Crystallographic map container. More...

#include <container_map.h>

Inheritance diagram for clipper::CXmap< T >:

Public Member Functions
	CXmap ()
	null constructor
	CXmap (Container &parent, const String name="")
	constructor: inherit spacegroup, cell and grid
void	init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sampling)
	initialiser: supply or inherit spacegroup, cell and grid
void	update ()
	hierarchical update
Public Member Functions inherited from clipper::Container
	Container (const String name="")
	constructor: make null object or top object in a tree
	Container (Container &parent, const String &path)
	constructor: from any other member and a relative path
String	path () const
	get the path of this tree object
String	name () const
	get the name of this tree object
void	set_name (const String &name)
	set the name of this tree object
bool	is_destroyed_with_parent () const
	is this object to be destroyed when parent is destroyed?
void	set_destroyed_with_parent (const bool d=true)
	set this object to be destroyed when parent is destroyed
void	move (const String &path)
	'move' method moves this object to somewhere else in the hierarchy
bool	has_parent () const
	test if this object has a parent
const Container &	parent () const
	get the parent of this object
Container &	parent ()
	get the parent of this object
int	num_children () const
	return number of children
const Container &	child (const int &i) const
	get the i'th child of this object
Container &	child (const int &i)
	get the i'th child of this object
const Container &	ultimate_parent () const
	get the ultimate parent of this object - the top of the tree
Container &	ultimate_parent ()
	get the ultimate parent of this object - the top of the tree
Container *	parent_ptr ()
	get the parent of this object (NULL on fail)
template<class T>
T *	parent_of_type_ptr ()
	search up the tree for a parent of the specified type (NULL on fail)
Container *	find_path_ptr (const String &path)
	find an object using a directory-like path (NULL on fail)
virtual	~Container ()
	destructor: virtual
void	debug ()
Public Member Functions inherited from clipper::Xmap< T >
	Xmap ()
	Null constructor, for later initialisation.
	Xmap (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	constructor: from spacegroup, cell, and grid
void	init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	initialiser: from spacegroup, cell, and grid
const T &	operator[] (const Xmap_base::Map_reference_index &ix) const
	get data by Map_reference_index
T &	operator[] (const Xmap_base::Map_reference_index &ix)
	set data by Map_reference_index
const T &	operator[] (const Xmap_base::Map_reference_coord &ix) const
	get data by Map_reference_coord
T &	operator[] (const Xmap_base::Map_reference_coord &ix)
	set data by Map_reference_coord
const T &	get_data (const Coord_grid &pos) const
	get a density value for an arbitrary position
void	set_data (const Coord_grid &pos, const T &val)
	set a density value for an arbitrary position
const T &	get_data (const int &index) const
	get data by index (not recommended)
bool	set_data (const int &index, const T &val)
	set data by index (not recommended)
template<class I>
T	interp (const Coord_frac &pos) const
	get map value for fractional coord using supplied interpolator
template<class I>
void	interp_grad (const Coord_frac &pos, T &val, Grad_frac< T > &grad) const
	get map value and grad for fractional coord using supplied interpolator
template<class I>
void	interp_curv (const Coord_frac &pos, T &val, Grad_frac< T > &grad, Curv_frac< T > &curv) const
	get map value and curv for fractional coord using supplied interpolator
template<class I>
T	interp (const Coord_map &pos) const
	get map value for map coord using supplied interpolator
template<class I>
void	interp_grad (const Coord_map &pos, T &val, Grad_map< T > &grad) const
	get map value and grad for map coord using supplied interpolator
template<class I>
void	interp_curv (const Coord_map &pos, T &val, Grad_map< T > &grad, Curv_map< T > &curv) const
	get map value and curv for map coord using supplied interpolator
template<class H>
void	fft_from (const H &fphidata, const FFTtype type=Default)
	FFT from reflection list to map.
template<class H>
void	fft_to (H &fphidata, const FFTtype type=Default) const
	FFT from map to reflection list.
const Cell &	cell () const
const Spacegroup &	spacegroup () const
const Grid_sampling &	grid_sampling () const
const Grid_range &	grid_asu () const
Coord_grid	coord_of (const int &index) const
int	index_of (const Coord_grid &coord) const
const int	multiplicity (const Coord_grid &pos) const
const Coord_grid	to_map_unit (const Coord_grid &pos) const
const Map_reference_index	first () const
const Map_reference_coord	first_coord () const
const T &	operator= (const T &value)
	assignment operator: assigns a single value to the whole map
const Xmap< T > &	operator+= (const Xmap< T > &other)
	add another map to this one
const Xmap< T > &	operator-= (const Xmap< T > &other)
	subtract another map from this one
Public Member Functions inherited from clipper::Xmap_base
bool	is_null () const
	test if object has been initialised
const Cell &	cell () const
	get the cell
const Spacegroup &	spacegroup () const
	get the spacegroup
const Grid_sampling &	grid_sampling () const
	get the cell grid
const Grid_range &	grid_asu () const
	get the ASU grid
Coord_grid	coord_of (const int &index) const
	map coordinate from index
int	index_of (const Coord_grid &coord) const
	map index from coordinate
Coord_grid	to_map_unit (const Coord_grid &pos) const
	function to pick right cell repeat for any grid coord
const RTop &	operator_orth_grid () const
	return the orthogonal-to-grid coordinate operator (translation is zero)
const RTop &	operator_grid_orth () const
	return the grid-to-orthogonal coordinate operator (translation is zero)
Coord_orth	coord_orth (const Coord_map &cm) const
	convert map coordinate to orthogonal
Coord_map	coord_map (const Coord_orth &co) const
	convert orthogonal coordinate to map
bool	in_map (const Coord_grid &) const
	(This method is for compatibility with NXmap - it always returns true)
template<class I>
bool	in_map (const Coord_map &cm) const
	(This method is for compatibility with NXmap - it always returns true)
int	multiplicity (const Coord_grid &pos) const
	get multiplicity of a map grid point
Map_reference_index	first () const
	return a Map_reference_index for this map
Map_reference_coord	first_coord () const
	return a Map_reference_coord for this map

Additional Inherited Members
Public Types inherited from clipper::Xmap_base
enum	FFTtype { Default , Normal , Sparse }
Static Public Member Functions inherited from clipper::Xmap_base
static FFTtype &	default_type ()
	set/get default backend type
Protected Member Functions inherited from clipper::Xmap_base
	Xmap_base ()
	Null constructor, for later initialisation.
void	init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
	initialiser
void	find_sym (const Coord_grid &base, int &index, int &sym) const
void	asu_error (const Coord_grid &pos) const
Protected Attributes inherited from clipper::Xmap_base
ObjectCache< Xmap_cacheobj >::Reference	cacheref
	object cache reference
const unsigned char *	asu
	fast access ptr
const Isymop *	isymop
	fast access ptr
const int *	du
	fast access ptr
const int *	dv
	fast access ptr
const int *	dw
	fast access ptr
Grid_range	asu_grid
	fast access copy
Grid_range	map_grid
	fast access copy
int	nsym
	fast access copy
Cell	cell_
	unit cell
Spacegroup	spacegroup_
	spacegroup
Grid_sampling	grid_sam_
	grid for the whole cell
RTop	rt_orth_grid
	orth->grid operator
RTop	rt_grid_orth
	grid->orth operator
Static Protected Attributes inherited from clipper::Xmap_base
static FFTtype	default_type_ = Xmap_base::Sparse
	default backend type

Detailed Description

template<class T>
class clipper::CXmap< T >

Crystallographic map container.

CXmap: This is a crystallographic map.

Constructor & Destructor Documentation

◆ CXmap()

template<class T>

clipper::CXmap< T >::CXmap	(	Container &	parent,
		const String	name = "" )

constructor: inherit spacegroup, cell and grid

The object is constructed at the given location in the hierarchy. An attempt is made to initialise the object using information from its parents in the hierarchy.

Parameters

parent	An object in the hierarchy (usually the parent of the new object).
name	The path from `parent` to the new object (usually just the name of the new object).

Member Function Documentation

◆ init()

template<class T>

void clipper::CXmap< T >::init	(	const Spacegroup &	spacegroup,
		const Cell &	cell,
		const Grid_sampling &	grid_sampling )

initialiser: supply or inherit spacegroup, cell and grid

An attempt is made to initialise the object using information from the supplied parameters, or if they are Null, from its parents in the hierarchy.

Parameters

spacegroup	The spacegroup for the map.
name	The cell for the map.
grid	The grid for the map.

◆ update()

template<class T>

void clipper::CXmap< T >::update ( )

virtual

hierarchical update

Hierarchical update. If this object is uninitialised, an attempt is made to initialise the object using information from its parents in the hierarchy. The childen of the object are then updated.

Reimplemented from clipper::Container.

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

container_map.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CXmap()

Member Function Documentation

◆ init()

◆ update()