cctbx.maptbx
index
/net/chevy/raid1/nat/src/cctbx_project/cctbx/maptbx/__init__.py

 
Package Contents
       
mem
real_space_refinement
real_space_refinement_simple
real_space_target_and_gradients
tst_asymmetric_map
tst_ccp
tst_get_percentile_cutoffs
tst_map_peak_3d_as_2d
tst_mask
tst_peak_volume_estimate
tst_real_space_refinement
tst_real_space_refinement_simple
tst_real_space_target_and_gradients

 
Classes
       
__builtin__.object
boxes
cluster_site_info
crystal_gridding
crystal_gridding_tags
local_scale
peak_cluster_analysis
peak_search_parameters
positivity_constrained_density_modification
spherical_variance_around_point
cctbx_maptbx_ext.peak_list(Boost.Python.instance)
peak_list
cctbx_maptbx_ext.statistics(Boost.Python.instance)
statistics

 
class boxes(__builtin__.object)
    Split box defined by n_real into boxes where each box is a fraction of the
whole box.
 
  Methods defined here:
__init__(self, n_real, fraction=None, log=None, prefix='')

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class cluster_site_info(__builtin__.object)
     Methods defined here:
__init__(self, peak_list_index, grid_index, grid_height, site, height)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class crystal_gridding(__builtin__.object)
     Methods defined here:
__init__(self, unit_cell, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, space_group_info=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True, pre_determined_n_real=None)
change_space_group(self, space_group_info)
crystal_symmetry(self)
d_min(self)
mandatory_factors(self)
max_prime(self)
n_grid_points(self)
n_real(self)
resolution_factor(self)
space_group(self)
space_group_info(self)
symmetry_flags(self)
tags(self)
unit_cell(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class crystal_gridding_tags(crystal_gridding)
    
Method resolution order:
crystal_gridding_tags
crystal_gridding
__builtin__.object

Methods defined here:
__init__(self, gridding)
peak_search(self, parameters, map, verify_symmetry=True)
tags(self)

Methods inherited from crystal_gridding:
change_space_group(self, space_group_info)
crystal_symmetry(self)
d_min(self)
mandatory_factors(self)
max_prime(self)
n_grid_points(self)
n_real(self)
resolution_factor(self)
space_group(self)
space_group_info(self)
symmetry_flags(self)
unit_cell(self)

Data descriptors inherited from crystal_gridding:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class local_scale(__builtin__.object)
     Methods defined here:
__init__(self, crystal_gridding, crystal_symmetry, f_map=None, map_data=None, miller_array=None, d_min=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class peak_cluster_analysis(__builtin__.object)
     Methods defined here:
__init__(self, peak_list, special_position_settings, general_positions_only=False, effective_resolution=None, significant_height_fraction=None, cluster_height_fraction=None, min_cross_distance=None, max_clusters=None, min_cubicle_edge=5)
__iter__(self)
all(self, max_clusters=None)
all_site_cluster_analysis(self, max_clusters=None)
all_with_effective_resolution(self, max_clusters=None)
append_fixed_site(self, site, height=0)
cluster_height_fraction(self)
discard_last(self)
effective_resolution(self)
fixed_site_indices(self)
general_positions_only(self)
heights(self)
max_clusters(self)
max_grid_height(self)
min_cross_distance(self)
next(self)
next_site_cluster_analysis(self)
next_with_effective_resolution(self)
peak_list(self)
peak_list_indices(self)
significant_height_fraction(self)
site_cluster_analysis(self)
sites(self)
special_position_settings(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class peak_list(cctbx_maptbx_ext.peak_list)
    
Method resolution order:
peak_list
cctbx_maptbx_ext.peak_list
Boost.Python.instance
__builtin__.object

Methods defined here:
__init__(self, data, tags, peak_search_level=1, max_peaks=0, peak_cutoff=None, interpolate=True)

Methods inherited from cctbx_maptbx_ext.peak_list:
__reduce__ = (...)
grid_heights(...)
grid_heights( (peak_list)arg1) -> double :
 
    C++ signature :
        scitbx::af::shared<double> grid_heights(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double> {lvalue})
grid_indices(...)
grid_indices( (peak_list)arg1, (int)arg2) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<long, 3ul> grid_indices(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double>,long)
gridding(...)
gridding( (peak_list)arg1) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<long, 3ul> gridding(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double> {lvalue})
heights(...)
heights( (peak_list)arg1) -> double :
 
    C++ signature :
        scitbx::af::shared<double> heights(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double> {lvalue})
sites(...)
sites( (peak_list)arg1) -> vec3_double :
 
    C++ signature :
        scitbx::af::shared<scitbx::vec3<double> > sites(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double> {lvalue})
size(...)
size( (peak_list)arg1) -> int :
 
    C++ signature :
        unsigned long size(cctbx::maptbx::peak_list<scitbx::af::tiny<long, 3ul>, scitbx::vec3<double>, double> {lvalue})

Data descriptors inherited from Boost.Python.instance:
__dict__
__weakref__

Data and other attributes inherited from Boost.Python.instance:
__new__ = <built-in method __new__ of Boost.Python.class object>
T.__new__(S, ...) -> a new object with type S, a subtype of T

 
class peak_search_parameters(__builtin__.object)
     Methods defined here:
__init__(self, peak_search_level=1, max_peaks=0, peak_cutoff=None, interpolate=True, min_distance_sym_equiv=None, general_positions_only=False, effective_resolution=None, significant_height_fraction=None, cluster_height_fraction=None, min_cross_distance=None, max_clusters=None, min_cubicle_edge=5)
cluster_height_fraction(self)
effective_resolution(self)
general_positions_only(self)
interpolate(self)
max_clusters(self)
max_peaks(self)
min_cross_distance(self)
min_cubicle_edge(self)
min_distance_sym_equiv(self)
peak_cutoff(self)
peak_search_level(self)
significant_height_fraction(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class positivity_constrained_density_modification(__builtin__.object)
     Methods defined here:
__init__(self, f, f_000, n_cycles=100, resolution_factor=0.25, d_min=None, crystal_gridding=None, complete_set=None)
assert_equal(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class spherical_variance_around_point(__builtin__.object)
     Methods defined here:
__init__(self, real_map, unit_cell, site_cart, radius, n_points=40, spline_interpolation=True, write_sphere_points_to_pdb_file=None)
show(self, out=None, prefix='')

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class statistics(cctbx_maptbx_ext.statistics)
    
Method resolution order:
statistics
cctbx_maptbx_ext.statistics
Boost.Python.instance
__builtin__.object

Methods defined here:
__init__(self, map)

Methods inherited from cctbx_maptbx_ext.statistics:
__reduce__ = (...)
max(...)
max( (statistics)arg1) -> float :
 
    C++ signature :
        double max(cctbx::maptbx::statistics<double> {lvalue})
mean(...)
mean( (statistics)arg1) -> float :
 
    C++ signature :
        double mean(cctbx::maptbx::statistics<double> {lvalue})
mean_sq(...)
mean_sq( (statistics)arg1) -> float :
 
    C++ signature :
        double mean_sq(cctbx::maptbx::statistics<double> {lvalue})
min(...)
min( (statistics)arg1) -> float :
 
    C++ signature :
        double min(cctbx::maptbx::statistics<double> {lvalue})
show_summary(self, f=None, prefix='')
sigma(...)
sigma( (statistics)arg1) -> float :
 
    C++ signature :
        double sigma(cctbx::maptbx::statistics<double> {lvalue})

Data descriptors inherited from Boost.Python.instance:
__dict__
__weakref__

Data and other attributes inherited from Boost.Python.instance:
__new__ = <built-in method __new__ of Boost.Python.class object>
T.__new__(S, ...) -> a new object with type S, a subtype of T

 
Functions
       
as_CObjectZYX(map_unit_cell, first, last, apply_sigma_scaling=True)
asu_eight_point_interpolation(...)
asu_eight_point_interpolation( (double)arg1, (direct_space_asu_asu_mappings)arg2, (object)arg3) -> float :
 
    C++ signature :
        double asu_eight_point_interpolation(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,cctbx::crystal::direct_space_asu::asu_mappings<double, int> {lvalue},cctbx::fractional<double>)
average_densities(...)
average_densities( (unit_cell)unit_cell, (double)data, (vec3_double)sites_frac, (float)radius) -> double :
 
    C++ signature :
        scitbx::af::shared<double> average_densities(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,float)
binarize(...)
binarize( (double)map_data, (float)threshold, (float)substitute_value_below, (float)substitute_value_above) -> None :
 
    C++ signature :
        void binarize(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,double,double)
cc_weighted_maps(...)
cc_weighted_maps( (double)arg1, (double)arg2) -> None :
 
    C++ signature :
        void cc_weighted_maps(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >)
ccv(map_1, map_2, modified, centered, cutoff=None, n_bins=10000)
center_of_mass(...)
center_of_mass( (double)map_data, (unit_cell)unit_cell, (float)cutoff) -> tuple :
 
    C++ signature :
        cctbx::cartesian<double> center_of_mass(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,cctbx::uctbx::unit_cell,double)
closest_grid_point(...)
closest_grid_point( (grid)arg1, (object)arg2) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<unsigned long, 3ul> closest_grid_point(scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >,cctbx::fractional<double>)
combine_and_maximize_maps(...)
combine_and_maximize_maps( (double)map_data_1, (double)map_data_2, (object)n_real) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > combine_and_maximize_maps(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>)
conditional_solvent_region_filter(...)
conditional_solvent_region_filter( (double)bulk_solvent_mask, (double)map_data, (float)threshold) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > conditional_solvent_region_filter(scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double)
convert_to_non_negative(...)
convert_to_non_negative( (double)data, (float)substitute_value) -> None :
 
    C++ signature :
        void convert_to_non_negative(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double)
copy(...)
copy( (float)map, (grid)result_grid) -> float :
 
    C++ signature :
        scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy(scitbx::af::const_ref<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >)
 
copy( (double)map, (grid)result_grid) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >)
 
copy( (float)map_unit_cell, (object)first, (object)last) -> float :
 
    C++ signature :
        scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy(scitbx::af::const_ref<float, cctbx::maptbx::c_grid_padded_p1<3ul> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
 
copy( (double)map_unit_cell, (object)first, (object)last) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy(scitbx::af::const_ref<double, cctbx::maptbx::c_grid_padded_p1<3ul> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
copy_box(...)
copy_box( (float)map, (object)first, (object)last) -> float :
 
    C++ signature :
        scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy_box(scitbx::af::const_ref<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
 
copy_box( (double)map, (object)first, (object)last) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > copy_box(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
 
copy_box( (double)map_data_from, (double)map_data_to, (object)start, (object)end) -> None :
 
    C++ signature :
        void copy_box(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
cut_by(...)
cut_by( (double)kick, (double)fem, (float)cut_by_threshold) -> None :
 
    C++ signature :
        void cut_by(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double)
denmod_simple(...)
denmod_simple( (double)map_data, (object)n_real, (float)cutoffp, (float)cutoffm) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > denmod_simple(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,double,double)
determine_gridding(...)
determine_gridding( (unit_cell)arg1, (float)arg2, (float)arg3, (object)arg4, (int)arg5, (bool)arg6) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<int, 3ul> determine_gridding(cctbx::uctbx::unit_cell,double,double,scitbx::af::tiny<int, 3ul>,int,bool)
 
determine_gridding( (unit_cell)arg1, (float)arg2, (float)arg3, (search_symmetry_flags)arg4, (space_group_type)arg5, (object)arg6, (int)arg7, (bool)arg8) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<int, 3ul> determine_gridding(cctbx::uctbx::unit_cell,double,double,cctbx::sgtbx::search_symmetry_flags,cctbx::sgtbx::space_group_type,scitbx::af::tiny<int, 3ul>,int,bool)
direct_summation_at_point(...)
direct_summation_at_point( (miller_index)miller_indices, (complex_double)data, (object)site_frac) -> complex :
 
    C++ signature :
        std::complex<double> direct_summation_at_point(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<std::complex<double>, scitbx::af::trivial_accessor>,scitbx::vec3<double>)
eight_point_interpolation(...)
eight_point_interpolation( (double)arg1, (object)arg2) -> float :
 
    C++ signature :
        double eight_point_interpolation(scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::vec3<double>)
fem_averaging_loop(...)
fem_averaging_loop( (complex_double)map_coefficients, (object)r_factors, (object)sigma_over_f_obs, (float)random_scale, (int)random_seed, (int)n_cycles) -> complex_double :
 
    C++ signature :
        scitbx::af::shared<std::complex<double> > fem_averaging_loop(scitbx::af::const_ref<std::complex<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double,int,int)
fft_to_real_map_unpadded(...)
fft_to_real_map_unpadded( (space_group)space_group, (object)n_real, (miller_index)miller_indices, (complex_double)data) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > fft_to_real_map_unpadded(cctbx::sgtbx::space_group,scitbx::af::tiny<int, 3ul>,scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<std::complex<double>, scitbx::af::trivial_accessor>)
flexible_boundary_mask(...)
flexible_boundary_mask( (double)data, (double)mask) -> None :
 
    C++ signature :
        void flexible_boundary_mask(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >)
get_asu_mapper(...)
get_asu_mapper( (object)coordinate, (space_group)space_group, (direct_space_asu_float_asu)float_asu, (float)min_distance_sym_equiv, (bool)assert_min_distance_sym_equiv) -> basic_mapper :
 
    C++ signature :
        cctbx::maptbx::basic_mapper<void, double, long> get_asu_mapper(cctbx::fractional<double>,cctbx::sgtbx::space_group,cctbx::crystal::direct_space_asu::float_asu<double>,double,bool)
get_non_symmetric_mapper(...)
get_non_symmetric_mapper( (object)coordinate) -> basic_mapper :
 
    C++ signature :
        cctbx::maptbx::basic_mapper<void, double, long> get_non_symmetric_mapper(cctbx::fractional<double>)
get_unit_cell_mapper(...)
get_unit_cell_mapper( (object)coordinate) -> basic_mapper :
 
    C++ signature :
        cctbx::maptbx::basic_mapper<void, double, long> get_unit_cell_mapper(cctbx::fractional<double>)
grid_indices_around_sites(...)
grid_indices_around_sites( (unit_cell)unit_cell, (object)fft_n_real, (object)fft_m_real, (vec3_double)sites_cart, (object)site_radii) -> unsigned :
 
    C++ signature :
        boost::shared_ptr<std::vector<unsigned int, std::allocator<unsigned int> > > grid_indices_around_sites(cctbx::uctbx::unit_cell,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>)
hoppe_gassman_modification(...)
hoppe_gassman_modification( (double)data, (float)mean_scale, (int)n_iterations) -> None :
 
    C++ signature :
        void hoppe_gassman_modification(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,int)
hoppe_gassman_modification2(...)
hoppe_gassman_modification2( (double)data, (float)mean_scale, (int)n_iterations) -> None :
 
    C++ signature :
        void hoppe_gassman_modification2(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,int)
intersection(...)
intersection( (double)map_data_1, (double)map_data_2, (object)thresholds, (bool)average) -> None :
 
    C++ signature :
        void intersection(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::trivial_accessor>,bool)
kuwahara_filter(...)
kuwahara_filter( (double)map_data, (int)index_span) -> None :
 
    C++ signature :
        void kuwahara_filter(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,int)
map_box_average(...)
map_box_average( (double)map_data, (float)cutoff, (int)index_span) -> None :
 
    C++ signature :
        void map_box_average(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,int)
 
map_box_average( (double)map_data, (unit_cell)unit_cell, (float)radius) -> None :
 
    C++ signature :
        void map_box_average(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,cctbx::uctbx::unit_cell,double)
map_peak_3d_as_2d(map_data, unit_cell, center_cart, radius, step=0.01, s_angle_sampling_step=10, t_angle_sampling_step=10)
map_sum_at_sites_frac(...)
map_sum_at_sites_frac( (double)map_data, (vec3_double)sites_frac) -> float :
 
    C++ signature :
        double map_sum_at_sites_frac(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
mask(xray_structure, n_real, solvent_radius)
median_filter(...)
median_filter( (double)map_data, (int)index_span) -> None :
 
    C++ signature :
        void median_filter(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,int)
non_crystallographic_eight_point_interpolation(...)
non_crystallographic_eight_point_interpolation( (double)map, (object)gridding_matrix, (object)site_cart [, (bool)allow_out_of_bounds=False [, (float)out_of_bounds_substitute_value=0]]) -> float :
 
    C++ signature :
        double non_crystallographic_eight_point_interpolation(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::mat3<double>,scitbx::vec3<double> [,bool=False [,double=0]])
peak_volume_estimate(map_data, sites_cart, crystal_symmetry, cutoff, atom_radius=2.0)
principal_axes_of_inertia(real_map, site_cart, unit_cell, radius)
real_space_gradients_simple(...)
real_space_gradients_simple( (unit_cell)unit_cell, (double)density_map, (vec3_double)sites_cart, (float)delta, (bool)selection) -> vec3_double :
 
    C++ signature :
        scitbx::af::shared<scitbx::vec3<double> > real_space_gradients_simple(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,double,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>)
real_space_refinement_gradients(...)
real_space_refinement_gradients( (basic_map)basic_map, (vec3_double)sites [, (float)delta_h=1.0 [, (int)max_iter=0]]) -> vec3_double :
 
    C++ signature :
        scitbx::af::shared<scitbx::vec3<double> > real_space_refinement_gradients(cctbx::maptbx::basic_map<double, long>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor> [,double=1.0 [,unsigned long=0]])
real_space_refinement_residual(...)
real_space_refinement_residual( (basic_map)basic_map, (vec3_double)sites, (object)weights) -> float :
 
    C++ signature :
        double real_space_refinement_residual(cctbx::maptbx::basic_map<double, long>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>)
real_space_target_simple(...)
real_space_target_simple( (unit_cell)unit_cell, (double)density_map, (vec3_double)sites_cart, (bool)selection) -> float :
 
    C++ signature :
        double real_space_target_simple(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>)
 
real_space_target_simple( (double)density_map, (vec3_double)sites_frac) -> float :
 
    C++ signature :
        double real_space_target_simple(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
real_space_target_simple_per_site(...)
real_space_target_simple_per_site( (unit_cell)unit_cell, (double)density_map, (vec3_double)sites_cart) -> double :
 
    C++ signature :
        scitbx::af::shared<double> real_space_target_simple_per_site(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
region_density_correlation(large_unit_cell, large_d_min, large_density_map, sites_cart, site_radii, work_scatterers)
remove_single_node_peaks(...)
remove_single_node_peaks( (double)map_data, (double)mask_data, (float)cutoff, (int)index_span) -> None :
 
    C++ signature :
        void remove_single_node_peaks(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,double,int)
reset(...)
reset( (double)data, (float)substitute_value, (float)less_than_threshold, (float)greater_than_threshold, (bool)use_and) -> None :
 
    C++ signature :
        void reset(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,double,double,bool)
rotate_translate_map(...)
rotate_translate_map( (unit_cell)unit_cell, (double)map_data, (object)rotation_matrix, (object)translation_vector, (object)start, (object)end) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > rotate_translate_map(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::mat3<double>,scitbx::vec3<double>,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
 
rotate_translate_map( (unit_cell)unit_cell, (double)map_data, (object)rotation_matrix, (object)translation_vector) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > rotate_translate_map(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::mat3<double>,scitbx::vec3<double>)
set_box(...)
set_box( (float)value, (double)map_data_to, (object)start, (object)end) -> None :
 
    C++ signature :
        void set_box(double,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
 
set_box( (double)map_data_from, (double)map_data_to, (object)start, (object)end) -> None :
 
    C++ signature :
        void set_box(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
set_box_copy(...)
set_box_copy( (float)value, (double)map_data_to, (object)start, (object)end) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > set_box_copy(double,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,scitbx::af::tiny<int, 3ul>)
set_if_less_than(...)
set_if_less_than( (float)arg1, (float)arg2, (float)arg3) -> None :
 
    C++ signature :
        void set_if_less_than(scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue},float,float)
 
set_if_less_than( (double)arg1, (float)arg2, (float)arg3) -> None :
 
    C++ signature :
        void set_if_less_than(scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue},double,double)
sharpen(...)
sharpen( (double)map_data, (int)index_span, (int)n_averages) -> None :
 
    C++ signature :
        void sharpen(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,int,int)
sphericity(...)
sphericity( (double)map_data, (unit_cell)unit_cell, (float)radius, (vec3_double)sites_frac) -> double :
 
    C++ signature :
        scitbx::af::shared<double> sphericity(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,cctbx::uctbx::unit_cell,double,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
sphericity_tensor(...)
sphericity_tensor( (double)map_data, (unit_cell)unit_cell, (float)radius, (object)site_frac) -> tuple :
 
    C++ signature :
        scitbx::sym_mat3<double> sphericity_tensor(scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,cctbx::uctbx::unit_cell,double,cctbx::fractional<double>)
standard_deviations_around_sites(...)
standard_deviations_around_sites( (unit_cell)unit_cell, (double)density_map, (vec3_double)sites_cart, (object)site_radii) -> double :
 
    C++ signature :
        scitbx::af::shared<double> standard_deviations_around_sites(cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>)
superpose_maps(...)
superpose_maps( (unit_cell)unit_cell_1, (unit_cell)unit_cell_2, (double)map_data_1, (object)n_real_2, (object)rotation_matrix, (object)translation_vector) -> double :
 
    C++ signature :
        scitbx::af::versa<double, scitbx::af::c_grid<3ul, unsigned long> > superpose_maps(cctbx::uctbx::unit_cell,cctbx::uctbx::unit_cell,scitbx::af::const_ref<double, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::tiny<int, 3ul>,scitbx::mat3<double>,scitbx::vec3<double>)
tricubic_interpolation(...)
tricubic_interpolation( (double)arg1, (object)arg2) -> float :
 
    C++ signature :
        double tricubic_interpolation(scitbx::af::const_ref<double, scitbx::af::c_grid_padded<3ul, unsigned long> >,scitbx::vec3<double>)
truncate(map_data, by_sigma_less_than, scale_by, set_value=0)
Trunate map inplace by standard deviation (sigma) while scale it with
specified scale, such as volume (scale_by=1/volume) or sigma
(scale_by=1/standard_deviation). Input map_data is expected to be unscaled (
right out of FT).
truncate_between_min_max(...)
truncate_between_min_max( (double)map_data, (float)min, (float)max) -> None :
 
    C++ signature :
        void truncate_between_min_max(scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >,double,double)
truncate_special(...)
truncate_special( (int)mask, (double)map_data) -> None :
 
    C++ signature :
        void truncate_special(scitbx::af::ref<int, scitbx::af::c_grid<3ul, unsigned long> >,scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >)
unpad_in_place(...)
unpad_in_place( (float)map) -> None :
 
    C++ signature :
        void unpad_in_place(scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue})
 
unpad_in_place( (double)map) -> None :
 
    C++ signature :
        void unpad_in_place(scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue})
value_at_closest_grid_point(map, x_frac)

 
Data
        debug_peak_cluster_analysis = ''
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
structure_factors = {'to_map': <class 'cctbx_maptbx_ext.structure_fa...s 'cctbx_maptbx_ext.structure_factors_from_map'>}
use_space_group_symmetry = <cctbx_sgtbx_ext.search_symmetry_flags object>