cctbx::maptbx Namespace Reference

Map algorithms. More...

Classes
class	c_grid_p1< 3 >
class	c_grid_padded_p1< 3 >
class	grid_points_in_sphere_around_atom_and_distances
class	find_gaussian_parameters
class	one_gaussian_peak_approximation
class	basic_map
struct	transformer_types
struct	transform< T, T >
struct	transform< fractional< FloatType >, grid_point< IntType > >
struct	transform< fractional< FloatType >, cartesian< FloatType > >
struct	transform< cartesian< FloatType >, grid_point< IntType > >
struct	transform< cartesian< FloatType >, fractional< FloatType > >
struct	transform< grid_point< IntType >, cartesian< FloatType > >
struct	transform< grid_point< IntType >, fractional< FloatType > >
class	get_corner
class	generic_grid< void, FloatType, IntType >
class	generic_grid< asu, FloatType, IntType >
class	generic_grid< unit_cell, FloatType, IntType >
class	generic_grid< non_symmetric, FloatType, IntType >
class	grid_tags
struct	out_of_bounds< void, FloatType, IntType >
struct	out_of_bounds< raise, FloatType, IntType >
struct	out_of_bounds< clamp, FloatType, IntType >
struct	out_of_bounds< substitute, FloatType, IntType >
struct	out_of_bounds< interpolate, FloatType, IntType >
struct	non_symmetric
struct	unit_cell
struct	asu
struct	basic_mapper< void, FloatType, IntType >
struct	basic_mapper< non_symmetric, FloatType, IntType >
struct	basic_mapper< unit_cell, FloatType, IntType >
struct	basic_mapper< asu, FloatType, IntType >
struct	mapper_factory< void, FloatType, IntType >
struct	mapper_factory_types< mapper_factory< SymmetryType, FloatType, IntType > >
struct	mapper_factory
struct	mapper_factory< asu, FloatType, IntType >
struct	transformer_mapper_factory
struct	peak_histogram
class	peak_list
class	target_and_gradients
class	statistics
	Determines simple map statistics. More...
class	more_statistics
	Determines higher order statistical central moments. More...
Namespaces
namespace	structure_factors
	Copy structure factors to and from complex maps.
Typedefs
typedef sgtbx::space_group	tbx_space_group
Functions
int	nint (double x)
	Fortran-like nearest integer.
af::versa< double, af::c_grid< 3 > >	box_map_averaging (cctbx::uctbx::unit_cell const &unit_cell, af::const_ref< double, af::c_grid< 3 > > const &data, double const &rad)
template<typename DataType>
af::shared< DataType >	average_densities (uctbx::unit_cell const &unit_cell, af::const_ref< DataType, af::c_grid< 3 > > const &data, af::const_ref< scitbx::vec3< double > > const &sites_frac, float radius)
template<typename FloatType, typename IntType>
fractional< FloatType >	grid_fractionalization (grid_point< IntType > const &coordinate, af::tiny< IntType, dimension_3 > const &extents)
template<typename IntType, typename FloatType>
scitbx::vec3< FloatType >	strange_fractional_gridization (fractional< FloatType > const &coordinate, af::tiny< IntType, dimension_3 > const &extents)
template<typename IntType, typename FloatType>
grid_point< IntType >	floor_fractional_gridization (fractional< FloatType > const &coordinate, af::tiny< IntType, dimension_3 > const &extents)
template<typename IntType, typename FloatType>
grid_point< IntType >	round_fractional_gridization (fractional< FloatType > const &coordinate, af::tiny< IntType, dimension_3 > const &extents)
template<typename FloatType, typename IndexType>
af::versa< FloatType, af::flex_grid< IndexType > >	copy (af::const_ref< FloatType, af::flex_grid< IndexType > > const &map, af::flex_grid< IndexType > const &result_grid)
template<typename ElementType>
void	copy (af::const_ref< ElementType, af::c_grid_padded< 3 > > const &source, af::ref< ElementType, af::c_grid< 3 > > const &target)
template<typename FloatType>
af::versa< FloatType, af::flex_grid<> >	copy (af::const_ref< FloatType, c_grid_padded_p1< 3 > > const &map_unit_cell, af::int3 const &first, af::int3 const &last)
template<typename ElementType, typename IndexType>
void	unpad_in_place (ElementType *map_begin, IndexType const &all, IndexType const &focus)
template<typename ElementType>
void	unpad_in_place (af::versa< ElementType, af::flex_grid<> > &map)
template<typename MapFloatType, typename SiteFloatType>
MapFloatType	eight_point_interpolation (af::const_ref< MapFloatType, af::c_grid_padded< 3 > > const &map, scitbx::vec3< SiteFloatType > const &x_frac)
template<typename FloatType>
af::c_grid_padded< 3 >::index_type	closest_grid_point (af::flex_grid<> const &map_accessor, fractional< FloatType > const &x_frac)
template<typename FloatType>
FloatType	non_crystallographic_eight_point_interpolation (af::const_ref< FloatType, af::flex_grid<> > const &map, scitbx::mat3< FloatType > const &gridding_matrix, scitbx::vec3< FloatType > const &site_cart, bool allow_out_of_bounds=false, FloatType const &out_of_bounds_substitute_value=0)
template<typename FloatType>
FloatType	asu_eight_point_interpolation (af::const_ref< FloatType, af::flex_grid<> > const &map, crystal::direct_space_asu::asu_mappings< FloatType > &am, fractional< FloatType > const &site_cart)
template<typename FloatType>
af::versa< FloatType, af::c_grid_padded< 3 > >	fft_to_real_map (sgtbx::space_group const &space_group, af::tiny< int, 3 > const &n_real, af::const_ref< miller::index<> > const &miller_indices, af::const_ref< std::complex< FloatType > > const &data)
	Computes FFT map from Fourier coefficients.
template<typename FloatType>
af::versa< FloatType, af::c_grid< 3 > >	fft_to_real_map_unpadded (sgtbx::space_group const &space_group, af::tiny< int, 3 > const &n_real, af::const_ref< miller::index<> > const &miller_indices, af::const_ref< std::complex< FloatType > > const &data)
	Computes unpadded FFT map from Fourier coefficients.
template<typename SetType>
std::auto_ptr< SetType >	grid_indices_around_sites (uctbx::unit_cell const &unit_cell, af::tiny< int, 3 > const &fft_n_real, af::tiny< int, 3 > const &fft_m_real, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< double > const &site_radii)
template<typename IndexValueType>
af::tiny< IndexValueType, 3 >	determine_gridding (uctbx::unit_cell const &unit_cell, double d_min, double resolution_factor, af::tiny< IndexValueType, 3 > const &mandatory_factors=detail::one_one_one, IndexValueType max_prime=5, bool assert_shannon_sampling=true)
template<typename IndexValueType>
af::tiny< IndexValueType, 3 >	determine_gridding (uctbx::unit_cell const &unit_cell, double d_min, double resolution_factor, sgtbx::search_symmetry_flags const &symmetry_flags, sgtbx::space_group_type const &space_group_type, af::tiny< IndexValueType, 3 > const &mandatory_factors=detail::one_one_one, IndexValueType max_prime=5, bool assert_shannon_sampling=true)
template<typename ToFracType, typename FactoryType, typename FromFracType>
transformer_types < FromFracType >::to_type	transformer_mapper (ToFracType const &to_frac, FactoryType const &factory, FromFracType const &from_frac, typename transformer_types< ToFracType >::from_type const &coordinate)
template<typename DataType, typename TagType>
void	peak_search_unit_cell (af::const_ref< DataType, af::c_grid_padded< 3 > > const &data, af::ref< TagType, af::c_grid< 3 > > const &tags, int level)
	Peak search in a 3d-map covering the unit cell.
template<typename MapFloatType, typename SiteFloatType>
MapFloatType	real_space_target_simple (uctbx::unit_cell const &unit_cell, af::const_ref< MapFloatType, af::c_grid_padded< 3 > > const &density_map, af::const_ref< scitbx::vec3< SiteFloatType > > const &sites_cart)
template<typename MapFloatType, typename SiteFloatType>
af::shared< scitbx::vec3 < SiteFloatType > >	real_space_gradients_simple (uctbx::unit_cell const &unit_cell, af::const_ref< MapFloatType, af::c_grid_padded< 3 > > const &density_map, af::const_ref< scitbx::vec3< SiteFloatType > > const &sites_cart, SiteFloatType delta)
template<typename IntegerType>
IntegerType	ih_as_h (IntegerType ih, std::size_t n_real)
	Miller index element corresponding to 1-dimensional array index.
template<typename IntegerType>
IntegerType	h_as_ih_exact (IntegerType h, IntegerType n_complex, bool positive_only)
	1-dimensional array index corresponding to Miller index element.
template<typename IndexTypeN>
af::int3	h_as_ih_exact_array (bool anomalous_flag, miller::index<> const &h, IndexTypeN const &n_complex)
	3-dimensional array indices corresponding to Miller index.
template<typename IntegerType>
IntegerType	h_as_ih_mod (IntegerType h, IntegerType const &n_real)
	1-dimensional array index corresponding to Miller index element.
template<typename IndexTypeN>
IndexTypeN	h_as_ih_mod_array (miller::index<> const &h, IndexTypeN const &n_real)
	3-dimensional array indices corresponding to Miller index.

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Detailed Description

Map algorithms.

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Function Documentation

af::versa<FloatType, af::c_grid_padded<3> > cctbx::maptbx::fft_to_real_map	(	sgtbx::space_group const &	space_group,
		af::tiny< int, 3 > const &	n_real,
		af::const_ref< miller::index<> > const &	miller_indices,
		af::const_ref< std::complex< FloatType > > const &	data
	)			[inline]

Computes FFT map from Fourier coefficients.

See also: scitbx::fftpack::real_to_complex_3d structure_factors::to_map

References real_to_complex_3d::backward(), to_map::complex_map(), real_to_complex_3d::m_real(), real_to_complex_3d::n_complex(), and real_to_complex_3d::n_real().

Referenced by fft_to_real_map_unpadded().

IntegerType cctbx::maptbx::h_as_ih_exact	(	IntegerType	h,
		IntegerType	n_complex,
		bool	positive_only
	)			[inline]

1-dimensional array index corresponding to Miller index element.

Returns -1 if h is out of range (see code).

Referenced by h_as_ih_exact_array().

af::int3 cctbx::maptbx::h_as_ih_exact_array	(	bool	anomalous_flag,
		miller::index<> const &	h,
		IndexTypeN const &	n_complex
	)			[inline]

3-dimensional array indices corresponding to Miller index.

Result is -1 for out-of-range elements (see code).

References h_as_ih_exact().

IntegerType cctbx::maptbx::h_as_ih_mod	(	IntegerType	h,
		IntegerType const &	n_real
	)			[inline]

1-dimensional array index corresponding to Miller index element.

Applies modulus operation (see code).

Referenced by h_as_ih_mod_array().

IndexTypeN cctbx::maptbx::h_as_ih_mod_array	(	miller::index<> const &	h,
		IndexTypeN const &	n_real
	)			[inline]

3-dimensional array indices corresponding to Miller index.

Applies modulus operation (see code).

See also: structure_factors::to_map

References h_as_ih_mod().

void cctbx::maptbx::peak_search_unit_cell	(	af::const_ref< DataType, af::c_grid_padded< 3 > > const &	data,
		af::ref< TagType, af::c_grid< 3 > > const &	tags,
		int	level
	)			[inline]

Peak search in a 3d-map covering the unit cell.

Dependencies due to symmetry (space group, Euclidean normalizer, or similar) are encoded in a 3d-map of tags.

Requirements:

• physical dimensions of maps are equal to generic dimensions
• dimensions of data and tags are equal

      tags:
        on input: < 0: independent grid point
                  >= 0: dependent grid point,
                        flag is 1d-index of corresponding
                        independent grid point
        on output: -1: independent, not a peak
                   -2: independent, peak
                   tags for dependent grid points are unchanged

      level = 1: compare to the 6 nearest neighbors
            = 2: also compare to the 12 second-nearest neighbors
            > 2: also compare to the 8 third-nearest neighbors

References CCTBX_ASSERT.