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Public Member Functions | Protected Attributes | Private Attributes | List of all members
core::scoring::epr_deer::metrics::DEERData Class Referenceabstract

Base class. More...

#include <DEERData.hh>

Inheritance diagram for core::scoring::epr_deer::metrics::DEERData:
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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, Realconvolute (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, 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...
 

Protected Attributes

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

Private Attributes

utility::vector1< PairSizeStringresidues_
 Residues used in this dataset. More...
 
Real score_ = 0.0
 Last computed score. More...
 
std::map< Size, Realdist_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

◆ append_dist_id()

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

Append distance ID to custom distance map.

Parameters
dist_idUnique distance ID used in distance map
distDistance value in angstroms @detail Only works when bins_per_a set to zero!

References dist_map_.

◆ avg_stdev()

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

◆ bins_per_a() [1/2]

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(), protocols::simple_moves::DEEROptimizeCoordsMover::init_data(), and core::scoring::epr_deer::DEERIO::parse_decay_info_lines().

◆ bins_per_a() [2/2]

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_aBins per angstrom

References bins_per_a(), and bins_per_a_.

◆ convolute()

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

◆ dist_map()

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) @detail Only works when bins_per_a set to zero!

References dist_map_.

◆ get_score() [1/2]

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

◆ get_score() [2/2]

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_histrSimulated DEER distribution
set_scoreBoolean to save score or not
Returns
Freshly computed score

References score(), and score_.

◆ print_histogram()

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_histrSimulated distance distribution
pose_nameName of the pose

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

◆ residues() [1/2]

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) @detail 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().

◆ residues() [2/2]

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

Sets residue for data set.

Parameters
residuesVector of residues (index and spin label type)

References residues(), and residues_.

◆ score() [1/2]

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

Returns the last computed score.

Returns
Score (0.0 if never set)

References score_.

Referenced by core::scoring::epr_deer::metrics::DEERMiscMethod::get_score(), core::scoring::epr_deer::metrics::DEEROverlapMethod::get_score(), and get_score().

◆ score() [2/2]

void core::scoring::epr_deer::metrics::DEERData::score ( Real const &  val)

Set the score of the data set.

Parameters
valScore to save

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

◆ stdev() [1/2]

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

Returns the standard deviation of the distributions to generate.

Parameters
Standarddeviation (in angstroms) @detail Function has a failsafe to avoid returning a nonzero value

References protocols::mean_field::max(), and stdev_.

◆ stdev() [2/2]

void core::scoring::epr_deer::metrics::DEERData::stdev ( Real const &  val)

Set the standard deviation of the distributions to generate.

Parameters
valSet the standard deviation to this value

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

Member Data Documentation

◆ bins_per_a_

Size core::scoring::epr_deer::metrics::DEERData::bins_per_a_ = 2
protected

Bins per angstrom for distributions stored and scored.

Referenced by avg_stdev(), bins_per_a(), convolute(), core::scoring::epr_deer::metrics::DEERDecayData::init_factory(), and print_histogram().

◆ dist_map_

std::map< Size, Real > core::scoring::epr_deer::metrics::DEERData::dist_map_ = {}
private

Map if distance indeces to distance values (NOT amplitudes!)

Referenced by append_dist_id(), and dist_map().

◆ residues_

utility::vector1< PairSizeString > core::scoring::epr_deer::metrics::DEERData::residues_
private

Residues used in this dataset.

Referenced by print_histogram(), and residues().

◆ score_

Real core::scoring::epr_deer::metrics::DEERData::score_ = 0.0
private

Last computed score.

Referenced by get_score(), and score().

◆ stdev_

Real core::scoring::epr_deer::metrics::DEERData::stdev_ = 1.0
private

Standard deviation of distribution.

Referenced by stdev().


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