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)