IMP Reference Guide
2.20.0
The Integrative Modeling Platform
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Basic utilities for handling cryo-electron microscopy 3D density maps. More...
Basic utilities for handling cryo-electron microscopy 3D density maps.
The main functionalities are:
The restraints vary based on how accurately the fit to the density is scored, which is usually related to the evaluation speed. Pick more accurate Restraints for higher resolution maps and models. Below is the Restraints list sorted from the fastest and most simple to the slowest and most accurate.
We also provide a number of command line tools to handle electron microscopy density maps and associated files:
Estimate EM density threshold.
Write out density map principal components in cmm format.
Write out protein principal components in cmm format.
Resample a density map.
Samples a protein into a simulated 3D density map.
Display the header information for a density map.
Author(s): Keren Lasker, Javier Velázquez-Muriel, Friedrich Förster, Daniel Russel, Dina Schneidman
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
Classes | |
class | CoarseCCatIntervals |
Cross correlation coefficient calculator. More... | |
class | CoarseConvolution |
Convolutes two grids. More... | |
class | DensityFillingRestraint |
Calculate score based on fit to EM map. More... | |
class | DensityHeader |
class | DensityMap |
Class for handling density maps. More... | |
class | DistanceMask |
Calculates and stores a distance mask. More... | |
class | EMReaderWriter |
class | EnvelopeFitRestraint |
A restraint for envelope-based scoring of particles in the density map. More... | |
class | EnvelopePenetrationRestraint |
Calculate score based on fit to EM map. More... | |
class | EnvelopeScore |
class for envelope based scoring using MapDistanceTransform More... | |
class | FitRestraint |
Calculate score based on fit to EM map. More... | |
class | FitRestraintBayesEM3D |
Calculate score based on fit to EM map. More... | |
class | FittingSolutions |
A simple list of fitting solutions. More... | |
class | HighDensityEmbedding |
class | ImageHeader |
Class to deal with the header of Electron Microscopy images in IMP. More... | |
class | KernelParameters |
Calculates and stores Gaussian kernel parameters. More... | |
class | MapDistanceTransform |
Class for getting the distance from the map envelope. More... | |
class | MapReaderWriter |
The base class to handle reading and writing of density maps. More... | |
class | MRCReaderWriter |
class | PCAAligner |
Fast alignment of points to a density map using principal components. More... | |
class | PCAFitRestraint |
Calculate score based on fit to EM map. More... | |
class | RadiusDependentDistanceMask |
class | SampledDensityMap |
Class for sampling a density map from particles. More... | |
struct | SpiderHeader |
Header for Spider images. IMP-EM is designed to be compatible with it. More... | |
class | SpiderMapReaderWriter |
Class to read EM maps (3D) in Spider and Xmipp formats. More... | |
class | SurfaceShellDensityMap |
The class represents a molecule as shells of distance from the surface. More... | |
class | Voxel |
class | XplorReaderWriter |
Typedefs | |
typedef IMP::Vector < IMP::Pointer< DensityMap > > | DensityMaps |
typedef IMP::Vector < IMP::WeakPointer< DensityMap > > | DensityMapsTemp |
typedef IMP::Vector < FittingSolutions > | FittingSolutionsList |
typedef IMP::Vector < KernelParameters > | KernelParametersList |
typedef IMP::Vector < IMP::Pointer < SampledDensityMap > > | SampledDensityMaps |
typedef IMP::Vector < IMP::WeakPointer < SampledDensityMap > > | SampledDensityMapsTemp |
typedef IMP::Vector < IMP::Pointer < SurfaceShellDensityMap > > | SurfaceShellDensityMaps |
typedef IMP::Vector < IMP::WeakPointer < SurfaceShellDensityMap > > | SurfaceShellDensityMapsTemp |
typedef IMP::Vector< Voxel > | Voxels |
Enumerations | |
enum | KernelType { GAUSSIAN, BINARIZED_SPHERE, SPHERE } |
Functions | |
Float | approximate_molecular_mass (DensityMap *m, Float threshold) |
Estimate the molecular mass from a map. More... | |
double | bayesem3d_get_cross_correlation_coefficient (const DensityMap *em1, const DensityMap *em2) |
Compute a normalized cross-correlation coefficient. More... | |
Floats | bayesem3d_get_cumulative_sum (DensityMap *em) |
Compute the cumulative sum of the histogram computed from EM map. More... | |
std::map< double, double > | bayesem3d_get_cumulative_sum_with_reference (DensityMap *em) |
Compute the cumulative sum of the histogram given a reference. More... | |
DensityMap * | bayesem3d_get_density_from_particle (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, const double window_size=1.0) |
std::map< double, int > | bayesem3d_get_distinct_and_counts (DensityMap *em) |
Get histogram of density in EM map. More... | |
FloatPair | 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 | bayesem3d_get_logabssumexp (double x, double y, double sx, double sy) |
Numerically stable logabssumexp. More... | |
FloatPair | bayesem3d_get_logabssumprodexp (double x, double y, double wx, double wy) |
Numerically stable logabssumprodexp. More... | |
double | bayesem3d_get_logsumexp (double x, double y) |
Numerically stable logsumexp. More... | |
double | bayesem3d_get_logsumprodexp (double x, double y, double wx, double wy) |
Numerically stable logsumexpprod. More... | |
void | bayesem3d_get_normalized_intensities (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution) |
std::pair< double, algebra::Vector3Ds > | 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 > | 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 > | 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 | bayesem3d_linear_interpolate (const Floats &x_data, const Floats &y_data, double x, bool extrapolate) |
Basic linear interpolation given vectors of values. More... | |
DensityMap * | binarize (DensityMap *orig_map, float threshold, bool reverse=false) |
Return a map with 0 for all voxels below the threshold and 1 for those above. More... | |
Float | calculate_intersection_score (const SurfaceShellDensityMap *d1, const SurfaceShellDensityMap *d2) |
Float | compute_fitting_score (const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key()) |
Compute fitting scores for a given set of rigid transformations. More... | |
FittingSolutions | compute_fitting_scores (const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key()) |
Compute fitting scores for a given set of rigid transformations. More... | |
FittingSolutions | compute_fitting_scores (DensityMap *em_map, core::RigidBody rb, Refiner *refiner, const algebra::Transformation3Ds &transformations) |
Compute fitting scores for a given set of rigid transformations. More... | |
double | convolute (const DensityMap *m1, const DensityMap *m2) |
Return a convolution between density maps m1 and m2. More... | |
DensityHeader | create_density_header (const algebra::BoundingBoxD< 3 > &bb, float spacing) |
Create a header from a bounding box in 3D. More... | |
DensityMap * | create_density_map (const DensityMap *other) |
Create a copy of another map. More... | |
DensityMap * | create_density_map (const algebra::BoundingBox3D &bb, double spacing) |
Create an empty density map from a bounding box. More... | |
DensityMap * | create_density_map (int nx, int ny, int nz, double spacing) |
Create an empty density map. More... | |
template<class S , class V , class E > | |
DensityMap * | create_density_map (const IMP::algebra::GridD< 3, S, V, E > &arg) |
Create a density map from an arbitrary IMP::algebra::GridD. More... | |
Particles | density2particles (DensityMap *dmap, Float threshold, Model *m, int step=1) |
Convert a density grid to a set of particles. More... | |
algebra::Vector3Ds | density2vectors (DensityMap *dmap, Float threshold) |
Convert a density grid to a set of vectors. More... | |
void | DensityHeader_to_ImageHeader (const DensityHeader &header, ImageHeader &h) |
double | EXP (float y) |
algebra::BoundingBoxD< 3 > | get_bounding_box (const DensityMap *m, Float threshold) |
Get the bounding box for a map. More... | |
algebra::BoundingBoxD< 3 > | get_bounding_box (const DensityMap *m) |
double | get_coarse_cc_coefficient (const DensityMap *grid1, const DensityMap *grid2, double grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.)) |
Calculates the cross correlation coefficient between two maps. More... | |
double | get_coarse_cc_local_coefficient (const DensityMap *em_map, DensityMap *model_map, double voxel_data_threshold) |
Local cross correlation function. More... | |
double | get_coarse_cc_score (DensityMap *data, SampledDensityMap *model_map, double scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.)) |
Calculates the value of the EM fitting term. More... | |
algebra::GridD < 3, algebra::DenseGridStorageD < 3, float >, float > | get_grid (DensityMap *in_map) |
Return a dense grid containing the voxels of the passed density map. More... | |
bool | get_interiors_intersect (const DensityMap *d1, const DensityMap *d2) |
DensityMap * | get_max_map (DensityMaps maps) |
Return a map where each voxel is the maximum value from the input maps. More... | |
Float | get_molecular_mass_at_threshold (DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ) |
Compute an approximate molecular mass. More... | |
long | get_number_of_particles_outside_of_the_density (DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0) |
Get the number of particles that are outside of the density. More... | |
Ints | get_numbers_of_particles_outside_of_the_density (DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0) |
Get numbers of particles (mult transforms) that are outside the density. More... | |
double | get_percentage_of_voxels_covered_by_particles (DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0) |
Get the number of density voxels that are not covered by particles. More... | |
DensityMap * | get_segment (DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end) |
Get a segment of the map according to xyz indexes. More... | |
DensityMap * | get_segment (DensityMap *map_to_segment, algebra::Vector3Ds vecs, float dist) |
Get a segment of the map covered by the input points. More... | |
DensityMap * | get_segment_by_masking (DensityMap *map_to_segment, DensityMap *mask, float mas_threshold) |
Get a segment of the map covered by another map. More... | |
double | get_sum (const DensityMap *m1) |
Return the sum of all voxels. More... | |
Float | get_threshold_for_approximate_mass (DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ) |
Computes the threshold to consider in an EM map to get a desired mass. More... | |
Float | get_threshold_for_approximate_volume (DensityMap *m, Float desired_volume) |
Computes the threshold consider in an EM map to get a desired volume. More... | |
DensityMap * | get_threshold_map (const DensityMap *orig_map, float threshold) |
Return a map with 0 for all voxels below the threshold. More... | |
void | get_transformed_into2 (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into) |
Float | get_volume_at_threshold (DensityMap *m, Float threshold) |
Compute an approximate volume. More... | |
void | ImageHeader_to_DensityHeader (const ImageHeader &h, DensityHeader &header) |
DensityMap * | interpolate_map (DensityMap *in_map, double new_spacing) |
Return a new map with an updated spacing. More... | |
FittingSolutions | local_rigid_fitting (Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true) |
Local rigid fitting of a rigid body. More... | |
FittingSolutions | local_rigid_fitting_around_point (Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false) |
Local rigid fitting of a rigid body around a center point. More... | |
FittingSolutions | local_rigid_fitting_around_points (Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) |
Local rigid fitting of a rigid body around a set of center points. More... | |
FittingSolutions | local_rigid_fitting_grid_search (const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100) |
Local grid search rigid fitting. More... | |
DensityMap * | mask_and_norm (em::DensityMap *dmap, em::DensityMap *mask) |
Return a masked density, and normalize the output map within the mask region. More... | |
DensityMap * | multiply (const DensityMap *m1, const DensityMap *m2) |
Return a density map for which voxel i contains the result of m1[i]*m2[i]. More... | |
SampledDensityMap * | particles2binarized_density (const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) |
SampledDensityMap * | particles2density (const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) |
Resample a set of particles into a density grid. More... | |
SurfaceShellDensityMap * | particles2surface (const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) |
Resample a set of particles into a density grid. More... | |
def | write_pca_cmm |
Write out principal components to a file in Chimera Marker format. More... | |
Variables | |
const double | EPS = 1e-16 |
Standard module functions | |
All | |
std::string | get_module_version () |
Return the version of this module, as a string. More... | |
std::string | get_module_name () |
std::string | get_data_path (std::string file_name) |
Return the full path to one of this module's data files. More... | |
std::string | get_example_path (std::string file_name) |
Return the full path to one of this module's example files. More... | |
typedef IMP::Vector<IMP::Pointer< DensityMap > > IMP::em::DensityMaps |
A vector of reference-counting object pointers.
Definition at line 546 of file DensityMap.h.
typedef IMP::Vector<IMP::WeakPointer< DensityMap > > IMP::em::DensityMapsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 546 of file DensityMap.h.
Pass or store a set of FittingSolutions .
Definition at line 120 of file rigid_fitting.h.
Pass or store a set of KernelParameters .
Definition at line 113 of file KernelParameters.h.
A vector of reference-counting object pointers.
Definition at line 136 of file SampledDensityMap.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 136 of file SampledDensityMap.h.
A vector of reference-counting object pointers.
Definition at line 96 of file SurfaceShellDensityMap.h.
typedef IMP::Vector<IMP::WeakPointer< SurfaceShellDensityMap > > IMP::em::SurfaceShellDensityMapsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 96 of file SurfaceShellDensityMap.h.
Float IMP::em::approximate_molecular_mass | ( | DensityMap * | m, |
Float | threshold | ||
) |
Estimate the molecular mass from a map.
[in] | m | a density map |
[in] | threshold | consider volume of only voxels above this threshold |
double IMP::em::bayesem3d_get_cross_correlation_coefficient | ( | const DensityMap * | em1, |
const DensityMap * | em2 | ||
) |
Compute a normalized cross-correlation coefficient.
Floats IMP::em::bayesem3d_get_cumulative_sum | ( | DensityMap * | em | ) |
Compute the cumulative sum of the histogram computed from EM map.
std::map<double, double> IMP::em::bayesem3d_get_cumulative_sum_with_reference | ( | DensityMap * | em | ) |
Compute the cumulative sum of the histogram given a reference.
DensityMap* IMP::em::bayesem3d_get_density_from_particle | ( | DensityMap * | em, |
const IMP::ParticlesTemp & | ps, | ||
double | resolution, | ||
const double | window_size = 1.0 |
||
) |
Compute a generated EM density map given particles. Header and box size is copied from reference EM density map
std::map<double, int> IMP::em::bayesem3d_get_distinct_and_counts | ( | DensityMap * | em | ) |
Get histogram of density in EM map.
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.
FloatPair IMP::em::bayesem3d_get_logabssumexp | ( | double | x, |
double | y, | ||
double | sx, | ||
double | sy | ||
) |
Numerically stable logabssumexp.
FloatPair IMP::em::bayesem3d_get_logabssumprodexp | ( | double | x, |
double | y, | ||
double | wx, | ||
double | wy | ||
) |
Numerically stable logabssumprodexp.
double IMP::em::bayesem3d_get_logsumexp | ( | double | x, |
double | y | ||
) |
Numerically stable logsumexp.
double IMP::em::bayesem3d_get_logsumprodexp | ( | double | x, |
double | y, | ||
double | wx, | ||
double | wy | ||
) |
Numerically stable logsumexpprod.
void IMP::em::bayesem3d_get_normalized_intensities | ( | DensityMap * | em, |
const IMP::ParticlesTemp & | ps, | ||
double | resolution | ||
) |
Normalization of an EM map by histogram matching against the CDF of the EM map generated from a set of particles.
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.
[in] | em | DensityMap class containing the EM map. Note: the EM density map must be normalized by the histogram matching routine. |
[in] | ps | ParticlesTemp class containing the particles of the tested model. |
[in] | resolution | the resolution of the input EM density map. Note: Usually is contained in the header but this is for safety. |
[in] | sigma | The expected variance of the difference between the normalized EM density map and the tested model. |
[in] | window_size | The size of the window to extend the blur of the model |
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.
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.
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.
DensityMap* IMP::em::binarize | ( | DensityMap * | orig_map, |
float | threshold, | ||
bool | reverse = false |
||
) |
Return a map with 0 for all voxels below the threshold and 1 for those above.
[in] | orig_map | the map to binarize |
[in] | threshold | values below the threshold are set to 0 and 1 otherwise |
[in] | reverse | if true values above the threshold are set to 0 and 1 otherwise |
Float IMP::em::compute_fitting_score | ( | const ParticlesTemp & | ps, |
DensityMap * | em_map, | ||
FloatKey | wei_key = atom::Mass::get_mass_key() |
||
) |
Compute fitting scores for a given set of rigid transformations.
Scores how well a set of particles fit a map
[in] | ps | The particles to be fitted |
[in] | em_map | The density map to fit to |
[in] | wei_key | The weight key of the particles in the rigid body |
FittingSolutions IMP::em::compute_fitting_scores | ( | const ParticlesTemp & | ps, |
DensityMap * | em_map, | ||
const algebra::Transformation3Ds & | transformations, | ||
bool | fast_version = false , |
||
bool | local_score = false , |
||
const FloatKey & | wei_key = atom::Mass::get_mass_key() |
||
) |
Compute fitting scores for a given set of rigid transformations.
Score how well a set of particles fit to the map in various rigid transformations.
[in] | ps | The particles to be fitted (treated rigid) |
[in] | em_map | The density map to fit to |
[in] | wei_key | The weight key of the particles in the rigid body |
[in] | fast_version | If fast_version is used the sampled density map of the input particles (ps) is not resampled for each transformation but instead the corresponding grid is rotated. This option significantly improves the running times but the returned scores are less accurate |
[in] | transformations | A set of rigid transformations |
[in] | fast_version | if true the density map of each transformation is interpolated |
[in] | local_score | if true a local cross correlation score is used |
FittingSolutions IMP::em::compute_fitting_scores | ( | DensityMap * | em_map, |
core::RigidBody | rb, | ||
Refiner * | refiner, | ||
const algebra::Transformation3Ds & | transformations | ||
) |
Compute fitting scores for a given set of rigid transformations.
Score how well a rigid body fits to the map
[in] | em_map | The density map to fit to |
[in] | rb | The rigid body |
[in] | refiner | The rigid body refiner |
[in] | transformations | Transformations of the rigid body |
Definition at line 289 of file rigid_fitting.h.
double IMP::em::convolute | ( | const DensityMap * | m1, |
const DensityMap * | m2 | ||
) |
Return a convolution between density maps m1 and m2.
The function assumes m1 and m2 are of the same dimensions.
DensityHeader IMP::em::create_density_header | ( | const algebra::BoundingBoxD< 3 > & | bb, |
float | spacing | ||
) |
Create a header from a bounding box in 3D.
DensityMap* IMP::em::create_density_map | ( | const DensityMap * | other | ) |
Create a copy of another map.
DensityMap* IMP::em::create_density_map | ( | const algebra::BoundingBox3D & | bb, |
double | spacing | ||
) |
Create an empty density map from a bounding box.
DensityMap* IMP::em::create_density_map | ( | int | nx, |
int | ny, | ||
int | nz, | ||
double | spacing | ||
) |
Create an empty density map.
DensityMap* IMP::em::create_density_map | ( | const IMP::algebra::GridD< 3, S, V, E > & | arg | ) |
Create a density map from an arbitrary IMP::algebra::GridD.
Definition at line 674 of file DensityMap.h.
Particles IMP::em::density2particles | ( | DensityMap * | dmap, |
Float | threshold, | ||
Model * | m, | ||
int | step = 1 |
||
) |
Convert a density grid to a set of particles.
Each such particle will have xyz attributes and a density_val attribute of type Float.
[in] | dmap | the density map |
[in] | threshold | only voxels with density above the given threshold will be converted to particles |
[in] | m | model to store the new particles |
[in] | step | sample every X steps in each direction |
algebra::Vector3Ds IMP::em::density2vectors | ( | DensityMap * | dmap, |
Float | threshold | ||
) |
Convert a density grid to a set of vectors.
[in] | dmap | the density map |
[in] | threshold | only voxels with density above the given threshold will be converted to vectors |
void IMP::em::DensityHeader_to_ImageHeader | ( | const DensityHeader & | header, |
ImageHeader & | h | ||
) |
Function to transfer the (compatible) information content from DensityHeader to ImageHeader
algebra::BoundingBoxD<3> IMP::em::get_bounding_box | ( | const DensityMap * | m, |
Float | threshold | ||
) |
Get the bounding box for a map.
[in] | m | a density map |
[in] | threshold | find the bounding box for voxels with value above the threshold |
double IMP::em::get_coarse_cc_coefficient | ( | const DensityMap * | grid1, |
const DensityMap * | grid2, | ||
double | grid2_voxel_data_threshold, | ||
bool | allow_padding = false , |
||
FloatPair | norm_factors = FloatPair(0., 0.) |
||
) |
Calculates the cross correlation coefficient between two maps.
Cross correlation coefficient between the em density and the density of a model. The function applied is: \(\frac{\sum_{i=1}^{N}{{td}_i}{{md}_i}-{N} {{mean}_{td}} {{mean}_{md}}} {N\sigma_{{td}}\sigma_{{md}}}\), where \(N\) is the number of voxels, \({td}\) is the target density, \({tm}\) is the model density,
[in] | grid1 | The first 3D grid |
[in] | grid2 | The second 3D grid |
[in] | grid2_voxel_data_threshold | voxels with value lower than threshold in grid2 are not summed (avoid calculating correlation on voxels below the threshold) |
[in] | allow_padding | determines whether the two maps should be padded to have the same size before the calculation is performed. If set to false and the grids are not of the same size, the function will throw an exception. |
[in] | norm_factors | if set these precalculated terms are used for normalization |
double IMP::em::get_coarse_cc_local_coefficient | ( | const DensityMap * | em_map, |
DensityMap * | model_map, | ||
double | voxel_data_threshold | ||
) |
Local cross correlation function.
double IMP::em::get_coarse_cc_score | ( | DensityMap * | data, |
SampledDensityMap * | model_map, | ||
double | scalefactor, | ||
bool | recalc_rms = true , |
||
bool | resample = true , |
||
FloatPair | norm_factors = FloatPair(0., 0.) |
||
) |
Calculates the value of the EM fitting term.
[in] | data | DensityMap class containing the EM map. note: correct RMSD and mean MUST be in the header! |
[in] | model_map | SampledDensityMap class prepared to contain the simulated EM map for the model. |
[in] | scalefactor | scale factor to apply to the value of the cross correlation term |
[in] | recalc_rms | determines whether the RMS of both maps should be recalculated prior to the correlation calculation. False is faster, but potentially inaccurate |
[in] | resample | if true, the model density map is resampled |
[in] | norm_factors | if set these precalculated terms are used for normalization |
std::string IMP::em::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::em::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
algebra::GridD<3, algebra::DenseGridStorageD<3, float>, float> IMP::em::get_grid | ( | DensityMap * | in_map | ) |
Return a dense grid containing the voxels of the passed density map.
The returned grid has the same bounding box as the map.
Definition at line 182 of file bayesianem/utilities.h.
DensityMap* IMP::em::get_max_map | ( | DensityMaps | maps | ) |
Return a map where each voxel is the maximum value from the input maps.
std::string IMP::em::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.
Float IMP::em::get_molecular_mass_at_threshold | ( | DensityMap * | m, |
Float | threshold, | ||
atom::ProteinDensityReference | ref = atom::HARPAZ |
||
) |
Compute an approximate molecular mass.
Compute an approximate molecular mass for the set of voxels with intensity under a given threshold
[in] | m | a density map |
[in] | threshold | only voxels above this threshold will be considered |
[in] | ref | the protein density reference to use in the computation. The default protein density for this computation is HARPAZ |
long IMP::em::get_number_of_particles_outside_of_the_density | ( | DensityMap * | dmap, |
const Particles & | ps, | ||
const IMP::algebra::Transformation3D & | t = IMP::algebra::get_identity_transformation_3d() , |
||
float | thr = 0.0 |
||
) |
Get the number of particles that are outside of the density.
Ints IMP::em::get_numbers_of_particles_outside_of_the_density | ( | DensityMap * | dmap, |
const Particles & | ps, | ||
const IMP::algebra::Transformation3Ds & | transformations, | ||
float | thr = 0.0 |
||
) |
Get numbers of particles (mult transforms) that are outside the density.
double IMP::em::get_percentage_of_voxels_covered_by_particles | ( | DensityMap * | dmap, |
const Particles & | ps, | ||
float | smoothing_radius = 3. , |
||
const IMP::algebra::Transformation3D & | t = IMP::algebra::get_identity_transformation_3d() , |
||
float | thr = 0.0 |
||
) |
Get the number of density voxels that are not covered by particles.
DensityMap* IMP::em::get_segment | ( | DensityMap * | map_to_segment, |
int | nx_start, | ||
int | nx_end, | ||
int | ny_start, | ||
int | ny_end, | ||
int | nz_start, | ||
int | nz_end | ||
) |
Get a segment of the map according to xyz indexes.
DensityMap* IMP::em::get_segment | ( | DensityMap * | map_to_segment, |
algebra::Vector3Ds | vecs, | ||
float | dist | ||
) |
Get a segment of the map covered by the input points.
DensityMap* IMP::em::get_segment_by_masking | ( | DensityMap * | map_to_segment, |
DensityMap * | mask, | ||
float | mas_threshold | ||
) |
Get a segment of the map covered by another map.
double IMP::em::get_sum | ( | const DensityMap * | m1 | ) |
Return the sum of all voxels.
Float IMP::em::get_threshold_for_approximate_mass | ( | DensityMap * | m, |
Float | desired_mass, | ||
atom::ProteinDensityReference | ref = atom::HARPAZ |
||
) |
Computes the threshold to consider in an EM map to get a desired mass.
Computes the threshold to consider in an EM map to get a desired mass (only voxels with intensity greater than the threshold are considered)
[in] | m | a density map |
[in] | desired_mass | (in Da) |
[in] | ref | the protein density reference to use in the computation. The default protein density for this computation is HARPAZ |
Float IMP::em::get_threshold_for_approximate_volume | ( | DensityMap * | m, |
Float | desired_volume | ||
) |
Computes the threshold consider in an EM map to get a desired volume.
Computes the threshold consider in an EM map to get a desired volume (i.e, the set of voxels with intensity greater than the threshold occupies that volume)
[in] | m | a density map |
[in] | desired_volume | (in A^3) |
DensityMap* IMP::em::get_threshold_map | ( | const DensityMap * | orig_map, |
float | threshold | ||
) |
Return a map with 0 for all voxels below the threshold.
[in] | orig_map | the map to threshold |
[in] | threshold | values below the threshold are set to 0 and left unchanged otherwise |
Float IMP::em::get_volume_at_threshold | ( | DensityMap * | m, |
Float | threshold | ||
) |
Compute an approximate volume.
Compute an approximate volume for the set of voxels with intensity under a given threshold
[in] | m | a density map |
[in] | threshold | consider volume of only voxels above this threshold |
void IMP::em::ImageHeader_to_DensityHeader | ( | const ImageHeader & | h, |
DensityHeader & | header | ||
) |
Function to transfer the (compatible) information content from ImageHeader to DensityHeader
DensityMap* IMP::em::interpolate_map | ( | DensityMap * | in_map, |
double | new_spacing | ||
) |
Return a new map with an updated spacing.
Input data is interpolated accordingly.
FittingSolutions IMP::em::local_rigid_fitting | ( | Particle * | p, |
Refiner * | refiner, | ||
const FloatKey & | weight_key, | ||
DensityMap * | dmap, | ||
OptimizerStates | display_log, | ||
Int | number_of_optimization_runs = 5 , |
||
Int | number_of_mc_steps = 10 , |
||
Int | number_of_cg_steps = 100 , |
||
Float | max_translation = 2. , |
||
Float | max_rotation = .3 , |
||
bool | fast = true |
||
) |
Local rigid fitting of a rigid body.
Fit a set of particles to a density map around their centroid. The fitting is assessed using the cross-correlation score. The optimization is a standard MC/CG procedure. The function returns a list of solutions sorted by the cross-correlation score.
[in] | p | The root of the hierarchy to fit |
[in] | refiner | The refiner to get the leaves of the particle |
[in] | weight_key | The weight key of the particles in the rigid body |
[in] | dmap | The density map to fit to |
[in] | display_log | If provided, then intermediate states during the optimization procedure are printed |
[in] | number_of_optimization_runs | number of Monte Carlo optimizations |
[in] | number_of_mc_steps | number of steps in a Monte Carlo optimization |
[in] | number_of_cg_steps | number of Conjugate Gradients steps in a Monte Carlo step |
[in] | max_translation | maximum translation step in a MC optimization step |
[in] | max_rotation | maximum rotation step in radians in a single MC optimization step |
[in] | fast | if true the density map of the rigid body is not resampled but transformed at each iteration of the optimization |
Definition at line 185 of file rigid_fitting.h.
FittingSolutions IMP::em::local_rigid_fitting_around_point | ( | Particle * | p, |
Refiner * | refiner, | ||
const FloatKey & | weight_key, | ||
DensityMap * | dmap, | ||
const algebra::Vector3D & | anchor_centroid, | ||
OptimizerStates | display_log, | ||
Int | number_of_optimization_runs = 5 , |
||
Int | number_of_mc_steps = 10 , |
||
Int | number_of_cg_steps = 100 , |
||
Float | max_translation = 2. , |
||
Float | max_rotation = .3 , |
||
bool | fast = false |
||
) |
Local rigid fitting of a rigid body around a center point.
Fit a set of particles to a density map around an anchor point. The fitting is assessed using the cross-correlation score. The optimization is a standard MC/CG procedure. The function returns a list of solutions sorted by the cross-correlation score.
[in] | p | The rigid body to fit |
[in] | refiner | Refiner to yield rigid body members |
[in] | weight_key | The weight key of the particles in the rigid body |
[in] | dmap | The density map to fit to |
[in] | anchor_centroid | The point to fit the particles around |
[in] | display_log | If provided, then intermediate states in during the optimization procedure are printed |
[in] | number_of_optimization_runs | number of Monte Carlo optimizations |
[in] | number_of_mc_steps | number of steps in a Monte Carlo optimization |
[in] | number_of_cg_steps | number of Conjugate Gradients steps in a Monte Carlo step |
[in] | max_translation | maximum translation step in a MC optimization step |
[in] | max_rotation | maximum rotation step in a single MC optimization step |
[in] | fast | if true the density map of the rigid body is not resampled but transformed at each iteration of the optimization |
FittingSolutions IMP::em::local_rigid_fitting_around_points | ( | Particle * | p, |
Refiner * | refiner, | ||
const FloatKey & | wei_key, | ||
DensityMap * | dmap, | ||
const algebra::Vector3Ds & | anchor_centroids, | ||
OptimizerStates | display_log, | ||
Int | number_of_optimization_runs = 5 , |
||
Int | number_of_mc_steps = 10 , |
||
Int | number_of_cg_steps = 100 , |
||
Float | max_translation = 2. , |
||
Float | max_rotation = .3 |
||
) |
Local rigid fitting of a rigid body around a set of center points.
Fit a set of particles to a density map around each of the input points. The function apply local_rigid_fitting_around_point around each center.
[in] | p | The rigid body to fit |
[in] | refiner | Refiner to yield rigid body members |
[in] | wei_key | The weight key of the particles in the rigid body |
[in] | dmap | The density map to fit to |
[in] | anchor_centroids | The points to fit the particles around |
[in] | display_log | If provided, then intermediate states in during the optimization procedure are printed |
[in] | number_of_optimization_runs | number of Monte Carlo optimizations |
[in] | number_of_mc_steps | number of steps in a Monte Carlo optimization |
[in] | number_of_cg_steps | number of Conjugate Gradients steps in a Monte Carlo step |
[in] | max_translation | maximum translation step in a MC optimization step |
[in] | max_rotation | maximum rotation step in a single MC optimization step |
FittingSolutions IMP::em::local_rigid_fitting_grid_search | ( | const ParticlesTemp & | ps, |
const FloatKey & | wei_key, | ||
DensityMap * | dmap, | ||
Int | max_voxels_translation = 2 , |
||
Int | translation_step = 1 , |
||
Float | max_angle_in_radians = 0.174 , |
||
Int | number_of_rotations = 100 |
||
) |
Local grid search rigid fitting.
Fit a set of particles to a density map around their centroid. The fitting is assessed using the cross-correlation score. The optimization is a grid search
[in] | ps | The particles to be fitted (treated rigid) |
[in] | wei_key | The weight key of the particles in the rigid body |
[in] | dmap | The density map to fit to |
[in] | max_voxels_translation | Sample translations within -max_voxel_translation to max_voxel_translation |
[in] | translation_step | The translation sampling step |
[in] | max_angle_in_radians | Sample rotations with +- max_angle_in_radians around the current rotation |
[in] | number_of_rotations | The number of rotations to sample |
DensityMap* IMP::em::mask_and_norm | ( | em::DensityMap * | dmap, |
em::DensityMap * | mask | ||
) |
Return a masked density, and normalize the output map within the mask region.
[in] | dmap | the density map to mask |
[in] | mask | the mask |
DensityMap* IMP::em::multiply | ( | const DensityMap * | m1, |
const DensityMap * | m2 | ||
) |
Return a density map for which voxel i contains the result of m1[i]*m2[i].
The function assumes m1 and m2 are of the same dimensions.
SampledDensityMap* IMP::em::particles2binarized_density | ( | const ParticlesTemp & | ps, |
Float | resolution, | ||
Float | apix, | ||
int | sig_cutoff = 3 , |
||
const FloatKey & | weight_key = IMP::atom::Mass::get_mass_key() |
||
) |
Resample a set of particles into a binarized density map 1 for voxels containing particles and 0 otherwise Each such particle should have xyz radius and weight attributes
[in] | ps | the particles to sample |
[in] | resolution | the resolution of the new sampled map |
[in] | apix | the voxel size of the sampled map |
[in] | sig_cutoff | sigma cutoff used in sampling |
[in] | weight_key | the weight attribute key of the particles |
Definition at line 76 of file converters.h.
SampledDensityMap* IMP::em::particles2density | ( | const ParticlesTemp & | ps, |
Float | resolution, | ||
Float | apix, | ||
int | sig_cutoff = 3 , |
||
const FloatKey & | weight_key = IMP::atom::Mass::get_mass_key() |
||
) |
Resample a set of particles into a density grid.
Each such particle should have xyz, radius and weight attributes
[in] | ps | the particles to sample |
[in] | resolution | the resolution of the new sampled map |
[in] | apix | the voxel size of the sampled map |
[in] | sig_cutoff | sigma cutoff used in sampling |
[in] | weight_key | the weight attribute key of the particles |
SurfaceShellDensityMap* IMP::em::particles2surface | ( | const ParticlesTemp & | ps, |
Float | apix, | ||
const FloatKey & | weight_key = IMP::atom::Mass::get_mass_key() |
||
) |
Resample a set of particles into a density grid.
Each such particle should have xyz radius and weight attributes
[in] | ps | the particles to sample |
[in] | apix | the voxel size of the surface map |
[in] | weight_key | the weight attribute key of the particles |
def IMP.em.write_pca_cmm | ( | pca, | |
fh | |||
) |
Write out principal components to a file in Chimera Marker format.
Definition at line 2501 of file em/__init__.py.