IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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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"
Go to the source code of this file.
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... | |
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.