#include <DEERIO.hh>

Public Member Functions
	DEERIO ()
	Constructor. More...

	~DEERIO ()
	Destructor. More...

std::map< Size, DEERDataOP >	generate_data (core::pose::Pose const &pose)
	Generates the data for use. Core function. More...

utility::vector1 < utility::vector1 < std::string > >	get_splitlines ()
	Reads the input file(s) and makes an unsorted vector of their whitespace-separated contents. More...

void	read_desc_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines, pose::Pose const &pose)
	Reads lines that start with DESC, which contain residue and spin label information. More...

void	read_info_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines)
	Reads lines that start with INFO, which gives additional options specific for each bit of data. More...

void	read_decay_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &data_lines)
	Read lines for decay data (raw data) More...

void	read_bounds_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines)
	Read lines for bounded distance restraints. More...

void	read_gauss_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines)
	Read lines for gaussian-distributed distance data. More...

void	read_dist_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines)
	Read lines for non-gaussian-distributed distance data. More...

void	read_pair_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines, pose::Pose const &pose)
	Read the lines starting with PAIR, which are for easy input. More...

Real	normalize_distribution (std::map< Size, Real > &in_map)
	Normalize distance distributions so their integrals equal 1. More...

utility::vector1< std::pair < EPRSpinLabel, Real > >	pull_coords () const
	Get custom spin label coordinates. More...

Private Attributes
Size	ANGSTROM_LIMIT_ = 100

Size	BINS_PER_ANGSTROM_ = 2

Constructor & Destructor Documentation

core::scoring::epr_deer::DEERIO::DEERIO ( )

Constructor.

core::scoring::epr_deer::DEERIO::~DEERIO ( )

Destructor.

Member Function Documentation

std::map< Size, DEERDataOP > core::scoring::epr_deer::DEERIO::generate_data ( core::pose::Pose const & pose )

Generates the data for use. Core function.

References get_splitlines(), read_bounds_lines(), read_decay_lines(), read_desc_lines(), read_dist_lines(), read_gauss_lines(), read_info_lines(), and read_pair_lines().

Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().

utility::vector1< utility::vector1< std::string > > core::scoring::epr_deer::DEERIO::get_splitlines ( )

Reads the input file(s) and makes an unsorted vector of their whitespace-separated contents.

References core::conformation::membrane::in, and protocols::sparta::split().

Referenced by generate_data().

Real core::scoring::epr_deer::DEERIO::normalize_distribution ( std::map< Size, Real > & in_map )

Normalize distance distributions so their integrals equal 1.

Referenced by read_dist_lines(), and read_gauss_lines().

utility::vector1< std::pair< EPRSpinLabel, Real > > core::scoring::epr_deer::DEERIO::pull_coords ( ) const

Get custom spin label coordinates.

References core::conformation::membrane::in, core::scoring::epr_deer::EPRSpinLabel::load_custom_electrons(), and protocols::sparta::split().

Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().

void core::scoring::epr_deer::DEERIO::read_bounds_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines
	)

Read lines for bounded distance restraints.

References core::scoring::epr_deer::TR().

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_decay_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	data_lines
	)

Read lines for decay data (raw data)

References ANGSTROM_LIMIT_, and core::scoring::epr_deer::TR().

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_desc_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines,
		pose::Pose const &	pose
	)

Reads lines that start with DESC, which contain residue and spin label information.

References BINS_PER_ANGSTROM_, core::pose::parse_resnum(), and core::scoring::epr_deer::TR().

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_dist_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines
	)

Read lines for non-gaussian-distributed distance data.

References BINS_PER_ANGSTROM_, protocols::mean_field::max(), protocols::mean_field::min(), normalize_distribution(), protocols::noesy_assign::round(), core::scoring::epr_deer::TR(), and protocols::hybridization::val.

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_gauss_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines
	)

Read lines for gaussian-distributed distance data.

References ANGSTROM_LIMIT_, core::scoring::epr_deer::DEERDistanceDistribution::best_fit(), BINS_PER_ANGSTROM_, core::sequence::end, core::scoring::epr_deer::EPRSpinLabel::gauss(), protocols::mean_field::max(), core::simple_metrics::metrics::mean, protocols::mean_field::min(), normalize_distribution(), and core::scoring::epr_deer::TR().

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_info_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines
	)

Reads lines that start with INFO, which gives additional options specific for each bit of data.

References core::scoring::epr_deer::TR().

Referenced by generate_data().

void core::scoring::epr_deer::DEERIO::read_pair_lines	(	std::map< Size, DEERDataOP > &	output,
		utility::vector1< utility::vector1< std::string > > const &	splitlines,
		pose::Pose const &	pose
	)

Read the lines starting with PAIR, which are for easy input.

References BINS_PER_ANGSTROM_, core::kinematics::distance(), core::pose::parse_resnum(), and core::scoring::epr_deer::DEERData::residues().

Referenced by generate_data().

Member Data Documentation

Size core::scoring::epr_deer::DEERIO::ANGSTROM_LIMIT_ = 100

private

Referenced by read_decay_lines(), and read_gauss_lines().

Size core::scoring::epr_deer::DEERIO::BINS_PER_ANGSTROM_ = 2

private

Referenced by read_desc_lines(), read_dist_lines(), read_gauss_lines(), and read_pair_lines().

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

src/core/scoring/epr_deer/DEERIO.hh
src/core/scoring/epr_deer/DEERIO.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation