def peak_cluster_reduction(crystal_symmetry, peak_list,
min_peak_distance, max_reduced_peaks):
special_position_settings = crystal.special_position_settings(
crystal_symmetry=crystal_symmetry,
min_distance_sym_equiv=min_peak_distance)
peaks = []
for i,site in enumerate(peak_list.sites()):
peaks.append(dicts.easy(
site=special_position_settings.site_symmetry(site).exact_site(),
height=peak_list.heights()[i]))
reduced_peaks = []
for peak in peaks:
site_symmetry = special_position_settings.site_symmetry(peak.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
keep = True
for reduced_peak in reduced_peaks:
dist = sgtbx.min_sym_equiv_distance_info(
equiv_sites, reduced_peak.site).dist()
if (dist < min_peak_distance):
keep = False
break
if (keep == True):
reduced_peaks.append(peak)
if (len(reduced_peaks) == max_reduced_peaks): break
return reduced_peaks
def match_refine_times():
return dicts.easy(exclude_pairs=0,
add_pairs=0,
eliminate_weak_pairs=0,
refine_adjusted_shift=0)
max_peaks=0,
peak_cutoff=None,
interpolate=True):
if (peak_cutoff is None):
ext.peak_list.__init__(self, data, tags, peak_search_level,
max_peaks, interpolate)
else:
ext.peak_list.__init__(self, data, tags, peak_search_level,
peak_cutoff, max_peaks, interpolate)
def as_CObjectZYX(map_unit_cell, first, last, apply_sigma_scaling=True):
return ext.as_CObjectZYX(map_unit_cell, first, last, apply_sigma_scaling)
structure_factors = dicts.easy(to_map=structure_factors_to_map,
from_map=structure_factors_from_map)
class crystal_gridding(object):
def __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):
if (pre_determined_n_real is None):
peak_search_level=1,
max_peaks=0,
peak_cutoff=None,
interpolate=True):
if (peak_cutoff is None):
ext.peak_list.__init__(self,
data, tags, peak_search_level, max_peaks, interpolate)
else:
ext.peak_list.__init__(self,
data, tags, peak_search_level, peak_cutoff, max_peaks, interpolate)
def as_CObjectZYX(map_unit_cell, first, last, apply_sigma_scaling=True):
return ext.as_CObjectZYX(map_unit_cell, first, last, apply_sigma_scaling)
structure_factors = dicts.easy(
to_map=structure_factors_to_map,
from_map=structure_factors_from_map)
class crystal_gridding(object):
def __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):
if (pre_determined_n_real is None):
def match_refine_times():
return dicts.easy(
exclude_pairs=0,
add_pairs=0,
eliminate_weak_pairs=0,
refine_adjusted_shift=0)
