xsel_.

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

inline

References xsel_refine_.

Member Data Documentation

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().

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().

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().

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().

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().

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().

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().

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().

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().

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

private

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

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().

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

private

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

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

private

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

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

private

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

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

private

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

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