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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
BayesEM3D.h File Reference

Compute a Bayesian formalism score and its derivatives to assess degree of match between a tested model and a density object. More...

#include <IMP/Refiner.h>
#include <IMP/core/rigid_bodies.h>
#include <IMP/em/KernelParameters.h>
#include <IMP/em/MRCReaderWriter.h>
#include <IMP/em/em_config.h>
#include <vector>
#include "DensityMap.h"
#include "def.h"
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Namespaces

 IMP
 Base functionality and abstract base classes for representation, scoring and sampling.
 
 IMP::em
 Basic utilities for handling cryo-electron microscopy 3D density maps.
 

Functions

double IMP::em::bayesem3d_get_cross_correlation_coefficient (const DensityMap *em1, const DensityMap *em2)
 Compute a normalized cross-correlation coefficient. More...
 
Floats IMP::em::bayesem3d_get_cumulative_sum (DensityMap *em)
 Compute the cumulative sum of the histogram computed from EM map. More...
 
std::map< double, double > IMP::em::bayesem3d_get_cumulative_sum_with_reference (DensityMap *em)
 Compute the cumulative sum of the histogram given a reference. More...
 
DensityMap * IMP::em::bayesem3d_get_density_from_particle (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, const double window_size=1.0)
 
std::map< double, int > IMP::em::bayesem3d_get_distinct_and_counts (DensityMap *em)
 Get histogram of density in EM map. More...
 
FloatPair IMP::em::bayesem3d_get_em_density_squared (DensityMap *em, long number_of_voxels)
 Compute the sum of the density and the sum of the squares of the density. More...
 
FloatPair IMP::em::bayesem3d_get_logabssumexp (double x, double y, double sx, double sy)
 Numerically stable logabssumexp. More...
 
FloatPair IMP::em::bayesem3d_get_logabssumprodexp (double x, double y, double wx, double wy)
 Numerically stable logabssumprodexp. More...
 
double IMP::em::bayesem3d_get_logsumexp (double x, double y)
 Numerically stable logsumexp. More...
 
double IMP::em::bayesem3d_get_logsumprodexp (double x, double y, double wx, double wy)
 Numerically stable logsumexpprod. More...
 
void IMP::em::bayesem3d_get_normalized_intensities (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
 
std::pair< double,
algebra::Vector3Ds > 
IMP::em::bayesem3d_get_score_and_derivative (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, double sigma, const double window_size=1.0)
 The function returns the negative log of the Normal distributed difference between a normalized EM density map and a tested model. To support sampling and optimization, the derivative of the score is also returned. More...
 
std::vector< double > IMP::em::bayesem3d_get_value (Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
 Compute the score and derivatives for a particle at a given voxel. More...
 
std::vector< double > IMP::em::bayesem3d_get_value_no_deriv (Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
 Compute the score without its derivative. More...
 
double IMP::em::bayesem3d_linear_interpolate (const Floats &x_data, const Floats &y_data, double x, bool extrapolate)
 Basic linear interpolation given vectors of values. More...
 

Detailed Description

Compute a Bayesian formalism score and its derivatives to assess degree of match between a tested model and a density object.

Copyright 2007-2020 IMP Inventors. All rights reserved.

Definition in file BayesEM3D.h.