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core::scoring::epr_deer::Simulated4PDEERTrace Class Reference

#include <Simulated4PDEERTrace.hh>

Public Member Functions

 Simulated4PDEERTrace ()
 Default constructor. More...
 
 Simulated4PDEERTrace (std::map< Real, Real > const &exp_trace, FittingInfo &fit_info, std::map< Size, Real > const &sim_histogram, Size const &bins_per_a)
 Custom constructor. More...
 
Real operator[] (Real const &t) const
 Bracket operator for accessing the DEER trace. More...
 
std::map< Real, Realsimulate_decay (std::map< Real, Real > const &exp_trace, FittingInfo &fit_info, std::map< Size, Real > const &sim_histogram, Size const &bins_per_a)
 Main function for simulating 4-pulse DEER trace This function first simulates the intramolecular dipolar coupling form factor using the evolution kernel described in "DEER Distance Measurements on Proteins" by Jeschke (2012). It then finds the best background fit for the experimental data, if necessary (3D by default, but can be set to "NONE" or "NON-3D") Background-fitted DEER trace is saved and returned. More...
 
std::map< Real, Realcalc_4pdeer (std::map< Real, Real > const &exp_trace, FittingInfo const &fit_info, std::map< Size, Real > const &sim_histogram, Size const &bins_per_a)
 Deterine the intramolecular DEER trace. More...
 
Real fit_k (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &trace, FittingInfo &fit_info, Real const &d, Real const &l)
 Fit the background decay using linear regression. More...
 
std::map< Real, Realoptimize_bckg (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &trace_no_bckg, FittingInfo &fit_info)
 Optimize the background function of the DEER trace: general function. More...
 
void optimize_mod_depth (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &trace, FittingInfo &fit_info, Real &d, Real &k, Real &l, bool fit_dim)
 Optimize the modulation depth using simple gradient descent. More...
 
std::map< Real, Realoptimize_bckg (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &trace, FittingInfo &fit_info, bool const &optimize_dim)
 Optimize the background function of the DEER trace: detailed function. More...
 
std::map< Real, Realfit_trace (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &trace, Real const &d, Real const &k, Real const &l)
 Convert an intramolecular trace to an intermolecular trace given background parameters. More...
 
Real sum_of_squares (std::map< Real, Real > const &exp_trace, Real const &noise=1.0)
 Determine the residuals between an experimental trace and a simulated trace. More...
 
Real sum_of_squares (std::map< Real, Real > const &exp_trace, std::map< Real, Real > const &sim_trace, Real const &noise=1.0)
 Determine the residuals between an experimental trace and a simulated trace. More...
 

Private Attributes

std::map< Real, Realtrace_
 

Constructor & Destructor Documentation

core::scoring::epr_deer::Simulated4PDEERTrace::Simulated4PDEERTrace ( )

Default constructor.

Default constructor

core::scoring::epr_deer::Simulated4PDEERTrace::Simulated4PDEERTrace ( std::map< Real, Real > const &  exp_trace,
FittingInfo fit_info,
std::map< Size, Real > const &  sim_histogram,
Size const &  bins_per_a 
)

Custom constructor.

References simulate_decay().

Member Function Documentation

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::calc_4pdeer ( std::map< Real, Real > const &  exp_trace,
FittingInfo const &  fit_info,
std::map< Size, Real > const &  sim_histogram,
Size const &  bins_per_a 
)
Real core::scoring::epr_deer::Simulated4PDEERTrace::fit_k ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  trace,
FittingInfo fit_info,
Real const &  d,
Real const &  l 
)

Fit the background decay using linear regression.

References core::scoring::epr_deer::FittingInfo::time_pts_sqd_.

Referenced by optimize_bckg(), and optimize_mod_depth().

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::fit_trace ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  trace,
Real const &  d,
Real const &  k,
Real const &  l 
)

Convert an intramolecular trace to an intermolecular trace given background parameters.

Referenced by optimize_bckg(), and optimize_mod_depth().

Real core::scoring::epr_deer::Simulated4PDEERTrace::operator[] ( Real const &  t) const

Bracket operator for accessing the DEER trace.

References trace_.

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::optimize_bckg ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  trace_no_bckg,
FittingInfo fit_info 
)

Optimize the background function of the DEER trace: general function.

References core::scoring::epr_deer::FittingInfo::bckg_.

Referenced by simulate_decay().

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::optimize_bckg ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  trace,
FittingInfo fit_info,
bool const &  optimize_dim 
)
void core::scoring::epr_deer::Simulated4PDEERTrace::optimize_mod_depth ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  trace,
FittingInfo fit_info,
Real d,
Real k,
Real l,
bool  fit_dim 
)

Optimize the modulation depth using simple gradient descent.

References fit_k(), fit_trace(), core::scoring::epr_deer::FittingInfo::mod_depth_bounds_, and sum_of_squares().

Referenced by optimize_bckg().

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::simulate_decay ( std::map< Real, Real > const &  exp_trace,
FittingInfo fit_info,
std::map< Size, Real > const &  sim_histogram,
Size const &  bins_per_a 
)

Main function for simulating 4-pulse DEER trace This function first simulates the intramolecular dipolar coupling form factor using the evolution kernel described in "DEER Distance Measurements on Proteins" by Jeschke (2012). It then finds the best background fit for the experimental data, if necessary (3D by default, but can be set to "NONE" or "NON-3D") Background-fitted DEER trace is saved and returned.

References calc_4pdeer(), optimize_bckg(), and trace_.

Referenced by core::scoring::epr_deer::DEERDecayData::get_score(), and Simulated4PDEERTrace().

Real core::scoring::epr_deer::Simulated4PDEERTrace::sum_of_squares ( std::map< Real, Real > const &  exp_trace,
Real const &  noise = 1.0 
)

Determine the residuals between an experimental trace and a simulated trace.

References trace_.

Referenced by core::scoring::epr_deer::DEERDecayData::get_score(), optimize_bckg(), and optimize_mod_depth().

Real core::scoring::epr_deer::Simulated4PDEERTrace::sum_of_squares ( std::map< Real, Real > const &  exp_trace,
std::map< Real, Real > const &  sim_trace,
Real const &  noise = 1.0 
)

Determine the residuals between an experimental trace and a simulated trace.

Member Data Documentation

std::map< Real, Real > core::scoring::epr_deer::Simulated4PDEERTrace::trace_
private

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