Base class. More...

#include <DEERData.hh>

Inheritance diagram for core::scoring::epr_deer::metrics::DEERData:

Public Member Functions
void	print_histogram (std::map< Size, Real > const &sim_histr, std::string const &pose_name="NO NAME GIVEN") const
	Print the simulated distance distribution. More...

Real	get_score (std::map< Size, Real > const &sim_histr, bool const &set_score)
	Function to evaluate score given a distribution. More...

std::map< Size, Real >	convolute (std::map< Size, Real > const &distr, Real const &std) const
	Convolute a distribution with a Gaussian of a specific width. More...

virtual Real	get_score (std::map< Size, Real > const &sim_histr)=0
	Virtual function to evaluate score given a distribution. More...

utility::vector1 < PairSizeString > const &	residues () const
	Returns the residues involved in this data set. More...

Size const &	bins_per_a () const
	Returns bins per angstrom for distribution (default: 2) More...

Real	score () const
	Returns the last computed score. More...

Real	stdev () const
	Returns the standard deviation of the distributions to generate. More...

void	residues (utility::vector1< PairSizeString > const &val)
	Sets residue for data set. More...

void	bins_per_a (Size const &val)
	Set the number of bins per angstrom for the data set. More...

void	score (Real const &val)
	Set the score of the data set. More...

void	stdev (Real const &val)
	Set the standard deviation of the distributions to generate. More...

std::map< Size, Real >	dist_map () const
	Returns the map of distance values used for custom distributions. More...

void	append_dist_id (Size dist_id, Real dist)
	Append distance ID to custom distance map. More...

utility::vector1< Real >	avg_stdev (std::map< Size, Real > const &histogram)
	Computes average distance of distribution for local functions. More...

Protected Attributes
Size	bins_per_a_ = 2
	Bins per angstrom for distributions stored and scored. More...

Private Attributes
utility::vector1< PairSizeString >	residues_
	Residues used in this dataset. More...

Real	score_ = 0.0
	Last computed score. More...

std::map< Size, Real >	dist_map_ = {}
	Map if distance indeces to distance values (NOT amplitudes!) More...

Real	stdev_ = 1.0
	Standard deviation of distribution. More...

Detailed Description

Base class.

Member Function Documentation

void core::scoring::epr_deer::metrics::DEERData::append_dist_id	(	Size	dist_id,
		Real	dist
	)

Append distance ID to custom distance map.

Parameters

dist_id	Unique distance ID used in distance map
dist	Distance value in angstroms Only works when bins_per_a set to zero!

References dist_map_.

utility::vector1< Real > core::scoring::epr_deer::metrics::DEERData::avg_stdev ( std::map< Size, Real > const & histogram )

Computes average distance of distribution for local functions.

Parameters

histogram Distance distribution

Returns: Vector with two items: Average and Standard Deviation

References bins_per_a_, and protocols::analysis::total.

Referenced by core::scoring::epr_deer::metrics::DEERDistanceDistribution::expand_hists(), core::scoring::epr_deer::metrics::DEERDecayData::get_score(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::get_score(), and core::scoring::epr_deer::metrics::DEERDistanceBounds::get_score().

Size const & core::scoring::epr_deer::metrics::DEERData::bins_per_a ( ) const

Returns bins per angstrom for distribution (default: 2)

Returns: Bins per angstrom

References bins_per_a_.

Referenced by bins_per_a(), and core::scoring::epr_deer::DEERIO::parse_decay_info_lines().

void core::scoring::epr_deer::metrics::DEERData::bins_per_a ( Size const & bins_per_a )

Set the number of bins per angstrom for the data set.

Parameters

bins_per_a Bins per angstrom

References bins_per_a(), and bins_per_a_.

std::map< Size, Real > core::scoring::epr_deer::metrics::DEERData::convolute	(	std::map< Size, Real > const &	distr,
		Real const &	std
	)		const

Convolute a distribution with a Gaussian of a specific width.

Parameters

distr	DEER Distribution
std	Width of Gaussian (mean=0)

Returns: New distribution

References core::scoring::epr_deer::add_to_map(), bins_per_a_, core::scoring::epr_deer::gauss(), protocols::mean_field::max(), protocols::noesy_assign::round(), protocols::loops::start, protocols::loops::stop, and protocols::analysis::total.

Referenced by core::scoring::epr_deer::metrics::DEERDistanceDistribution::expand_hists(), and core::scoring::epr_deer::metrics::DEERDecayData::get_score().

std::map< Size, Real > core::scoring::epr_deer::metrics::DEERData::dist_map ( ) const

Returns the map of distance values used for custom distributions.

Returns: Map of values (indeces to distances in Angstroms) Only works when bins_per_a set to zero!

References dist_map_.

Real core::scoring::epr_deer::metrics::DEERData::get_score	(	std::map< Size, Real > const &	sim_histr,
		bool const &	set_score
	)

Function to evaluate score given a distribution.

Parameters

sim_histr	Simulated DEER distribution
set_score	Boolean to save score or not

Returns: Freshly computed score

References score(), and score_.

virtual Real core::scoring::epr_deer::metrics::DEERData::get_score ( std::map< Size, Real > const & sim_histr )

pure virtual

Virtual function to evaluate score given a distribution.

Parameters

sim_histr Simulated DEER distribution

Returns: Freshly computed score

Implemented in core::scoring::epr_deer::metrics::DEERDistanceBounds, core::scoring::epr_deer::metrics::DEERDistanceDistribution, core::scoring::epr_deer::metrics::DEERDecayData, core::scoring::epr_deer::metrics::DEERChiSqMethod, core::scoring::epr_deer::metrics::DEERJaccardMethod, core::scoring::epr_deer::metrics::DEERJSMethod, core::scoring::epr_deer::metrics::DEERMiscMethod, and core::scoring::epr_deer::metrics::DEEROverlapMethod.

void core::scoring::epr_deer::metrics::DEERData::print_histogram	(	std::map< Size, Real > const &	sim_histr,
		std::string const &	pose_name = `"NO NAME GIVEN"`
	)		const

Print the simulated distance distribution.

Parameters

sim_histr	Simulated distance distribution
pose_name	Name of the pose

References bins_per_a_, residues_, and core::scoring::epr_deer::metrics::TR().

utility::vector1< PairSizeString > const & core::scoring::epr_deer::metrics::DEERData::residues ( ) const

Returns the residues involved in this data set.

Returns: Vector of residues (ID and spin label type) Residues are saved with two parameters: the residue ID, and the label type. Label type is set to "DEFAULT" by default. Other options include DEFAULT_FAST and CUSTOM

References residues_.

Referenced by residues().

void core::scoring::epr_deer::metrics::DEERData::residues ( utility::vector1< PairSizeString > const & residues )

Sets residue for data set.

Parameters

residues Vector of residues (index and spin label type)

References residues(), and residues_.

Real core::scoring::epr_deer::metrics::DEERData::score ( ) const

Returns the last computed score.