cctbx.crystal package

Module contents

class cctbx.crystal.calculate_angles(pair_asu_table, sites_frac, skip_j_seq_less_than_i_seq=True, covariance_matrix=None, cell_covariance_matrix=None, parameter_map=None, conformer_indices=None)

Bases: object

Methods

next()
next()
class cctbx.crystal.calculate_distances(pair_asu_table, sites_frac, skip_j_seq_less_than_i_seq=True, covariance_matrix=None, cell_covariance_matrix=None, parameter_map=None)

Bases: object

Methods

next()
next()
cctbx.crystal.cluster_erosion(sites_cart, box_size, fraction_to_be_retained)
cctbx.crystal.correct_special_position(crystal_symmetry, special_op, site_frac=None, site_cart=None, site_label=None, tolerance=1, error_message='Excessive special position correction:')
class cctbx.crystal.distance_based_clustering(special_position_settings, sites_cart, distance_cutoff, discard_special_positions=False)

Bases: cctbx.crystal._clustering_mix_in

Methods

sites_cart()
tidy_index_groups_in_place()
class cctbx.crystal.incremental_clustering(special_position_settings, sites_cart, distance_cutoffs, scores=None, discard_special_positions=False, discard_not_strictly_inside_asu=False, initial_required_cluster_size=0)

Bases: cctbx.crystal._clustering_mix_in

Methods

sites_cart()
tidy_index_groups_in_place()
cctbx.crystal.non_crystallographic_symmetry(sites_cart=None, sites_cart_min=None, sites_cart_max=None, buffer_layer=None, default_buffer_layer=0.5, min_unit_cell_length=0)
cctbx.crystal.select_crystal_symmetry(from_command_line=None, from_parameter_file=None, from_coordinate_files=[None], from_reflection_files=[None])

Select/construct a crystal symmetry from a list of various options

class cctbx.crystal.show_angles(pair_asu_table, site_labels=None, sites_frac=None, sites_cart=None, show_cartesian=False, keep_pair_asu_table=False, out=None)

Bases: object

class cctbx.crystal.show_distances(pair_asu_table, site_labels=None, sites_frac=None, sites_cart=None, show_cartesian=False, keep_pair_asu_table=False, skip_j_seq_less_than_i_seq=False, out=None)

Bases: libtbx.slots_getstate_setstate

distances_info
have_sym
pair_asu_table
class cctbx.crystal.special_position_settings(crystal_symmetry, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)

Bases: cctbx.crystal.symmetry

Methods

as_cif_block()
as_py_code([indent])
as_reference_setting()
assert_min_distance_sym_equiv()
asu_mappings(buffer_thickness[, sites_frac, ...])
average_b_cart(b_cart)
average_u_cart(u_cart)
best_cell([angular_tolerance])
build_miller_set(anomalous_flag, d_min[, d_max])
cell_equivalent_p1()
change_basis(cb_op)
change_of_basis_op_to_best_cell([...])
change_of_basis_op_to_inverse_hand()
change_of_basis_op_to_minimum_cell()
change_of_basis_op_to_niggli_cell([...])
change_of_basis_op_to_primitive_setting()
change_of_basis_op_to_reference_setting()
customized_copy([unit_cell, ...])
direct_space_asu()
gridding([d_min, resolution_factor, step, ...])
incremental_pairs(distance_cutoff[, ...])
inverse_hand()
is_compatible_unit_cell()
is_patterson_symmetry()
is_similar_symmetry(other[, ...])
join_symmetry(other_symmetry[, force, ...])
miller_set(indices, anomalous_flag)
min_distance_sym_equiv()
minimum_cell()
niggli_cell([relative_epsilon, iteration_limit])
pair_asu_table(distance_cutoff[, ...])
pair_generator(distance_cutoff[, ...])
patterson_symmetry()
primitive_setting()
reflection_intensity_symmetry(anomalous_flag)
show_summary([f, prefix])
site_cluster_analysis([min_distance, ...])
site_symmetry([site, site_cart])
site_symmetry_table([sites_frac, ...])
space_group()
space_group_info()
special_position_settings([...])
subtract_continuous_allowed_origin_shifts(...)
sym_equiv_sites(site)
u_star_tolerance()
unit_cell()
xray_structure([scatterers])
assert_min_distance_sym_equiv()
asu_mappings(buffer_thickness, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_is_inside_epsilon=None)
change_basis(cb_op)
incremental_pairs(distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
min_distance_sym_equiv()
pair_asu_table(distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, min_cubicle_edge=5, distance_cutoff_epsilon=None)
pair_generator(distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, minimal=False)
site_cluster_analysis(min_distance=None, min_cross_distance=None, min_self_distance=None, general_positions_only=False, estimated_reduction_factor=4, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, min_cubicle_edge=5, cubicle_epsilon=-1)
site_symmetry(site=None, site_cart=None)
site_symmetry_table(sites_frac=None, sites_cart=None, unconditional_general_position_flags=None)
sym_equiv_sites(site)
u_star_tolerance()
xray_structure(scatterers=None)
class cctbx.crystal.sym_pair(i_seq, j_seq, rt_mx_ji)

Bases: libtbx.slots_getstate_setstate

Methods

i_seqs()
i_seq
i_seqs()
j_seq
rt_mx_ji
class cctbx.crystal.symmetry(unit_cell=None, space_group_symbol=None, space_group_info=None, space_group=None, correct_rhombohedral_setting_if_necessary=False, assert_is_compatible_unit_cell=True, raise_sorry_if_incompatible_unit_cell=False, force_compatible_unit_cell=True)

Bases: object

This class represents the symmetry of a crystal and bundles information on its unit cell and space group.

Methods

as_cif_block()
as_py_code([indent])
as_reference_setting()
asu_mappings(buffer_thickness[, ...])
average_b_cart(b_cart)
average_u_cart(u_cart)
best_cell([angular_tolerance])
build_miller_set(anomalous_flag, d_min[, d_max])
cell_equivalent_p1()
change_basis(cb_op)
change_of_basis_op_to_best_cell([...])
change_of_basis_op_to_inverse_hand()
change_of_basis_op_to_minimum_cell()
change_of_basis_op_to_niggli_cell([...])
change_of_basis_op_to_primitive_setting()
change_of_basis_op_to_reference_setting()
customized_copy([unit_cell, ...])
direct_space_asu()
gridding([d_min, resolution_factor, step, ...])
inverse_hand()
is_compatible_unit_cell()
is_patterson_symmetry()
is_similar_symmetry(other[, ...])
join_symmetry(other_symmetry[, force, ...])
miller_set(indices, anomalous_flag)
minimum_cell()
niggli_cell([relative_epsilon, iteration_limit])
patterson_symmetry()
primitive_setting()
reflection_intensity_symmetry(anomalous_flag)
show_summary([f, prefix])
space_group()
space_group_info()
special_position_settings([...])
subtract_continuous_allowed_origin_shifts(...)
unit_cell()
as_cif_block()
as_py_code(indent='')
as_reference_setting()
asu_mappings(buffer_thickness, asu_is_inside_epsilon=None)
average_b_cart(b_cart)
average_u_cart(u_cart)
best_cell(angular_tolerance=None)
build_miller_set(anomalous_flag, d_min, d_max=None)
cell_equivalent_p1()
change_basis(cb_op)
change_of_basis_op_to_best_cell(angular_tolerance=None, best_monoclinic_beta=True)
change_of_basis_op_to_inverse_hand()
change_of_basis_op_to_minimum_cell()
change_of_basis_op_to_niggli_cell(relative_epsilon=None, iteration_limit=None)
change_of_basis_op_to_primitive_setting()
change_of_basis_op_to_reference_setting()
customized_copy(unit_cell=Keep, space_group_info=Keep, raise_sorry_if_incompatible_unit_cell=False)
direct_space_asu()
gridding(d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
inverse_hand()
is_compatible_unit_cell()
is_patterson_symmetry()
is_similar_symmetry(other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0)
join_symmetry(other_symmetry, force=False, raise_sorry_if_incompatible_unit_cell=False)
miller_set(indices, anomalous_flag)
minimum_cell()
niggli_cell(relative_epsilon=None, iteration_limit=None)
patterson_symmetry()
primitive_setting()
reflection_intensity_symmetry(anomalous_flag)
show_summary(f=None, prefix='')
space_group()
space_group_info()
special_position_settings(min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
subtract_continuous_allowed_origin_shifts(translation_cart)
unit_cell()

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