clipper::Xmap_base Class Reference

Xmap_base: base for crystallographic map class. More...

#include <xmap.h>

Inheritance diagram for clipper::Xmap_base:

List of all members.

Classes
class	Map_reference_base
	Map reference base class. More...
class	Map_reference_coord
	Map reference with coordinate-like behaviour. More...
class	Map_reference_index
	Map reference with index-like behaviour. More...
Public Types
enum	FFTtype { Default, Normal, Sparse }
Public Member Functions
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
Static Public Member Functions
static FFTtype &	default_type ()
	set/get default backend type
Protected Member Functions
	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
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
static FFTtype	default_type_ = Xmap_base::Sparse
	default backend type
Friends
class	Xmap_base::Map_reference_base
class	Xmap_base::Map_reference_index
class	Xmap_base::Map_reference_coord

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Detailed Description

Xmap_base: base for crystallographic map class.

The crystallographic map class stores a map of arbitrary data type. Its main difference from a 3-d array is that the data extent appears to be infinite, and yet internally only a unique ASU is stored. Iterators provide efficient access to data.

This base contains everything except the data, which is templated in the derived type Xmap<T>

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Constructor & Destructor Documentation

clipper::Xmap_base::Xmap_base

(

)

[protected]

Null constructor, for later initialisation.

For later initialisation: see init()

References clipper::Message::message().

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Member Function Documentation

bool clipper::Xmap_base::is_null

(

)

const

test if object has been initialised

Returns:

true if the object has not been initalised.

References cell_, grid_sam_, clipper::Grid_sampling::is_null(), clipper::Cell::is_null(), clipper::Spacegroup::is_null(), and spacegroup_.

Referenced by init(), and clipper::CXmap< T >::update().

Coord_grid clipper::Xmap_base::coord_of

(

const int &

index

)

const [inline]

map coordinate from index

Parameters:

index

The index.

Returns:

The corresponding grid coordinate.

Reimplemented in clipper::Xmap< T >.

References cacheref.

int clipper::Xmap_base::index_of

(

const Coord_grid &

coord

)

const [inline]

map index from coordinate

This does not check symmetry equivalents.

Parameters:

coord

The coordinate.

Returns:

The index, or -1 if it does not exist.

Reimplemented in clipper::Xmap< T >.

References asu, and cacheref.

Coord_orth clipper::Xmap_base::coord_orth

(

const Coord_map &

cm

)

const [inline]

convert map coordinate to orthogonal

Parameters:

cm	The grid coordinate to be converted.

Returns:

The equivalent orthogonal coordinate.

References clipper::RTop< T >::rot(), and rt_grid_orth.

Coord_map clipper::Xmap_base::coord_map

(

const Coord_orth &

co

)

const [inline]

convert orthogonal coordinate to map

Parameters:

co	The orthogonal coordinate to be converted.

Returns:

The equivalent grid coordinate.

References clipper::RTop< T >::rot(), and rt_orth_grid.

int clipper::Xmap_base::multiplicity

(

const Coord_grid &

pos

)

const

get multiplicity of a map grid point

The multiplicity is the number of times the spacegroup operators map a particular grid point onto itself. This is required in order to properly weight map statistics so as to get the same result from just an ASU as using the whole cell.

Parameters:

pos	The coordinate of the grid point.

Returns:

The multiplicty of the point.

Reimplemented in clipper::Xmap< T >.

References cacheref, grid_sam_, isymop, clipper::Coord_grid::transform(), and clipper::Coord_grid::unit().

void clipper::Xmap_base::init	(	const Spacegroup &	spacegroup,
		const Cell &	cell,
		const Grid_sampling &	grid_sam
	)		[protected]

initialiser

The Xmap is initialised with a given cell, spacegroup, and grid sampling. A unique assymetric unit (ASU) of grid cells is selected and will be used to store a unique set of data.

If any of the parameters have null values, the existing values will be unchanged. The object will only be fully initialised once all parameters are available.

Parameters:

spacegroup	The spacegroup for the map
cell	The cell for the map
grid_sam	The grid sampling for the map, i.e. the sampling along each axis for one whole cell

Reimplemented in clipper::CXmap< T >, and clipper::Xmap< T >.

References asu, asu_grid, clipper::ObjectCache< T >::cache(), cacheref, cell(), cell_, du, dv, dw, grid_sam_, clipper::RTop< T >::inverse(), is_null(), isymop, map_grid, clipper::Grid_sampling::matrix_grid_frac(), clipper::Cell::matrix_orth(), nsym, rt_grid_orth, rt_orth_grid, spacegroup(), and spacegroup_.

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

• xmap.h
• xmap.cpp