IMP::em::SampledDensityMap Class Reference

Detailed Description

Class for sampling a density map from particles.

Inheritance diagram for IMP::em::SampledDensityMap:


Public Member Functions
void	calc_sampling_bounding_box (const emreal &x, const emreal &y, const emreal &z, const emreal &kdist, int &iminx, int &iminy, int &iminz, int &imaxx, int &imaxy, int &imaxz) const
KernelParameters *	get_kernel_params ()
FloatKey	get_radius_key () const
const Particles &	get_sampled_particles () const
FloatKey	get_weight_key () const
const core::XYZRs &	get_xyzr_particles () const
virtual void	resample ()
	Resampling beads on an EM grid.
	SampledDensityMap (const Particles &ps, emreal resolution, emreal voxel_size, IMP::FloatKey radius_key=IMP::core::XYZR::get_default_radius_key(), IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3)
	Generatea a sampled density map from the particles.
	SampledDensityMap (const DensityHeader &header)
	The size of the map is determined by the header and the data is allocated.
	SampledDensityMap ()
	Creates a new density map for sampled map.
void	set_particles (IMP::Particles &ps, IMP::FloatKey radius_key=IMP::core::XYZR::get_default_radius_key(), IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key())
	setting particles in case they were not set by the constructor
Protected Member Functions
IMP::algebra::BoundingBoxD< 3 >	calculate_particles_bounding_box (const Particles &ps)
	Calculate the parameters of the particles bounding box.
int	lower_voxel_shift (const emreal &loc, const emreal &kdist, const emreal &orig, int ndim) const
void	set_header (const algebra::VectorD< 3 > &lower_bound, const algebra::VectorD< 3 > &upper_bound, emreal maxradius, emreal resolution, emreal voxel_size, int sig_offset)
int	upper_voxel_shift (const emreal &loc, const emreal &kdist, const emreal &orig, int ndim) const
Protected Attributes
KernelParameters	kernel_params_
	kernel handling
Particles	ps_
FloatKey	radius_key_
FloatKey	weight_key_
FloatKey	x_key_
core::XYZRs	xyzr_
FloatKey	y_key_
FloatKey	z_key_
Friends
template<class T >
void	IMP::internal::unref (T *)
Related Functions
(Note that these are not member functions.)
SampledDensityMap *	particles2density (Particles &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &rad_key=IMP::core::XYZR::get_default_radius_key(), const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
	Resample a set of particles into a density grid.

Constructor & Destructor Documentation

IMP::em::SampledDensityMap::SampledDensityMap ( )

Creates a new density map for sampled map.

The header of the map is not determined and no data is being allocated

IMP::em::SampledDensityMap::SampledDensityMap	(	const Particles &	ps,
		emreal	resolution,
		emreal	voxel_size,
		IMP::FloatKey	radius_key = `IMP::core::XYZR::get_default_radius_key()`,
		IMP::FloatKey	mass_key = `IMP::atom::Mass::get_mass_key()`,
		int	sig_cuttoff = `3`
	)

Generatea a sampled density map from the particles.

/param[in] ps particles with XYZ, radius and weight attributes /param[in] resolution half width the Gaussian /param[in] voxel_size /param[in] sig_cutoff Choose what should be the sigma cutoff for accurate sampling. It is used in two functions; (i) to determine the size of the grid dimensions (ii) to determine the voxels around the coords participating in the sampling procedure.

Member Function Documentation

IMP::algebra::BoundingBoxD<3> IMP::em::SampledDensityMap::calculate_particles_bounding_box ( const Particles & ps ) [protected]

Calculate the parameters of the particles bounding box.

Parameters:

[in] ps particles with XYZ, radius and weight attributes

Returns:: the particles bounding box

virtual void IMP::em::SampledDensityMap::resample ( ) [virtual]

Resampling beads on an EM grid.

Note:: The density of a particle p centered at pl at position gl is: $\frac{{Z}e^{\frac{{-0.5}({p_l}-{g_l})}{\sigma}}}{\sqrt{{2}{\pi}\sigma}}$ , such that is the weight of the particle and ${\sigma}$ is defined to be times the resolution, to follow the 'full width at half maxima' criterion. For more details please refer to Topf et al, Structure, 2008.

Reimplemented in IMP::em::SurfaceShellDensityMap.

Friends And Related Function Documentation

SampledDensityMap * particles2density	(	Particles &	ps,
		Float	resolution,
		Float	apix,
		int	sig_cutoff = `3`,
		const FloatKey &	rad_key = `IMP::core::XYZR::get_default_radius_key()`,
		const FloatKey &	weight_key = `IMP::atom::Mass::get_mass_key()`
	)			`[related]`

Resample a set of particles into a density grid.

Each such particle should be 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]`	rad_key	the radius attribute key of the particles
`[in]`	weight_key	the weight attribute key of the particles

Returns:: the sampled density grid

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

IMP::em::SampledDensityMap Class Reference

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Related Functions

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation