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

Derived class that stores DEER decay data, either raw or background-corrected. More...

#include <DEERData.hh>

Inheritance diagram for core::scoring::epr_deer::DEERDecayData:
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Public Member Functions

Real get_score (std::map< Size, Real > const &simulated_histogram, bool const &set_score=false) override
 Computes sum-of-squares of experimental to simulated DEER trace A DEER trace is calculated from the simulated histogram. For details, please read del Alamo et al Biophysical Journal 2019. 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. More...
 
std::map< Size, Realmod_distr (Real const &avg, Real const &stdev) const
 Returns a gaussian distribution with certain avg and stdev. Used for generating distributions when the standard deviation is used as a fitting parameter. More...
 
std::map< Real, Real > const & trace () const
 Returns the experimental DEER trace. Key is time point in microseconds. More...
 
Real const & k_fit () const
 Returns the last value obtained when fitting background slope (stored in fitting info) More...
 
Real const & modulation_depth_fit () const
 Returns the last value obtained when fitting modulation depth (stored in fitting info) More...
 
Real const & time_points_sqd () const
 Returns the time points squared, used to fit slope and avoids unnecessary calculation. More...
 
Real const & noise () const
 Returns the noise from the imaginary component, provided manually as an option. More...
 
Real const & spin_val (Size const &dist_bin, Real const &time_pt) const
 Returns the spin value for a given time point and distance. Computed at the front end. More...
 
std::pair< Real, Real > const & mod_depth_bounds () const
 Returns the upper and lower bounds of the modulation depth. More...
 
bool const & fit_stdev () const
 Returns whether or not the standard deviation is used as a fitting parameter. More...
 
std::string const & bckg () const
 Returns whether the dimensionality is used as a fitting parameter - typical for membrane proteins. More...
 
void trace (std::map< Real, Real > const &trace)
 Sets the experimental DEER trace. More...
 
void append_trace_data (Real const &time, Real const &signal)
 Appends time point and signal values for the experimental DEER trace. More...
 
void k_fit (Real const &k)
 Sets the value obtained when fitting background slope (stored in fitting info) More...
 
void modulation_depth_fit (Real const &modulation_depth)
 Sets the value obtained when fitting modulation depth (stored in fitting info) More...
 
void time_pts_sqd (Real const &time_pts_sqd)
 Sets the value for time points squared, used to fit slope and avoids unnecessary calculation. More...
 
void noise (Real const &noise)
 Sets the noise from the imaginary component, provided manually as an option. More...
 
void spin_map (std::map< Size, std::map< Real, Real > > const &spin_map)
 Sets the "spin map" that contains trace values at all time points and distances. More...
 
void mod_depth_bounds (Real const &lower, Real const &upper)
 Sets lower and upper bounds for modulation depth. More...
 
void fit_stdev (bool const &fit_stdev)
 Sets whether the standard deviation is a parameter when fitting DEER traces. More...
 
void bckg (std::string const &bckg)
 Sets what type of background is used for fitting: options are 3D, NON-3D, NONE. More...
 
void append_trace_data_and_calculate (Real const &time, Real const &signal, Size const &max_bin)
 Appends data to experimental decay trace and values to relevant variables. More...
 
Real calculate_decay_2_spin (Real const &t, Real const &r) const
 Calculates the DEER trace given a time point (microseconds) and distance (A) More...
 
- Public Member Functions inherited from core::scoring::epr_deer::DEERData
void print_histogram (std::map< Size, Real > const &simulated_histogram) const
 Print the simulated distance distribution. More...
 
utility::vector1< std::pair
< Size, std::string > > const & 
residues () const
 Returns the residues involved in this data set. Residues are saves with two parameters: the residue ID, and the label type Label type is set to "DEFAULT" by default (duh). Other options include DEFAULT_FAST and CUSTOM. More...
 
Size const & bins_per_angstrom () const
 Returns the granularity of the distance distribution. Default is 2 bins per A. More...
 
Real score () const
 Returns the last computed score. Obtained using get_score() or manually set. More...
 
Real relative_weight () const
 Returns the relative weight. Default: 1. Can be lowered when the data is less trustworthy. More...
 
void residues (utility::vector1< std::pair< Size, std::string > > const &val)
 Sets residue for data set; info for each "residue" consists of the index and the spin label type. More...
 
void bins_per_angstrom (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 relative_weight (Real const &val)
 Set the relative weight of the data set. More...
 

Private Attributes

std::map< Real, Realtrace_
 
FittingInfo fit_info_
 
Real noise_ = 1.0
 
bool fit_stdev_ = false
 
utility::vector0< Realtheta_terms_
 

Additional Inherited Members

- Protected Member Functions inherited from core::scoring::epr_deer::DEERData
Real compute_avg_dist (std::map< Size, Real > const &simulated_histogram) const
 Computes average distance of distribution for local functions. More...
 
- Protected Attributes inherited from core::scoring::epr_deer::DEERData
utility::vector1< std::pair
< Size, std::string > > 
residues_
 
Size bins_per_angstrom_ = 2
 
Real score_
 
Real rel_weight_ = 1.0
 

Detailed Description

Derived class that stores DEER decay data, either raw or background-corrected.

Member Function Documentation

void core::scoring::epr_deer::DEERDecayData::append_trace_data ( Real const &  time,
Real const &  signal 
)

Appends time point and signal values for the experimental DEER trace.

References trace_.

void core::scoring::epr_deer::DEERDecayData::append_trace_data_and_calculate ( Real const &  time,
Real const &  signal,
Size const &  max_bin 
)
std::string const & core::scoring::epr_deer::DEERDecayData::bckg ( ) const

Returns whether the dimensionality is used as a fitting parameter - typical for membrane proteins.

References core::scoring::epr_deer::FittingInfo::bckg_, and fit_info_.

Referenced by bckg().

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

Sets what type of background is used for fitting: options are 3D, NON-3D, NONE.

References bckg(), core::scoring::epr_deer::FittingInfo::bckg_, and fit_info_.

Real core::scoring::epr_deer::DEERDecayData::calculate_decay_2_spin ( Real const &  t,
Real const &  r 
) const

Calculates the DEER trace given a time point (microseconds) and distance (A)

Referenced by append_trace_data_and_calculate().

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

Returns whether or not the standard deviation is used as a fitting parameter.

References fit_stdev_.

Referenced by fit_stdev().

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

Sets whether the standard deviation is a parameter when fitting DEER traces.

References fit_stdev(), and fit_stdev_.

Real core::scoring::epr_deer::DEERDecayData::get_score ( std::map< Size, Real > const &  simulated_histogram,
bool const &  set_score = false 
)
overridevirtual

Computes sum-of-squares of experimental to simulated DEER trace A DEER trace is calculated from the simulated histogram. For details, please read del Alamo et al Biophysical Journal 2019. 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.

Computes sum-of-squares of experimental to simulated DEER trace.

Reimplemented from core::scoring::epr_deer::DEERData.

References core::scoring::epr_deer::DEERData::bins_per_angstrom_, core::scoring::epr_deer::DEERData::compute_avg_dist(), fit_info_, fit_stdev_, mod_distr(), noise_, core::scoring::epr_deer::DEERData::score(), core::scoring::epr_deer::DEERData::score_, core::scoring::epr_deer::Simulated4PDEERTrace::simulate_decay(), core::scoring::epr_deer::Simulated4PDEERTrace::sum_of_squares(), and trace_.

Real const & core::scoring::epr_deer::DEERDecayData::k_fit ( ) const

Returns the last value obtained when fitting background slope (stored in fitting info)

References fit_info_, and core::scoring::epr_deer::FittingInfo::last_slope_.

void core::scoring::epr_deer::DEERDecayData::k_fit ( Real const &  k)

Sets the value obtained when fitting background slope (stored in fitting info)

References fit_info_, and core::scoring::epr_deer::FittingInfo::last_slope_.

std::pair< Real, Real > const & core::scoring::epr_deer::DEERDecayData::mod_depth_bounds ( ) const

Returns the upper and lower bounds of the modulation depth.

References fit_info_, and core::scoring::epr_deer::FittingInfo::mod_depth_bounds_.

void core::scoring::epr_deer::DEERDecayData::mod_depth_bounds ( Real const &  lower,
Real const &  upper 
)
std::map< Size, Real > core::scoring::epr_deer::DEERDecayData::mod_distr ( Real const &  avg,
Real const &  stdev 
) const

Returns a gaussian distribution with certain avg and stdev. Used for generating distributions when the standard deviation is used as a fitting parameter.

Returns a gaussian distribution with certain avg and stdev.

References core::scoring::epr_deer::DEERData::bins_per_angstrom_, protocols::mean_field::max(), and protocols::noesy_assign::round().

Referenced by get_score().

Real const & core::scoring::epr_deer::DEERDecayData::modulation_depth_fit ( ) const

Returns the last value obtained when fitting modulation depth (stored in fitting info)

References fit_info_, and core::scoring::epr_deer::FittingInfo::last_mod_depth_.

void core::scoring::epr_deer::DEERDecayData::modulation_depth_fit ( Real const &  modulation_depth)

Sets the value obtained when fitting modulation depth (stored in fitting info)

References fit_info_, and core::scoring::epr_deer::FittingInfo::last_mod_depth_.

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

Returns the noise from the imaginary component, provided manually as an option.

References noise_.

Referenced by noise().

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

Sets the noise from the imaginary component, provided manually as an option.

References noise(), and noise_.

void core::scoring::epr_deer::DEERDecayData::spin_map ( std::map< Size, std::map< Real, Real > > const &  spin_map)

Sets the "spin map" that contains trace values at all time points and distances.

References fit_info_, and core::scoring::epr_deer::FittingInfo::spin_map_.

Real const & core::scoring::epr_deer::DEERDecayData::spin_val ( Size const &  dist_bin,
Real const &  time_pt 
) const

Returns the spin value for a given time point and distance. Computed at the front end.

References fit_info_, and core::scoring::epr_deer::FittingInfo::spin_map_.

Real const & core::scoring::epr_deer::DEERDecayData::time_points_sqd ( ) const

Returns the time points squared, used to fit slope and avoids unnecessary calculation.

References fit_info_, and core::scoring::epr_deer::FittingInfo::time_pts_sqd_.

void core::scoring::epr_deer::DEERDecayData::time_pts_sqd ( Real const &  time_pts_sqd)

Sets the value for time points squared, used to fit slope and avoids unnecessary calculation.

References fit_info_, and core::scoring::epr_deer::FittingInfo::time_pts_sqd_.

std::map< Real, Real > const & core::scoring::epr_deer::DEERDecayData::trace ( ) const

Returns the experimental DEER trace. Key is time point in microseconds.

References trace_.

Referenced by trace().

void core::scoring::epr_deer::DEERDecayData::trace ( std::map< Real, Real > const &  trace)

Sets the experimental DEER trace.

References trace(), and trace_.

Member Data Documentation

FittingInfo core::scoring::epr_deer::DEERDecayData::fit_info_
private
bool core::scoring::epr_deer::DEERDecayData::fit_stdev_ = false
private

Referenced by fit_stdev(), and get_score().

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

Referenced by get_score(), and noise().

utility::vector0< Real > core::scoring::epr_deer::DEERDecayData::theta_terms_
private
std::map< Real, Real > core::scoring::epr_deer::DEERDecayData::trace_
private

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