Derived class that stores DEER decay data. More...

#include <DEERDecayData.hh>

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

Public Member Functions
Real	get_score (std::map< Size, Real > const &sim_histr) override
	Virtual function to evaluate score given a distribution. More...

Real	sum_of_squares (utility::vector1< Real > const &sim_trace, bool const &normalize=true) const
	Calculate sum of squares of simulated DEER trace. More...

void	init_factory (utility::vector1< Real > const &trace, utility::vector1< Real > const &time_pts)
	Initialize DEER factory object. More...

Simulated4PDEERTraceFactory &	factory ()
	Returns DEER trace factory object. More...

Real const &	noise () const
	Returns the noise from the imaginary component. More...

bool const &	fit_stdev () const
	Returns whether standard deviation is a fitting parameter. More...

std::string	bckg () const
	Returns background type. More...

Size	max_dist () const
	Returns maximum distance for kernel calculation. More...

void	factory (Simulated4PDEERTraceFactory const &val)
	Sets DEER trace factory object. More...

void	noise (Real const &val)
	Sets the noise from the imaginary component. More...

void	fit_stdev (bool const &val)
	Sets if standard deviation is varied as a parameter. More...

void	bckg (std::string const &val)
	Sets background type. More...

void	max_dist (Size const &val)
	Sets maximum distance for kernel calculation. More...

Public Member Functions inherited from core::scoring::epr_deer::metrics::DEERData
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...

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...

Private Attributes
Simulated4PDEERTraceFactory	factory_
	DEER trace factory object. More...

Real	noise_ = 1.0
	Noise level in experimental DEER data. More...

bool	fit_stdev_ = false
	Whether standard deviation should be varied as a parameter. More...

std::string	bckg_ = "3D"
	Intermolecular background coupling type. More...

Size	max_dist_ = 100
	Maximum distance considered for kernel calculation. More...

Additional Inherited Members
Protected Attributes inherited from core::scoring::epr_deer::metrics::DEERData
Size	bins_per_a_ = 2
	Bins per angstrom for distributions stored and scored. More...

Detailed Description

Derived class that stores DEER decay data.

Member Function Documentation

std::string core::scoring::epr_deer::metrics::DEERDecayData::bckg ( ) const

Returns background type.

Returns: Intermolecular coupling background type

References bckg_.

void core::scoring::epr_deer::metrics::DEERDecayData::bckg ( std::string const & val )

Sets background type.

Parameters

val	Type of intermolecular coupling background

References bckg_, and protocols::hybridization::val.

Simulated4PDEERTraceFactory & core::scoring::epr_deer::metrics::DEERDecayData::factory ( )

Returns DEER trace factory object.

Returns: Factory object

References factory_.

void core::scoring::epr_deer::metrics::DEERDecayData::factory ( Simulated4PDEERTraceFactory const & val )

Sets DEER trace factory object.

Parameters

factory Factory object

References factory_, and protocols::hybridization::val.

bool const & core::scoring::epr_deer::metrics::DEERDecayData::fit_stdev ( ) const

Returns whether standard deviation is a fitting parameter.

Returns: Boolean

References fit_stdev_.

void core::scoring::epr_deer::metrics::DEERDecayData::fit_stdev ( bool const & val )

Sets if standard deviation is varied as a parameter.

Parameters

val Boolean

References fit_stdev_, and protocols::hybridization::val.

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

overridevirtual

Virtual function to evaluate score given a distribution.

Parameters

sim_histr Simulated DEER distribution

Returns: Freshly computed score A DEER trace is calculated from the simulated histogram. For details, please read del Alamo Biophysical Journal 2020. The score is the average sum-of-squares residuals between the two. Note that there is a slight noise-dependence to this; noisier data will always return higher scores.

Implements core::scoring::epr_deer::metrics::DEERData.

References core::scoring::epr_deer::metrics::DEERData::avg_stdev(), core::scoring::epr_deer::metrics::DEERData::convolute(), factory_, fit_stdev_, sum_of_squares(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::trace_from_distr().

void core::scoring::epr_deer::metrics::DEERDecayData::init_factory	(	utility::vector1< Real > const &	trace,
		utility::vector1< Real > const &	time_pts
	)

Initialize DEER factory object.

Parameters

trace	Experimental DEER trace
tiem_pts	Time points corresponding to DEER trace

References bckg_, core::scoring::epr_deer::metrics::DEERData::bins_per_a_, factory_, and max_dist_.

Size core::scoring::epr_deer::metrics::DEERDecayData::max_dist ( ) const

Returns maximum distance for kernel calculation.

Returns: Maximum distance for kernel calculation

References max_dist_.

void core::scoring::epr_deer::metrics::DEERDecayData::max_dist ( Size const & val )

Sets maximum distance for kernel calculation.

Parameters

val	Maximum distance to set

References max_dist_, and protocols::hybridization::val.

Real const & core::scoring::epr_deer::metrics::DEERDecayData::noise ( ) const

Returns the noise from the imaginary component.

Returns: Noise level

References noise_.

void core::scoring::epr_deer::metrics::DEERDecayData::noise ( Real const & val )

Sets the noise from the imaginary component.

Parameters

val	Noise level

References noise_, and protocols::hybridization::val.

Real core::scoring::epr_deer::metrics::DEERDecayData::sum_of_squares	(	utility::vector1< Real > const &	sim_trace,
		bool const &	normalize = `true`
	)		const