Clipper
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Crystallographic map container. More...
#include <container_map.h>
Public Member Functions | |
CXmap () | |
null constructor | |
CXmap (Container &parent, const String name="") | |
constructor: inherit spacegroup, cell and grid More... | |
void | init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sampling) |
initialiser: supply or inherit spacegroup, cell and grid More... | |
void | update () |
hierarchical update More... | |
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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 () |
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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 More... | |
void | set_data (const Coord_grid &pos, const T &val) |
set a density value for an arbitrary position More... | |
const T & | get_data (const int &index) const |
get data by index (not recommended) More... | |
bool | set_data (const int &index, const T &val) |
set data by index (not recommended) More... | |
template<class I > | |
T | interp (const Coord_frac &pos) const |
get map value for fractional coord using supplied interpolator More... | |
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 More... | |
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 More... | |
template<class I > | |
T | interp (const Coord_map &pos) const |
get map value for map coord using supplied interpolator More... | |
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 More... | |
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 More... | |
template<class H > | |
void | fft_from (const H &fphidata, const FFTtype type=Default) |
FFT from reflection list to map. More... | |
template<class H > | |
void | fft_to (H &fphidata, const FFTtype type=Default) const |
FFT from map to reflection list. More... | |
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 More... | |
const Xmap< T > & | operator+= (const Xmap< T > &other) |
add another map to this one More... | |
const Xmap< T > & | operator-= (const Xmap< T > &other) |
subtract another map from this one More... | |
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bool | is_null () const |
test if object has been initialised More... | |
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 More... | |
int | index_of (const Coord_grid &coord) const |
map index from coordinate More... | |
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 More... | |
Coord_map | coord_map (const Coord_orth &co) const |
convert orthogonal coordinate to map More... | |
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 More... | |
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 | |
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enum | FFTtype { Default, Normal, Sparse } |
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static FFTtype & | default_type () |
set/get default backend type | |
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Xmap_base () | |
Null constructor, for later initialisation. More... | |
void | init (const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam) |
initialiser More... | |
void | find_sym (const Coord_grid &base, int &index, int &sym) const |
void | asu_error (const Coord_grid &pos) const |
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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 | |
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static FFTtype | default_type_ = Xmap_base::Sparse |
default backend type | |
Crystallographic map container.
CXmap: This is a crystallographic map.
clipper::CXmap< T >::CXmap | ( | Container & | parent, |
const String | name = "" |
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) |
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.
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). |
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.
spacegroup | The spacegroup for the map. |
name | The cell for the map. |
grid | The grid for the map. |
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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.