Detailed Description

The class represents a molecule as shells of distance from the surface.

Definition at line 27 of file SurfaceShellDensityMap.h.

Public Member Functions
	SurfaceShellDensityMap ()
	Creates a new density map. More...

	SurfaceShellDensityMap (const DensityHeader &header)

	SurfaceShellDensityMap (const ParticlesTemp &ps, float voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int num_shells=5)
	Generate a surface shell density map from the input particles. More...

void	binaries (float scene_val)

void	binarize (float scene_val)
	Set the value of the map voxels as either scene or background. More...

bool	has_background_neighbor (long voxel_ind) const
	Checks if the one of the neighbors of the voxel is a background voxel. More...

void	resample ()
	Resample the grid to consist of density shells of a model. More...

Public Member Functions inherited from IMP::em::SampledDensityMap
	SampledDensityMap (KernelType kt=GAUSSIAN)
	Creates a new density map for sampled map. More...

	SampledDensityMap (const DensityHeader &header, KernelType kt=GAUSSIAN)
	The size of the map is determined by the header and the data is allocated. More...

	SampledDensityMap (const ParticlesTemp &ps, emreal resolution, emreal voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cutoff=3, KernelType kt=GAUSSIAN)
	Generate a sampled density map from the particles. More...

KernelParameters *	get_kernel_params ()

float	get_minimum_resampled_value ()
	Get minimum density value between voxels that correspond to particles. More...

const Particles &	get_sampled_particles () const

FloatKey	get_weight_key () const

const core::XYZRs &	get_xyzr_particles () const

void	project (const ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key())
	Project particles on the grid by their mass value. More...

void	set_particles (const ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key())
	setting particles in case they were not set by the constructor More...

void	update_resolution (Float res)
	Update the simulation resolution. More...

Public Member Functions inherited from IMP::em::DensityMap
	DensityMap (std::string name="DensityMap%1%")

	DensityMap (const DensityHeader &header, std::string name="DensityMap%1%")
	Construct a density map as instructed in the input header. More...

void	add (const DensityMap *other)
	Sums two grids; the result is kept in the map. More...

void	calc_all_voxel2loc ()
	Calculates the coordinates that correspond to all voxels. More...

emreal	calcRMS ()
	Calculates RMSD and mean of a map values as stored in the header. More...

void	copy_map (const DensityMap *other)
	Copy map into this map. More...

algebra::Vector3D	get_centroid (emreal threshold=0.0) const
	Get the centroid of all voxels with density above a given threshold. More...

DensityMap *	get_cropped (float threshold)
	Create and return a new cropped map. More...

DensityMap *	get_cropped (const algebra::BoundingBox3D &bb)
	Create and return a new cropped map with the given bounding box extent. More...

int	get_dim_index_by_location (const algebra::Vector3D &v, int ind) const
	Calculate dimension index of a given location. More...

int	get_dim_index_by_location (float loc_val, int ind) const

const DensityHeader *	get_header () const
	Returns a read-only pointer to the header of the map. More...

DensityHeader *	get_header_writable ()
	Returns a pointer to the header of the map in a writable version. More...

algebra::Vector3D	get_location_by_voxel (long index) const
	Calculate the location of a given voxel. More...

float	get_location_in_dim_by_voxel (long index, int dim) const
	Calculate the location of a given voxel in a given dimension. More...

std::string	get_locations_string (float t)
	Print the locations of all voxels with value above a given threshold. More...

emreal	get_max_value () const
	Returns the value of the voxel with the highest density. More...

float	get_maximum_value_in_xy_plane (int z_ind)
	Get the maximum value in a XY plane indicated by a Z index. More...

float	get_maximum_value_in_xz_plane (int y_ind)
	Get the maximum value in a XZ plane indicated by a Y index. More...

float	get_maximum_value_in_yz_plane (int x_ind)
	Get the maximum value in a YZ plane indicated by a X index. More...

emreal	get_min_value () const
	Returns the value of the voxel with the lowest density. More...

long	get_number_of_voxels () const
	Get the number of map voxels. More...

algebra::Vector3D	get_origin () const

bool	get_rms_calculated () const

Float	get_spacing () const
	Get the voxel size of the map. More...

algebra::Vector3D	get_top () const

virtual std::string	get_type_name () const

emreal	get_value (float x, float y, float z) const
	Gets the value of the voxel located at (x,y,z) More...

emreal	get_value (const algebra::Vector3D &point) const

emreal	get_value (long index) const
	Gets the value of the voxel at a given index. More...

virtual ::IMP::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

long	get_voxel_by_location (float x, float y, float z) const
	Calculate the voxel of a given location. More...

long	get_voxel_by_location (const algebra::Vector3D &v) const
	Calculate the voxel of a given location. More...

bool	is_normalized () const

bool	is_part_of_volume (float x, float y, float z) const
	Checks whether a given point is in the grid. More...

bool	is_part_of_volume (const algebra::Vector3D &v) const
	Checks whether a given point is in the grid. More...

bool	is_xyz_ind_part_of_volume (int ix, int iy, int iz) const

int	lower_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const

void	multiply (float factor)
	Multiply in place each voxel in the map by the input factor. More...

void	pad (int nx, int ny, int nz, float val=0.0)
	Increase the dimension of the map. More...

DensityMap *	pad_margin (int mrg_x, int mrg_y, int mrg_z, float val=0.0)
	Create a new padded map. More...

void	pick_max (const DensityMap *other)
	Pick the max value between two corresponding voxels between two maps. More...

void	reset_data (float value=0.0)
	Set the density voxels to some value and reset the management flags. More...

bool	same_dimensions (const DensityMap *other) const
	Checks if two maps have the same dimensions. More...

bool	same_origin (const DensityMap *other) const
	Checks if two maps have the same origin. More...

bool	same_voxel_size (const DensityMap *other) const
	Checks if two maps have the same voxel size. More...

void	set_origin (float x, float y, float z)
	Sets the origin of the header. More...

void	set_origin (const IMP::algebra::Vector3D &v)

void	set_value (long index, emreal value)
	Set the value of the voxel at a given index. More...

void	set_value (float x, float y, float z, emreal value)
	Set the value of the voxel at given coordinates. More...

void	set_void_map (int nx, int ny, int nz)
	Set the map dimension and reset all voxels to 0. More...

void	std_normalize ()
	Normalize the density voxels according to standard deviation (stdv). More...

void	update_voxel_size (float new_apix)
	Update the voxel size of the map. More...

int	upper_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const

long	xyz_ind2voxel (int x, int y, int z) const
	Calculate the voxel of a given xyz index. More...

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
void	set_kernel ()

void	set_neighbor_mask ()

void	set_surface_shell (std::vector< long > *shell)

Protected Member Functions inherited from IMP::em::SampledDensityMap
IMP::algebra::BoundingBoxD< 3 >	calculate_particles_bounding_box (const Particles &ps)
	Calculate the parameters of the particles bounding box. More...

void	determine_grid_size (emreal resolution, emreal voxel_size, int sig_cutoff)

void	set_header (const algebra::Vector3D &lower_bound, const algebra::Vector3D &upper_bound, emreal maxradius, emreal resolution, emreal voxel_size, int sig_offset)

void	set_neighbor_mask (float radius)

Protected Member Functions inherited from IMP::em::DensityMap
void	allocated_data ()

void	float2real (float *f_data, boost::scoped_array< emreal > &r_data)

void	real2float (emreal *r_data, boost::scoped_array< float > &f_data)

void	reset_all_voxel2loc ()

void	update_header ()
	update the header values – still in work More...

Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes
std::vector< emreal >	neighbor_dist_

std::vector< long >	neighbor_shift_

int	num_shells_

float	surface_val_

Protected Attributes inherited from IMP::em::SampledDensityMap
KernelParameters	kernel_params_
	kernel handling More...

KernelType	kt_

Particles	ps_

FloatKey	weight_key_

FloatKey	x_key_

core::XYZRs	xyzr_

FloatKey	y_key_

FloatKey	z_key_

Protected Attributes inherited from IMP::em::DensityMap
boost::scoped_array< emreal >	data_

bool	data_allocated_

DensityHeader	header_

bool	loc_calculated_
	true if the locations have already been computed More...

bool	normalized_

bool	rms_calculated_

boost::scoped_array< float >	x_loc_

boost::scoped_array< float >	y_loc_

boost::scoped_array< float >	z_loc_

Additional Inherited Members
Related Functions inherited from IMP::em::DensityMap
void	add_to_map (DensityMap *dm, const Particles &pis)
	Rasterize the particles into an existing density map. More...

DensityMap *	create_density_map (const algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > &grid)
	Return a density map with the values taken from the grid. More...

DensityMap *	get_binarized_interior (DensityMap *dmap)
	Return a binarized map with 1 for voxels that are internal in the input map. More...

double	get_density (const DensityMap *m, const algebra::Vector3D &v)
	Get density value at point v, interpolating linearly from the sample values. More...

DensityMap *	get_resampled (DensityMap *input, double scaling)
	Get a resampled version of the map. More...

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...

DensityMap *	read_map (std::string filename, MapReaderWriter *reader)
	Read a density map from a file (using the given reader) 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 using the given writer. More...

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

Constructor & Destructor Documentation

IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap ( )

Creates a new density map.

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

IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap ( const DensityHeader & header )

Creates a new density map. The size of the map is determined by the header and the data is allocated.

IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap	(	const ParticlesTemp &	ps,
		float	voxel_size,
		IMP::FloatKey	mass_key = `IMP::atom::Mass::get_mass_key()`,
		int	num_shells = `5`
	)

Generate a surface shell density map from the input particles.

Parameters

[in]	ps	particles with XYZ, radius and weight attributes
[in]	voxel_size	the voxel size.
[in]	mass_key	key to use to weight particles
[in]	num_shells	number of shells

Note: the voxel size and the number of shells determines the resolution/accuracy of the surface rasterization.

Member Function Documentation

void IMP::em::SurfaceShellDensityMap::binarize ( float scene_val )

Set the value of the map voxels as either scene or background.

Parameters

[in] scene_val all voxels corresponding to particles will be set to this value

bool IMP::em::SurfaceShellDensityMap::has_background_neighbor ( long voxel_ind ) const

Checks if the one of the neighbors of the voxel is a background voxel.

Parameters

[in] voxel_ind the index of the voxel

Returns: true if at least one of the neighbors of the voxel is in the background

void IMP::em::SurfaceShellDensityMap::resample ( )

virtual

Resample the grid to consist of density shells of a model.

All voxels that are outside of the model defined by the particles will be set to zero. Voxels on the surface between the model and the background will be set of 1. The interior voxels will be assign value according to their corresponding shell ( the value increases as the voxel is further away from the surface).

Reimplemented from IMP::em::SampledDensityMap.

void IMP::em::SurfaceShellDensityMap::set_surface_shell ( std::vector< long > * shell )

protected

Finds all of the voxels that are part of the surface (i.e, separate background from scene)

Parameters

[in] shell indexes of all of the surface particles will be stored here.

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

SurfaceShellDensityMap.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation