cctbx::maptbx Namespace Reference

Map algorithms. More...


Classes

class  c_grid_p1< 3 >
class  c_grid_padded_p1< 3 >
class  mapped_grid_loop
class  asymmetric_map
class  volume_scale
class  non_linear_map_modification_to_match_average_cumulative_histogram
class  grid_points_in_sphere_around_atom_and_distances
class  find_gaussian_parameters
class  one_gaussian_peak_approximation
class  basic_map
class  connectivity
 Map connectivity analysis. More...
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 >
struct  grid_indices_around_sites_enumerator
class  grid_tags
class  histogram
 Compute map histogram and cumulative functions. More...
class  map_accumulator
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
struct  join_t
class  skeleton
class  shortest_paths
class  statistics
 Determines simple map statistics. More...
class  more_statistics
 Determines higher order statistical central moments. More...
class  mem_iteration

Namespaces

namespace  structure_factors
 Copy structure factors to and from complex maps.

Typedefs

typedef sgtbx::space_group tbx_space_group
typedef scitbx::af::versa
< double,
scitbx::af::c_grid_padded< 3 > > 
map_t
typedef scitbx::af::const_ref
< double,
scitbx::af::c_grid_padded< 3 > > 
const_map_t
typedef scitbx::af::versa
< unsigned,
cctbx::maptbx::asymmetric_map::asu_grid_t > 
marks_t
typedef scitbx::vec3< int > int3_t
typedef tuple< int3_t, double > xyzm_t
typedef std::set< join_t > joins_t

Functions

void translate_into_cell (scitbx::int3 &num, const scitbx::int3 &den)
unsigned short site_symmetry_order (const std::vector< cctbx::sgtbx::grid_symop > &symops, const scitbx::int3 &num, const scitbx::int3 &den)
af::versa< double, af::c_grid< 3 > > denmod_simple (af::const_ref< double, af::c_grid< 3 > > const &map_data, af::tiny< int, 3 > const &n_real, double cutoffp, double cutoffm)
af::versa< double, af::c_grid< 3 > > combine_and_maximize_maps (af::const_ref< double, af::c_grid< 3 > > const &map_data_1, af::const_ref< double, af::c_grid< 3 > > const &map_data_2, af::tiny< int, 3 > const &n_real)
af::versa< double, af::c_grid< 3 > > superpose_maps (cctbx::uctbx::unit_cell const &unit_cell_1, cctbx::uctbx::unit_cell const &unit_cell_2, af::const_ref< double, af::c_grid< 3 > > const &map_data_1, af::tiny< int, 3 > const &n_real_2, scitbx::mat3< double > const &rotation_matrix, scitbx::vec3< double > const &translation_vector)
af::versa< double, af::c_grid< 3 > > rotate_translate_map (cctbx::uctbx::unit_cell const &unit_cell, af::const_ref< double, af::c_grid< 3 > > const &map_data, scitbx::mat3< double > const &rotation_matrix, scitbx::vec3< double > const &translation_vector, af::tiny< int, 3 > const &start, af::tiny< int, 3 > const &end)
af::versa< double, af::c_grid< 3 > > rotate_translate_map (cctbx::uctbx::unit_cell const &unit_cell, af::const_ref< double, af::c_grid< 3 > > const &map_data, scitbx::mat3< double > const &rotation_matrix, scitbx::vec3< double > const &translation_vector)
void cc_weighted_maps (af::ref< double, af::c_grid< 3 > > data_1, af::ref< double, af::c_grid< 3 > > data_2)
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 FloatType>
af::versa< FloatType,
af::flex_grid<> > 
copy_box (af::const_ref< FloatType, af::flex_grid<> > const &map, 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 MapFloatType, typename SiteFloatType>
MapFloatType eight_point_interpolation (af::const_ref< MapFloatType, af::c_grid< 3 > > const &map, scitbx::vec3< SiteFloatType > const &x_frac)
template<typename MapFloatType, typename SiteFloatType>
MapFloatType tricubic_interpolation (af::const_ref< MapFloatType, af::c_grid_padded< 3 > > const &map, scitbx::vec3< SiteFloatType > const &x_frac)
template<typename MapFloatType, typename SiteFloatType>
MapFloatType tricubic_interpolation (af::const_ref< MapFloatType, af::c_grid< 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 FloatType>
std::complex< FloatType > direct_summation_at_point (af::const_ref< miller::index<> > const &miller_indices, af::const_ref< std::complex< FloatType > > const &data, scitbx::vec3< FloatType > site_frac)
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 FloatType>
af::versa< FloatType,
af::c_grid< 3 > > 
mask (af::const_ref< scitbx::vec3< FloatType > > const &sites_frac, uctbx::unit_cell const &unit_cell, af::tiny< int, 3 > const &n_real, af::const_ref< FloatType > const &radii)
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, af::const_ref< bool > const &selection)
template<typename MapFloatType, typename SiteFloatType>
MapFloatType real_space_target_simple (af::const_ref< MapFloatType, af::c_grid< 3 > > const &density_map, af::const_ref< scitbx::vec3< SiteFloatType > > const &sites_frac)
template<typename MapFloatType, typename SiteFloatType>
af::shared< MapFloatType > real_space_target_simple_per_site (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, af::const_ref< bool > const &selection)
bool operator< (const join_t &a, const join_t &b)
skeleton swanson (const const_map_t &map, const cctbx::sgtbx::space_group_type &spgr, double sigma)
skeleton swanson (const cctbx::maptbx::asymmetric_map &map, double sigma)
std::vector< std::size_t > find_clusters (const skeleton &skelet)
std::vector< std::size_t > mask_components (marks_t &mask, const std::vector< int > &components)
void mask_density_map (asymmetric_map::data_ref_t map, const marks_t &mask, unsigned val)
std::pair< size_t, std::vector
< int > > 
skeleton_components (const joins_t &joins, size_t nv)
template<typename FloatType>
scitbx::sym_mat3< FloatType > sphericity_tensor (af::const_ref< FloatType, af::c_grid< 3 > > const &map_data, uctbx::unit_cell const &unit_cell, FloatType const &radius, cctbx::fractional<> const &site_frac)
template<typename FloatType>
af::shared< FloatType > sphericity (af::const_ref< FloatType, af::c_grid< 3 > > const &map_data, uctbx::unit_cell const &unit_cell, FloatType const &radius, af::const_ref< scitbx::vec3< FloatType > > const &sites_frac)
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.
template<typename DataType>
void hoppe_gassman_modification2 (af::ref< DataType, af::c_grid< 3 > > map_data, DataType mean_scale, int n_iterations)
template<typename DataType>
void hoppe_gassman_modification (af::ref< DataType, af::c_grid< 3 > > map_data, DataType mean_scale, int n_iterations)
template<typename DataType>
DataType map_sum_at_sites_frac (af::const_ref< DataType, af::c_grid< 3 > > const &map_data, af::const_ref< scitbx::vec3< DataType > > const &sites_frac)
template<typename DataType>
af::versa< DataType,
af::c_grid< 3 > > 
set_box_copy (DataType const &value, af::ref< DataType, af::c_grid< 3 > > map_data_to, af::tiny< int, 3 > const &start, af::tiny< int, 3 > const &end)
template<typename ComplexType, typename FloatType>
af::shared< ComplexType > fem_averaging_loop (af::const_ref< ComplexType > const &map_coefficients, af::const_ref< FloatType > const &r_factors, af::const_ref< FloatType > const &sigma_over_f_obs, FloatType const &random_scale, int const &random_seed, int const &n_cycles)
template<typename FloatType>
cctbx::cartesian center_of_mass (af::const_ref< FloatType, af::c_grid< 3 > > const &map_data, cctbx::uctbx::unit_cell const &unit_cell, FloatType const &cutoff)
template<typename DataType>
af::versa< DataType,
af::c_grid< 3 > > 
conditional_solvent_region_filter (af::const_ref< DataType, af::c_grid_padded< 3 > > const &bulk_solvent_mask, af::const_ref< DataType, af::c_grid< 3 > > const &map_data, DataType const &threshold)
template<typename DataType>
void set_box (DataType const &value, af::ref< DataType, af::c_grid< 3 > > map_data_to, af::tiny< int, 3 > const &start, af::tiny< int, 3 > const &end)
template<typename DataType>
void copy_box (af::const_ref< DataType, af::c_grid< 3 > > const &map_data_from, af::ref< DataType, af::c_grid< 3 > > map_data_to, af::tiny< int, 3 > const &start, af::tiny< int, 3 > const &end)
template<typename DataType>
void set_box (af::const_ref< DataType, af::c_grid< 3 > > const &map_data_from, af::ref< DataType, af::c_grid< 3 > > map_data_to, af::tiny< int, 3 > const &start, af::tiny< int, 3 > const &end)
template<typename DataType>
void cut_by (af::ref< DataType, af::c_grid< 3 > > kick, af::ref< DataType, af::c_grid< 3 > > fem, DataType cut_by_threshold)
template<typename DataType1, typename DataType2>
void truncate_special (af::ref< DataType2, af::c_grid< 3 > > mask, af::ref< DataType1, af::c_grid< 3 > > map_data)
template<typename DataType>
void truncate_between_min_max (af::ref< DataType, af::c_grid< 3 > > map_data, DataType const &min, DataType const &max)
template<typename DataType>
void binarize (af::ref< DataType, af::c_grid< 3 > > map_data, DataType const &threshold, DataType const &substitute_value_below, DataType const &substitute_value_above)
template<typename DataType>
void truncate (af::ref< DataType, af::c_grid< 3 > > map_data, DataType const &standard_deviation, DataType const &by_sigma_less_than, DataType const &scale_by, DataType const &set_value)
template<typename DataType>
void intersection (af::ref< DataType, af::c_grid< 3 > > map_data_1, af::ref< DataType, af::c_grid< 3 > > map_data_2, af::ref< DataType > const &thresholds, bool average)
template<typename DataType>
void convert_to_non_negative (af::ref< DataType, af::c_grid< 3 > > map_data, DataType substitute_value)
template<typename DataType>
void flexible_boundary_mask (af::ref< DataType, af::c_grid< 3 > > map_data, af::ref< DataType, af::c_grid< 3 > > mask_data)
template<typename DataType>
void reset (af::ref< DataType, af::c_grid< 3 > > map_data, DataType substitute_value, DataType less_than_threshold, DataType greater_than_threshold, bool use_and)
template<typename DataType>
void median_filter (af::ref< DataType, af::c_grid< 3 > > map_data, int const &index_span)
template<typename DataType>
void kuwahara_filter (af::ref< DataType, af::c_grid< 3 > > map_data, int const &index_span)
template<typename DataType>
void remove_single_node_peaks (af::ref< DataType, af::c_grid< 3 > > map_data, af::ref< DataType, af::c_grid_padded< 3 > > mask_data, DataType const &cutoff, int const &index_span)
template<typename DataType>
void map_box_average (af::ref< DataType, af::c_grid< 3 > > map_data, cctbx::uctbx::unit_cell const &unit_cell, double const &radius)
template<typename DataType>
void map_box_average (af::ref< DataType, af::c_grid< 3 > > map_data, DataType const &cutoff, int const &index_span)
template<typename DataType>
void sharpen (af::ref< DataType, af::c_grid< 3 > > map_data, int const &index_span, int const &n_averages)


Detailed Description

Map algorithms.

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]

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.

unsigned short cctbx::maptbx::site_symmetry_order ( const std::vector< cctbx::sgtbx::grid_symop > &  symops,
const scitbx::int3 num,
const scitbx::int3 den 
) [inline]

Todo:
: code duplication, see atom_mask.h

References CCTBX_ASSERT, and translate_into_cell().

scitbx::sym_mat3<FloatType> cctbx::maptbx::sphericity_tensor ( af::const_ref< FloatType, af::c_grid< 3 > > const &  map_data,
uctbx::unit_cell const &  unit_cell,
FloatType const &  radius,
cctbx::fractional<> const &  site_frac 
) [inline]

Compute peak sphericity as the ratio of min/max eigen-values of spericity tensor using coordinates of grid points in a box around peak center selected above one-nth (n=3) of peak max height value. Tensor elements are weighted with map values at respective grid nodes though it isn't clear whether it is necessary conceptially or useful practically. Known (fixable) limitation: may consider two closely standing peaks as one.

References scitbx::deg_as_rad(), unit_cell::orthogonalize(), unit_cell::parameters(), and unit_cell::volume().

void cctbx::maptbx::translate_into_cell ( scitbx::int3 num,
const scitbx::int3 den 
) [inline]

Todo:
code duplication: mmtbx/masks/atom_mask.cpp

Referenced by site_symmetry_order().


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