Basic utilities for handling cryo-electron microscopy 3D density maps. More...

Detailed Description

Basic utilities for handling cryo-electron microscopy 3D density maps.

The main functionalities are:

Reading and writing various density map formats such as XPLOR, MRC, EM and SPIDER.
Simulating density maps of particles, supports particles of any radii and mass.
Calculating cross-correlation scores between a density map and a set of particles.
Implements several Restraints.

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.

PCAFitRestraint - compares how well the principal components of the density map fit to the principal components of the particles
DensityFillingRestraint - estimates the percentage of volume of the density map that is covered by particles
EnvelopePenetrationRestraint - estimates the number of particles that fall outside the density map
EnvelopeFitRestraint - scores how well the particles fit the density map using MapDistanceTransform that transforms a density map into a Distance Transform of the map envelope
FitRestraint - computes the fit using cross correlation

We also provide a number of command line tools to handle electron microscopy density maps and associated files:

estimate_threshold_from_molecular_mass

Estimate EM density threshold.

map2pca

Write out density map principal components in cmm format.

mol2pca

Write out protein principal components in cmm format.

resample_density

Resample a density map.

simulate_density_from_pdb

Samples a protein into a simulated 3D density map.

view_density_header

Display the header information for a density map.

Info

Author(s): Keren Lasker, Javier Velazquez-Muriel, Friedrich Foerster, 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:

See main IMP papers list.

Classes
class	CoarseCC
	Responsible for performing coarse fitting between two density objects. More...

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	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

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

class	PCAFitRestraint
	Calculate score based on fit to EM map. More...

class	RadiusDependentDistanceMask

class	RadiusDependentKernelParameters
	Calculates kernel parameters as a function of a specific radius. More...

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::base::Vector < IMP::base::Pointer < DensityMap > >	DensityMaps

typedef IMP::base::Vector < IMP::base::WeakPointer < DensityMap > >	DensityMapsTemp

typedef double	emreal

typedef IMP::base::Vector < FittingSolutions >	FittingSolutionsList

typedef IMP::base::Vector < KernelParameters >	KernelParametersList

typedef IMP::base::Vector < RadiusDependentKernelParameters >	RadiusDependentKernelParametersList

typedef IMP::base::Vector < IMP::base::Pointer < SampledDensityMap > >	SampledDensityMaps

typedef IMP::base::Vector < IMP::base::WeakPointer < SampledDensityMap > >	SampledDensityMapsTemp

typedef IMP::base::Vector < IMP::base::Pointer < SurfaceShellDensityMap > >	SurfaceShellDensityMaps

typedef IMP::base::Vector < IMP::base::WeakPointer < SurfaceShellDensityMap > >	SurfaceShellDensityMapsTemp

typedef IMP::base::Vector< Voxel >	Voxels

Enumerations
enum	KernelType { GAUSSIAN, BINARIZED_SPHERE, SPHERE }

Functions
void	add_to_map (DensityMap *dm, const kernel::Particles &pis)

Float	approximate_molecular_mass (DensityMap *m, Float threshold)

DensityMap *	binarize (DensityMap *orig_map, float threshold, bool reverse=false)

Float	calculate_intersection_score (const SurfaceShellDensityMap d1, const SurfaceShellDensityMap d2)

Float	compute_fitting_score (const kernel::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 kernel::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)

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)

DensityMap *	create_density_map (const algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > &grid)

kernel::Particles	density2particles (DensityMap dmap, Float threshold, kernel::Model m, int step=1)
	Converts a density grid to a set of paritlces. More...

algebra::Vector3Ds	density2vectors (DensityMap *dmap, Float threshold)
	Converts a density grid to a set of paritlces. More...

void	DensityHeader_to_ImageHeader (const DensityHeader &header, ImageHeader &h)

double	EXP (float y)

DensityMap *	get_binarized_interior (DensityMap *dmap)
	Return a binaries density map with 1 for voxels that are internal. More...

algebra::BoundingBoxD< 3 >	get_bounding_box (const DensityMap *m, Float threshold)

algebra::BoundingBoxD< 3 >	get_bounding_box (const DensityMap *m)

double	get_density (const DensityMap *m, const algebra::Vector3D &v)

algebra::GridD < 3, algebra::DenseGridStorageD < 3, float >, float >	get_grid (DensityMap *in_map)

bool	get_interiors_intersect (const DensityMap d1, const DensityMap d2)

DensityMap *	get_max_map (DensityMaps maps)

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 kernel::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 kernel::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 kernel::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_resampled (DensityMap *input, double scaling)
	Get a resampled version of the map. 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)

DensityMap *	get_transformed (const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
	Return a new density map containing a rotated version of the old one. More...

DensityMap *	get_transformed (DensityMap *input, const algebra::Transformation3D &tr)
	Return a new density map containing a rotated version of the old one. More...

void	get_transformed_into (const DensityMap source, const algebra::Transformation3D &tr, DensityMap into, bool calc_rms=true)
	Rotate a density map into another map. 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)

FittingSolutions	local_rigid_fitting (kernel::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 (kernel::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 (kernel::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 kernel::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)

SampledDensityMap *	particles2binarized_density (const kernel::ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())

SampledDensityMap *	particles2density (const kernel::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 kernel::ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
	Resample a set of particles into a density grid. More...

DensityMap *	read_map (std::string filename, MapReaderWriter *reader)
	Read a density map from a file and return it. More...

DensityMap *	read_map (std::string filename)
	Read a density map from a file and return it. More...

void	write_map (DensityMap m, std::string filename, MapReaderWriter writer)
	Write a density map to a file. More...

void	write_map (DensityMap *m, std::string filename)
	Write a density map to a file. 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 `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< DensityMap > > IMP::em::DensityMaps

Store a set of objects.

Definition at line 499 of file DensityMap.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DensityMap > > IMP::em::DensityMapsTemp

Pass a set of objects.

See Also: DensityMap

Definition at line 499 of file DensityMap.h.

typedef IMP::base::Vector< FittingSolutions > IMP::em::FittingSolutionsList

Pass or store a set of FittingSolutions .

Definition at line 103 of file rigid_fitting.h.

typedef IMP::base::Vector< KernelParameters > IMP::em::KernelParametersList

Pass or store a set of KernelParameters .

Definition at line 139 of file KernelParameters.h.

typedef IMP::base::Vector< RadiusDependentKernelParameters > IMP::em::RadiusDependentKernelParametersList

Pass or store a set of RadiusDependentKernelParameters .

Definition at line 71 of file KernelParameters.h.

typedef IMP::base::Vector<IMP::base::Pointer< SampledDensityMap > > IMP::em::SampledDensityMaps

Store a set of objects.

Definition at line 131 of file SampledDensityMap.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SampledDensityMap > > IMP::em::SampledDensityMapsTemp

Pass a set of objects.

See Also: SampledDensityMap

Definition at line 131 of file SampledDensityMap.h.

typedef IMP::base::Vector<IMP::base::Pointer< SurfaceShellDensityMap > > IMP::em::SurfaceShellDensityMaps

Store a set of objects.

Definition at line 93 of file SurfaceShellDensityMap.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SurfaceShellDensityMap > > IMP::em::SurfaceShellDensityMapsTemp

Pass a set of objects.

See Also: SurfaceShellDensityMap

Definition at line 93 of file SurfaceShellDensityMap.h.

Function Documentation

void IMP::em::add_to_map	(	DensityMap *	dm,
		const kernel::Particles &	pis
	)

Rasterize the particles into an existing density map.

Float IMP::em::approximate_molecular_mass	(	DensityMap *	m,
		Float	threshold
	)

Parameters

[in]	m	a density map
[in]	threshold	consider volume of only voxels above this threshold

Note: The method assumes 1.21 cubic A per Dalton (Harpaz 1994).

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

Parameters

[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 kernel::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

Parameters

[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

Note: the function assumes the density map holds its density

FittingSolutions IMP::em::compute_fitting_scores	(	const kernel::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.

Parameters

[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

Returns: The scored fitting solutions

Note: the function assumes the density map holds its density

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

Parameters

[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

Returns: The scored fitting solutions

Note: the function assumes the density map holds its density

Definition at line 272 of file rigid_fitting.h.

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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.

See Also: DensityHeader

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.

template<class S , class V , class E >

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 628 of file DensityMap.h.

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DensityMap* IMP::em::create_density_map ( const algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > & grid )

Return a density map with the values taken from the grid.

kernel::Particles IMP::em::density2particles	(	DensityMap *	dmap,
		Float	threshold,
		kernel::Model *	m,
		int	step = `1`
	)

Converts a density grid to a set of paritlces.

Each such particle will be have xyz attributes and a density_val attribute of type Float.

Parameters

[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

Returns: particles corresponding to all voxels above the threshold

algebra::Vector3Ds IMP::em::density2vectors	(	DensityMap *	dmap,
		Float	threshold
	)

Converts a density grid to a set of paritlces.

Each such particle will be have xyz attributes and a density_val attribute of type Float.

Parameters

[in]	dmap	the density map
[in]	threshold	only voxels with density above the given threshold will be converted to particles

Returns: a set of vector3Ds corresponding to the positions of all voxels above the threshold

void IMP::em::DensityHeader_to_ImageHeader	(	const DensityHeader &	header,
		ImageHeader &	h
	)

Function to transfer the (compatible) information content from DensityHeader to ImageHeader

DensityMap* IMP::em::get_binarized_interior ( DensityMap * dmap )

Return a binaries density map with 1 for voxels that are internal.

algebra::BoundingBoxD<3> IMP::em::get_bounding_box	(	const DensityMap *	m,
		Float	threshold
	)

Parameters

[in]	m	a density map
[in]	threshold	find the bounding box for voxels with value above the threshold

std::string IMP::em::get_data_path ( std::string file_name )

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

double IMP::em::get_density	(	const DensityMap *	m,
		const algebra::Vector3D &	v
	)

Return the value for the density map, m, at point v, interpolating linearly from the sample values. The resulting function is C0 over R3.

See Also: DensityMap

std::string IMP::em::get_example_path ( std::string file_name )

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",

model));

This will ensure that the code works when IMP is installed or 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 as well as the same bounding box.

DensityMap* IMP::em::get_max_map ( DensityMaps maps )

Return a density map for which each voxel is the maximum value from the input densities.

Note: all input maps should have the same extent

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

Parameters

[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

Returns: an approximate molecular mass for the set of voxels with intensity under the provided threshold (mass in Da)

long IMP::em::get_number_of_particles_outside_of_the_density	(	DensityMap *	dmap,
		const kernel::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.

/note the function assumes that all of the particles have XYZ coordinates

Ints IMP::em::get_numbers_of_particles_outside_of_the_density	(	DensityMap *	dmap,
		const kernel::Particles &	ps,
		const IMP::algebra::Transformation3Ds &	transformations,
		float	thr = `0.0`
	)

Get numbers of particles (mult transforms) that are outside the density.

/note the function assumes that all of the particles have XYZ coordinates

double IMP::em::get_percentage_of_voxels_covered_by_particles	(	DensityMap *	dmap,
		const kernel::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.

/note the function assumes that all of the particles have XYZ coordinates

DensityMap* IMP::em::get_resampled	(	DensityMap *	input,
		double	scaling
	)

Get a resampled version of the map.

The spacing is multiplied by scaling. That means, scaling values greater than 1 increase the voxel size.

See Also: DensityMap

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.

Note: the output map will be cover the region [[nx_start,nx_end],[]ny_start,ny_end,[nz_start,nz_end]]

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)

Parameters

[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)

Parameters

[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

Parameters

[in]	orig_map	the map to binarize
[in]	threshold	values below the threshold are set to 0 and 1 otherwise

DensityMap* IMP::em::get_transformed	(	const DensityMap *	input,
		const algebra::Transformation3D &	tr,
		double	threshold
	)

Return a new density map containing a rotated version of the old one.

Only voxels whose value is above threshold are considered when computing the bounding box of the new map (set IMP::em::get_bounding_box()).

See Also: DensityMap

DensityMap* IMP::em::get_transformed	(	DensityMap *	input,
		const algebra::Transformation3D &	tr
	)

Return a new density map containing a rotated version of the old one.

The dimension of the new map is the same as the old one.

See Also: DensityMap

void IMP::em::get_transformed_into	(	const DensityMap *	source,
		const algebra::Transformation3D &	tr,
		DensityMap *	into,
		bool	calc_rms = `true`
	)

Rotate a density map into another map.

Parameters

[in]	source	the map to transform
[in]	tr	transform the from density map by this transformation
[out]	into	the map to transform into
[in]	calc_rms	if true RMS is calculated on the transformed map

See Also: DensityMap

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

Parameters

[in]	m	a density map
[in]	threshold	consider volume of only voxels above this threshold

Returns: a volume for the set of voxels with intensity under the provided 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 and interpolate input data accordingly

FittingSolutions IMP::em::local_rigid_fitting	(	kernel::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.

Note: The returned cross-correlation score is 1-cc, as we usually want to minimize a scoring function. Thus a score of 1 means no correlation and a score of 0 is perfect correlation.; The input rigid body should be also IMP::atom::Hierarchy

Parameters

[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

Returns: the refined fitting solutions

Definition at line 168 of file rigid_fitting.h.

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FittingSolutions IMP::em::local_rigid_fitting_around_point	(	kernel::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.

Note: The returned cross-correlation score is 1-cc, as we usually want to minimize a scoring function. Thus a score of 1 means no-correlation and a score of 0. is perfect correlation.; The input rigid body should be also IMP::atom::Hierarchy

Parameters

[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

Returns: the refined fitting solutions

FittingSolutions IMP::em::local_rigid_fitting_around_points	(	kernel::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.

Note: The input rigid body should be also IMP::atom::Hierarchy

Parameters

[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

Returns: the refined fitting solutions

FittingSolutions IMP::em::local_rigid_fitting_grid_search	(	const kernel::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

Note: The transformations are not clustered.; The returned cross-correlation score is 1-cc, as we usually want to minimize a scoring function. Thus a score of 1 means no-correlation and a score of 0. is perfect correlation.

Parameters

[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

Returns: the refined fitting solutions

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.

Parameters

[in]	dmap	the density map to mask
[in]	mask	the mask

Returns: the masked and normalized map

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 kernel::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

Parameters

[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

Returns: the sampled density grid

See Also: SampledDensityMap

Definition at line 80 of file converters.h.

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SampledDensityMap* IMP::em::particles2density	(	const kernel::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

Parameters

[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

Returns: the sampled density grid

See Also: SampledDensityMap

SurfaceShellDensityMap* IMP::em::particles2surface	(	const kernel::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

Parameters

[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

Returns: the surface grid

See Also: SampledDensityMap

DensityMap* IMP::em::read_map	(	std::string	filename,
		MapReaderWriter *	reader
	)

Read a density map from a file and return it.

See Also: DensityMap

DensityMap* IMP::em::read_map ( std::string filename )

Read a density map from a file and return it.

Guess the file type from the file name. The file formats supported are:

.mrc
.em
.vol
.xplor
See Also
DensityMap

void IMP::em::write_map	(	DensityMap *	m,
		std::string	filename,
		MapReaderWriter *	writer
	)

Write a density map to a file.

See Also: DensityMap

void IMP::em::write_map	(	DensityMap *	m,
		std::string	filename
	)

Write a density map to a file.

Guess the file type from the file name. The file formats supported are:

.mrc
.em
.vol
.xplor
See Also
DensityMap

def IMP.em.write_pca_cmm	(	pca,
		fh
	)

Write out principal components to a file in Chimera Marker format.

Definition at line 2418 of file em/__init__.py.

Detailed Description

estimate_threshold_from_molecular_mass

map2pca

mol2pca

resample_density

simulate_density_from_pdb

view_density_header

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