core::io::rna Namespace Reference

Classes
class	RDAT
class	RNA_DataReader

Typedefs
typedef utility::pointer::shared_ptr< RDAT >	RDATOP
typedef utility::pointer::shared_ptr< RDAT const >	RDATCOP
typedef std::pair< std::string, std::string >	Annotation
typedef utility::pointer::shared_ptr< RNA_DataReader >	RNA_DataReaderOP

Functions
std::string	get_tag (utility::vector1< Annotation > const &annotations, std::string const &tag)
utility::vector1< std::string >	get_tags (utility::vector1< utility::vector1< Annotation > > const &data_annotations, std::string const &tag)
static basic::Tracer	TR ("protocols.rna.RNA_DataReader")
core::pose::rna::RNA_DataInfo const &	get_rna_data_info (pose::Pose &pose, std::string const &rna_data_file, core::scoring::ScoreFunctionOP scorefxn)

Variables
std::string const	RDAT_VERSION_NUM_STRING = "0.33"
vector1< std::string > const	ok_annotations = utility::tools::make_vector1( "chemical","modifier","experimentType","temperature","chemical","mutation","processing","ERROR","warning","EteRNA","sequence","structure","MAPseq","sequenceSource","signal_to_noise","feature","lig_pos","offset","scaling" )
std::string const	numbers = "0123456789-"

Typedef Documentation

Annotation

typedef std::pair< std::string, std::string > core::io::rna::Annotation

RDATCOP

typedef utility::pointer::shared_ptr< RDAT const > core::io::rna::RDATCOP

RDATOP

typedef utility::pointer::shared_ptr< RDAT > core::io::rna::RDATOP

RNA_DataReaderOP

typedef utility::pointer::shared_ptr< RNA_DataReader > core::io::rna::RNA_DataReaderOP

Function Documentation

get_rna_data_info()

pose::rna::RNA_DataInfo const & core::io::rna::get_rna_data_info	(	pose::Pose &	pose,
		std::string const &	rna_data_file,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References core::pose::full_model_info::const_full_model_info(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::full_model_info::FullModelInfo::other_pose_list(), core::scoring::rna_chem_map, core::scoring::rna::RNA_ScoringInfo::rna_data_info(), and core::scoring::rna::rna_scoring_info_from_pose().

get_tag()

std::string core::io::rna::get_tag	(	utility::vector1< Annotation > const &	annotations,
		std::string const &	tag
	)

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

get_tags()

utility::vector1< std::string > core::io::rna::get_tags	(	utility::vector1< utility::vector1< Annotation > > const &	data_annotations,
		std::string const &	tag
	)

References get_tag().

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

TR()

static basic::Tracer core::io::rna::TR ( "protocols.rna.RNA_DataReader"  )

static

Referenced by core::io::rna::RDAT::check_annotations(), core::io::rna::RDAT::check_rdat(), core::io::rna::RDAT::check_sequence_seqpos(), core::io::rna::RDAT::fill_if_empty(), core::io::rna::RDAT::fill_sequences_if_empty(), core::io::rna::RDAT::output_rdat_to_file(), core::io::rna::RNA_DataReader::read_data_from_file(), and core::io::rna::RDAT::read_rdat_file().

Variable Documentation

numbers

std::string const core::io::rna::numbers = "0123456789-"

Referenced by core::io::rna::RDAT::fill_seqpos(), core::io::rna::RDAT::fill_sequences_if_empty(), protocols::antibody::design::get_resnums_from_strings_with_ranges(), and protocols::denovo_design::components::StructureData::retrieve_remarks().

ok_annotations

vector1< std::string > const core::io::rna::ok_annotations = utility::tools::make_vector1( "chemical","modifier","experimentType","temperature","chemical","mutation","processing","ERROR","warning","EteRNA","sequence","structure","MAPseq","sequenceSource","signal_to_noise","feature","lig_pos","offset","scaling" )

Referenced by core::io::rna::RDAT::check_annotation().

RDAT_VERSION_NUM_STRING

std::string const core::io::rna::RDAT_VERSION_NUM_STRING = "0.33"