cctbx::miller Namespace Reference

Miller index namespace. More...


Classes

class  amplitude_normalisation
 Amplitudes normalisation transforming so-called F's into E's, and vice-versa. More...
class  index_table_layout_adaptor
 Support for common layouts of tables of asymmetric Miller indices. More...
class  asym_index
 Selection of an asymmetric Miller index. More...
struct  map_to_asu_policy< data_classes::scalar_type >
struct  map_to_asu_policy< data_classes::complex_type >
struct  map_to_asu_policy< data_classes::hendrickson_lattman_type >
struct  map_to_asu_policy< data_classes::phase_type >
struct  map_to_asu_policy< double >
struct  map_to_asu_policy< std::complex< double > >
struct  map_to_asu_policy< hendrickson_lattman<> >
class  binning
class  binner
struct  change_basis_phase_policy
struct  change_basis_complex_policy
struct  change_basis_hendrickson_lattman_policy
struct  change_basis
struct  expand_to_p1_iselection
 Expands an array of Miller indices to P1 symmetry. More...
struct  expand_to_p1_complex
 Expands an array of Miller indices and associated complex data to P1 symmetry. More...
struct  expand_to_p1_hendrickson_lattman
 Expands an array of Miller indices and associated Hendrickson-Lattman coefficients to P1 symmetry. More...
struct  expand_to_p1_phases
 Expands an array of Miller indices and associated phases to P1 symmetry. More...
class  hermitian_accessor
 The accessor doing the magic behind the class f_calc_map. More...
class  f_calc_map
 A mapping of miller indices to f_calc values with fast readonly access. More...
class  index_generator
 Efficient, easy-to-use algorithm for building an asymmetric unit of Miller indices up to a given high-resolution limit or up to a given maximum Miller index. More...
class  index_span
 Determines min(indices[i]) and max(indices[i])+1, i=1..3, for an array of Miller indices. More...
class  match_bijvoet_mates
class  match_indices
class  match_multi_indices
struct  merge_equivalents_impl
struct  merge_equivalents_generic
struct  merge_equivalents_exact
struct  merge_equivalents_real
class  merge_equivalents_obs
class  merge_equivalents_shelx
class  split_unmerged
class  phase_integrator
class  phase_entropy
class  sym_equiv_index
 Class for symmetrically equivalent Miller indices. More...
class  sym_equiv_indices
 class for the handling of symmetrically equivalent Miller indices. More...
struct  union_of_indices_registry
class  index
 Miller index class. More...
class  fast_less_than
 Definition of fast comparison for use in, e.g., std::map<miller::index<> >. More...

Typedefs

typedef af::tiny< std::size_t, 2 > pair_type

Functions

void map_to_asu (sgtbx::space_group_type const &sg_type, bool anomalous_flag, af::ref< index<> > const &miller_indices)
void map_to_asu_isym (sgtbx::space_group_type const &sg_type, bool anomalous_flag, af::ref< index<> > const &miller_indices, af::ref< int > const &isym)
template<typename ValueType>
void map_to_asu (sgtbx::space_group_type const &sg_type, bool anomalous_flag, af::ref< index<> > const &miller_indices, af::ref< ValueType > const &data)
template<typename ValueType>
void map_to_asu (sgtbx::space_group_type const &sg_type, bool anomalous_flag, af::ref< index<> > const &miller_indices, af::ref< ValueType > const &data, bool deg)
bool is_unique_set_under_symmetry (sgtbx::space_group_type const &space_group_type, bool anomalous_flag, af::const_ref< index<> > const &miller_indices)
af::shared< std::size_t > unique_under_symmetry_selection (sgtbx::space_group_type const &space_group_type, bool anomalous_flag, af::const_ref< index<> > const &miller_indices)
template<typename FloatType>
FloatType sphere_volume (FloatType const &radius)
af::shared< index<> > expand_to_p1_indices (sgtbx::space_group const &space_group, bool anomalous_flag, af::const_ref< index<> > const &indices)
 Expands an array of Miller indices to P1 symmetry.
template<typename FloatType>
FloatType statistical_mean (sgtbx::space_group const &space_group, bool anomalous_flag, af::const_ref< index<> > const &miller_indices, af::const_ref< FloatType > const &data)
template<typename FloatType>
af::shared< std::complex
< FloatType > > 
phase_transfer (sgtbx::space_group const &space_group, af::const_ref< index<> > const &miller_indices, af::const_ref< FloatType > const &amplitude_source, af::const_ref< std::complex< FloatType > > const &phase_source, FloatType const &epsilon=1.e-10)
 Transfer the phase of phase_source[i] onto amplitude_source[i].
template<typename FloatType>
af::shared< std::complex
< FloatType > > 
phase_transfer (sgtbx::space_group const &space_group, af::const_ref< index<> > const &miller_indices, af::const_ref< FloatType > const &amplitude_source, af::const_ref< FloatType > const &phase_source, bool deg=false)
 Another overload of phase_transfer passing the source phases directly.
template<typename ComplexType, typename FloatType>
af::shared< ComplexType > randomize_amplitude_and_phase (af::const_ref< ComplexType > const &data, af::const_ref< bool > const &selection, FloatType const &amplitude_error, FloatType const &phase_error_deg, int random_seed)
af::shared< bool > simple_slice (af::const_ref< index< int > > const &indices, unsigned slice_axis, int slice_index)
af::shared< bool > multi_slice (af::const_ref< index< int > > const &indices, unsigned slice_axis, int slice_start, int slice_end)


Detailed Description

Miller index namespace.

Function Documentation

af::shared<index<> > cctbx::miller::expand_to_p1_indices ( sgtbx::space_group const &  space_group,
bool  anomalous_flag,
af::const_ref< index<> > const &  indices 
) [inline]

Expands an array of Miller indices to P1 symmetry.

The symmetry operations are applied to each element of the input array.

If anomalous_flag == false, centric indices are treated in a special way: Friedel mates are suppressed. If N is the number of unique symmetrically equivalent indices for a given centric index, only N/2 indices will be generated.

See also: sym_equiv_indices

af::shared<std::complex<FloatType> > cctbx::miller::phase_transfer ( sgtbx::space_group const &  space_group,
af::const_ref< index<> > const &  miller_indices,
af::const_ref< FloatType > const &  amplitude_source,
af::const_ref< std::complex< FloatType > > const &  phase_source,
FloatType const &  epsilon = 1.e-10 
) [inline]

Transfer the phase of phase_source[i] onto amplitude_source[i].

The sign of phase_source[i] is kept.

The phase is actually the nearest phase compatible with space-group restriction for centric reflections.

References CCTBX_ASSERT, and space_group::phase_restriction().

FloatType cctbx::miller::statistical_mean ( sgtbx::space_group const &  space_group,
bool  anomalous_flag,
af::const_ref< index<> > const &  miller_indices,
af::const_ref< FloatType > const &  data 
) [inline]

sum((w/epsilon)*data) / sum(w) anomalous_flag = true: w = 1 anomalous_flag = false: w = 1 for centric reflections w = 2 for acentric reflections

See also: sgtbx::space_group::epsilon()

References space_group::epsilon(), and space_group::is_centric().


Generated on Thu Jun 19 15:34:56 2014 for cctbx by  doxygen 1.5.6