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core::scoring::epr_deer::metrics::DEERDecayData Class Reference

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

#include <DEERDecayData.hh>

Inheritance diagram for core::scoring::epr_deer::metrics::DEERDecayData:
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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...
 
Simulated4PDEERTraceFactoryfactory ()
 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, Realconvolute (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, Realdist_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< Realavg_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
valType 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
factoryFactory 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
valBoolean

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_histrSimulated 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
traceExperimental DEER trace
tiem_ptsTime 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
valMaximum 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
valNoise 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

Calculate sum of squares of simulated DEER trace.

Parameters
trace1Simulated DEER trace
trace2Reference DEER trace; experimental by default
normalizeNormalize by number of time points; recommended
Returns
Sum of squared residuals

References factory_, noise_, and core::scoring::epr_deer::Simulated4PDEERTraceFactory::trace().

Referenced by get_score().

Member Data Documentation

std::string core::scoring::epr_deer::metrics::DEERDecayData::bckg_ = "3D"
private

Intermolecular background coupling type.

Referenced by bckg(), and init_factory().

Simulated4PDEERTraceFactory core::scoring::epr_deer::metrics::DEERDecayData::factory_
private

DEER trace factory object.

Referenced by factory(), get_score(), init_factory(), and sum_of_squares().

bool core::scoring::epr_deer::metrics::DEERDecayData::fit_stdev_ = false
private

Whether standard deviation should be varied as a parameter.

Referenced by fit_stdev(), and get_score().

Size core::scoring::epr_deer::metrics::DEERDecayData::max_dist_ = 100
private

Maximum distance considered for kernel calculation.

Referenced by init_factory(), and max_dist().

Real core::scoring::epr_deer::metrics::DEERDecayData::noise_ = 1.0
private

Noise level in experimental DEER data.

Referenced by noise(), and sum_of_squares().


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