cctbx.sgtbx package

Subpackages

• cctbx.sgtbx.direct_space_asu package
  • Subpackages
    • cctbx.sgtbx.direct_space_asu.proto package
      • Submodules
        • cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module
          • base_symbol_cpp()
          • make_md5()
          • out_cpp()
          • run()
          • show_cpp()
      • Module contents
        • asu_show_()
  • Submodules
    • cctbx.sgtbx.direct_space_asu.check_redundancies module
      • analyze_redundancies()
      • check_asu()
      • check_compatibility_with_sampling_grid()
      • check_multiplicities()
      • color_server
        • color_server.next()
      • colored_grid_point
      • compare_redundancies()
      • grid_asu()
      • iround()
      • recolor_grid_points()
      • rt_mx_analysis()
      • rt_plus_unit_shifts()
      • rt_times_grid_point()
      • sample_asu()
      • slice()
      • sort_redundancies()
      • str_ev()
      • test_all()
      • u_index_as_r_index()
    • cctbx.sgtbx.direct_space_asu.cut_plane module
      • cut
        • cut.as_float_cut_plane()
        • cut.as_xyz()
        • cut.base_symbol()
        • cut.c
        • cut.change_basis()
        • cut.cut_expr
        • cut.evaluate()
        • cut.extract_all_cuts()
        • cut.get_point_in_plane()
        • cut.has_cuts()
        • cut.inclusive
        • cut.is_inside()
        • cut.lcm_of_denominators()
        • cut.n
        • cut.one()
        • cut.strip()
      • cut_expr_ops
      • cut_expression
        • cut_expression.as_xyz()
        • cut_expression.change_basis()
        • cut_expression.extract_all_cuts()
        • cut_expression.is_inside()
        • cut_expression.lhs
        • cut_expression.op
        • cut_expression.rhs
    • cctbx.sgtbx.direct_space_asu.facet_analysis module
      • all_cut_points()
      • asu_polygons()
      • collect_cuts()
      • consolidated_edges_with_cut_points
        • consolidated_edges_with_cut_points.add()
        • consolidated_edges_with_cut_points.asu
        • consolidated_edges_with_cut_points.get_all_segments()
        • consolidated_edges_with_cut_points.get_segments()
        • consolidated_edges_with_cut_points.list
        • consolidated_edges_with_cut_points.verify_edge_segments()
      • depth1_cuts()
      • edge_position()
      • edge_segment
        • edge_segment.edge_inclusive_flag
        • edge_segment.vertex
        • edge_segment.vertex_inclusive_flag
      • edge_with_cut_points
        • edge_with_cut_points.all_points()
        • edge_with_cut_points.cut_point_positions()
        • edge_with_cut_points.cut_points
        • edge_with_cut_points.end_points
        • edge_with_cut_points.join_edge()
        • edge_with_cut_points.join_point()
        • edge_with_cut_points.show_points()
        • edge_with_cut_points.sort_cut_points()
        • edge_with_cut_points.sorted_cut_points()
      • eliminate_outside_vertices()
      • extract_polygon_vertices()
      • face_polygons()
      • face_vertices()
      • get_all_edge_segments()
      • get_all_vertices()
      • get_edge_vertices()
      • intersection()
      • is_one_of()
      • line_sample_point()
      • polygon_vertices()
      • sense_of_polygon()
      • shape_vertices()
      • trace_polygon()
      • verify_asu_polygons()
    • cctbx.sgtbx.direct_space_asu.plane_group_reference_table module
      • asu_01()
      • asu_02()
      • asu_03()
      • asu_04()
      • asu_05()
      • asu_06()
      • asu_07()
      • asu_08()
      • asu_09()
      • asu_10()
      • asu_11()
      • asu_12()
      • asu_13()
      • asu_14()
      • asu_15()
      • asu_16()
      • asu_17()
      • get_asu()
    • cctbx.sgtbx.direct_space_asu.reference_table module
      • apply_change_of_basis()
      • asu_001()
      • asu_002()
      • asu_003()
      • asu_004()
      • asu_005()
      • asu_006()
      • asu_007()
      • asu_008()
      • asu_009()
      • asu_010()
      • asu_011()
      • asu_012()
      • asu_013()
      • asu_014()
      • asu_015()
      • asu_016()
      • asu_017()
      • asu_018()
      • asu_019()
      • asu_020()
      • asu_021()
      • asu_022()
      • asu_023()
      • asu_024()
      • asu_025()
      • asu_026()
      • asu_027()
      • asu_028()
      • asu_029()
      • asu_030()
      • asu_031()
      • asu_032()
      • asu_033()
      • asu_034()
      • asu_035()
      • asu_036()
      • asu_037()
      • asu_038()
      • asu_039()
      • asu_040()
      • asu_041()
      • asu_042()
      • asu_043()
      • asu_044()
      • asu_045()
      • asu_046()
      • asu_047()
      • asu_048()
      • asu_049()
      • asu_050()
      • asu_051()
      • asu_052()
      • asu_053()
      • asu_054()
      • asu_055()
      • asu_056()
      • asu_057()
      • asu_058()
      • asu_059()
      • asu_060()
      • asu_061()
      • asu_062()
      • asu_063()
      • asu_064()
      • asu_065()
      • asu_066()
      • asu_067()
      • asu_068()
      • asu_069()
      • asu_070()
      • asu_071()
      • asu_072()
      • asu_073()
      • asu_074()
      • asu_075()
      • asu_076()
      • asu_077()
      • asu_078()
      • asu_079()
      • asu_080()
      • asu_081()
      • asu_082()
      • asu_083()
      • asu_084()
      • asu_085()
      • asu_086()
      • asu_087()
      • asu_088()
      • asu_089()
      • asu_090()
      • asu_091()
      • asu_092()
      • asu_093()
      • asu_094()
      • asu_095()
      • asu_096()
      • asu_097()
      • asu_098()
      • asu_099()
      • asu_100()
      • asu_101()
      • asu_102()
      • asu_103()
      • asu_104()
      • asu_105()
      • asu_106()
      • asu_107()
      • asu_108()
      • asu_109()
      • asu_110()
      • asu_111()
      • asu_112()
      • asu_113()
      • asu_114()
      • asu_115()
      • asu_116()
      • asu_117()
      • asu_118()
      • asu_119()
      • asu_120()
      • asu_121()
      • asu_122()
      • asu_123()
      • asu_124()
      • asu_125()
      • asu_126()
      • asu_127()
      • asu_128()
      • asu_129()
      • asu_130()
      • asu_131()
      • asu_132()
      • asu_133()
      • asu_134()
      • asu_135()
      • asu_136()
      • asu_137()
      • asu_138()
      • asu_139()
      • asu_140()
      • asu_141()
      • asu_142()
      • asu_143()
      • asu_144()
      • asu_145()
      • asu_146()
      • asu_147()
      • asu_148()
      • asu_149()
      • asu_150()
      • asu_151()
      • asu_152()
      • asu_153()
      • asu_154()
      • asu_155()
      • asu_156()
      • asu_157()
      • asu_158()
      • asu_159()
      • asu_160()
      • asu_161()
      • asu_162()
      • asu_163()
      • asu_164()
      • asu_165()
      • asu_166()
      • asu_167()
      • asu_168()
      • asu_169()
      • asu_170()
      • asu_171()
      • asu_172()
      • asu_173()
      • asu_174()
      • asu_175()
      • asu_176()
      • asu_177()
      • asu_178()
      • asu_179()
      • asu_180()
      • asu_181()
      • asu_182()
      • asu_183()
      • asu_184()
      • asu_185()
      • asu_186()
      • asu_187()
      • asu_188()
      • asu_189()
      • asu_190()
      • asu_191()
      • asu_192()
      • asu_193()
      • asu_194()
      • asu_195()
      • asu_196()
      • asu_197()
      • asu_198()
      • asu_199()
      • asu_200()
      • asu_201()
      • asu_202()
      • asu_203()
      • asu_204()
      • asu_205()
      • asu_206()
      • asu_207()
      • asu_208()
      • asu_209()
      • asu_210()
      • asu_211()
      • asu_212()
      • asu_213()
      • asu_214()
      • asu_215()
      • asu_216()
      • asu_217()
      • asu_218()
      • asu_219()
      • asu_220()
      • asu_221()
      • asu_222()
      • asu_223()
      • asu_224()
      • asu_225()
      • asu_226()
      • asu_227()
      • asu_228()
      • asu_229()
      • asu_230()
      • get_asu()
    • cctbx.sgtbx.direct_space_asu.short_cuts module
  • Module contents
    • direct_space_asu
      • direct_space_asu.add_buffer()
      • direct_space_asu.add_plane()
      • direct_space_asu.add_planes()
      • direct_space_asu.box_max()
      • direct_space_asu.box_min()
      • direct_space_asu.change_basis()
      • direct_space_asu.define_metric()
      • direct_space_asu.extract_all_cuts()
      • direct_space_asu.in_which_cuts()
      • direct_space_asu.is_inside()
      • direct_space_asu.shape_only()
      • direct_space_asu.shape_vertices()
      • direct_space_asu.show_comprehensive_summary()
      • direct_space_asu.show_summary()

Submodules

• cctbx.sgtbx.bravais_types module
  • bravais_lattice
    • bravais_lattice.crystal_family_symbols
  • exercise()
  • tst_bravais_types()
• cctbx.sgtbx.cosets module
  • construct_nice_cb_op()
  • double_cosets
    • double_cosets.clear_up_cosets()
    • double_cosets.have_duplicates()
    • double_cosets.is_in_coset()
    • double_cosets.is_in_list_of_cosets()
    • double_cosets.show()
  • double_unique()
  • left_decomposition
    • left_decomposition.is_subgroup()
    • left_decomposition.show()
    • left_decomposition.sort_cosets()
  • left_decomposition_point_groups_only
    • left_decomposition_point_groups_only.best_partition_representatives()
  • partition_t
  • run()
  • test_double_coset_decomposition()
  • test_lattice_translation_aware_left_decomposition()
• cctbx.sgtbx.harker module
  • dot3()
  • mod_positive3()
  • plane_cartesian
    • plane_cartesian.distance()
  • plane_fractional
    • plane_fractional.algebraic()
    • plane_fractional.operation()
  • planes_cartesian
    • planes_cartesian.count()
    • planes_cartesian.min_distance()
  • planes_fractional
  • test()
  • test_call_back()
• cctbx.sgtbx.lattice_symmetry module
  • metric_subgroups
    • metric_subgroups.change_input_to_minimum_cell()
    • metric_subgroups.change_of_basis_op_to_best_cell()
    • metric_subgroups.derive_result_group_list()
    • metric_subgroups.lattice_group_info()
    • metric_subgroups.show()
    • metric_subgroups.show_groups()
    • metric_subgroups.show_input()
  • metric_supergroup()
• cctbx.sgtbx.literal_description module
  • literal_description
    • literal_description.cosets_form()
    • literal_description.labelit_check_pdb_symmetry_form()
    • literal_description.labelit_check_pdb_symmetry_short()
    • literal_description.long_form()
    • literal_description.select()
  • str_ev()
• cctbx.sgtbx.plane_groups module
• cctbx.sgtbx.pointgroup_tools module
  • compatible_symmetries()
  • coset_lookup()
  • edge_object
    • edge_object.return_unused()
    • edge_object.return_used()
  • find_compatible_space_groups
    • find_compatible_space_groups.compare_abs_lists()
    • find_compatible_space_groups.find_absent_indices()
    • find_compatible_space_groups.full_sys_abs_mask()
    • find_compatible_space_groups.get_space_groups_compatible_with_likely_point_group()
    • find_compatible_space_groups.make_sys_abs_list()
    • find_compatible_space_groups.show()
  • node_object
  • point_group_graph
    • point_group_graph.build_it()
    • point_group_graph.get_maximal_subgroup()
    • point_group_graph.make_and_place_nodes_and_connections()
    • point_group_graph.remove_point_group_and_its_super_groups_from_graph()
    • point_group_graph.reverse_dict()
  • reference_setting_choices()
  • space_group_graph_from_cell_and_sg
    • space_group_graph_from_cell_and_sg.graphviz_pg_graph()
    • space_group_graph_from_cell_and_sg.return_likely_sg_and_cell()
    • space_group_graph_from_cell_and_sg.show()
  • sub_super_point_group_relations
    • sub_super_point_group_relations.assemble_symops()
    • sub_super_point_group_relations.find_left_over_symops()
    • sub_super_point_group_relations.get_symops_from_supergroup_that_are_not_in_subgroup()
    • sub_super_point_group_relations.return_next_index()
    • sub_super_point_group_relations.return_next_left_over_set()
    • sub_super_point_group_relations.return_next_set()
    • sub_super_point_group_relations.return_next_sg()
    • sub_super_point_group_relations.show()
• cctbx.sgtbx.rational_matrices_point_groups module
  • as_hkl()
  • cb_op_as_rational()
  • compare_groups()
  • construct_rational_point_group()
  • rat_rot_group
    • rat_rot_group.change_basis()
    • rat_rot_group.expand()
    • rat_rot_group.is_in_group()
    • rat_rot_group.show()
  • rt_mx_as_rational()
  • run()
  • tst_compare()
  • tst_groups()
• cctbx.sgtbx.reticular_pg_tools module
  • as_hkl()
  • build_reticular_twin_laws()
  • cb_op_as_rational()
  • compare_groups()
  • construct_rational_point_group()
  • cosets()
  • extra_operators()
  • is_reticular_polyholohedral()
  • is_subgroup()
  • rat_rot_group
    • rat_rot_group.change_basis()
    • rat_rot_group.expand()
    • rat_rot_group.is_in_group()
    • rat_rot_group.show()
  • recurring_operators()
  • rt_mx_as_rational()
  • run()
  • tst_build_reticular_twin_laws()
  • tst_compare()
  • tst_groups()
• cctbx.sgtbx.reticular_twin_laws module
  • exercise()
  • ret_twin_law_info
    • ret_twin_law_info.show()
  • reticular_twin_laws
    • reticular_twin_laws.construct_twin_laws()
    • reticular_twin_laws.show()
  • symmetry_safe_sublattice_xs
    • symmetry_safe_sublattice_xs.make_new_xs()
    • symmetry_safe_sublattice_xs.metric_r()
• cctbx.sgtbx.show_cosets module
  • run()
• cctbx.sgtbx.sub_lattice_tools module
  • compare_lattice
    • compare_lattice.make_new_cell_and_symmetry()
    • compare_lattice.show_basic_info()
    • compare_lattice.show_solution()
  • divisor()
  • exercise()
  • find_triples()
  • find_triples_slowly()
  • generate_cb_op_up_to_order()
  • generate_inverse_matrix_up_to_order()
  • generate_matrix()
  • generate_matrix_up_to_order()
  • make_list_of_target_xs_up_to_order
    • make_list_of_target_xs_up_to_order.make_new_xs()
  • make_permutations()
  • make_triples()
  • rt_mx_as_rational()
  • sort_triple()
  • tst_centered_cells()
  • tst_compare()
  • tst_make_bigger_cell()
  • tst_sublattice()
• cctbx.sgtbx.subgroups module
  • anomalous_reflection_intensity_primitive_cell()
  • show()
  • subgroups
    • subgroups.groups_parent_setting()
    • subgroups.groups_primitive_setting()
• cctbx.sgtbx.symbol_confidence module
  • level()
• cctbx.sgtbx.sys_abs_equiv module

Module contents

class cctbx.sgtbx.any_generator_set(space_group, z2c_r_den=12, z2c_t_den=144)

Bases: object

cctbx.sgtbx.compare_cb_op_as_hkl(a, b)

class cctbx.sgtbx.empty

Bases: object

class cctbx.sgtbx.le_page_1982_delta_details(reduced_cell, rot_mx, deg=False)

Bases: object

cctbx.sgtbx.reference_space_group_infos()

class cctbx.sgtbx.space_group_info(symbol=None, table_id=None, group=None, number=None, space_group_t_den=None)

Bases: object

any_compatible_crystal_symmetry(volume=None, asu_volume=None)

any_compatible_unit_cell(volume=None, asu_volume=None)

Generate a unit cell of arbitrary dimensions (optionally filling the desired volume) with parameters compatible with the specified space group.

Parameters:

• volume – desired unit cell volume

• asu_volume – desired volume of the asymmetric unit

Returns:

uctbx.unit_cell object

any_generator_set()

as_reference_setting()

brick()

change_basis(cb_op)

change_hand()

change_of_basis_op_to(other)

The change of basis from self to other. This method strives to return a mere origin shift.

change_of_basis_op_to_other_hand()

change_of_basis_op_to_primitive_setting()

change_of_basis_op_to_reference_setting()

cif_symmetry_code(rt_mx, full_code=False, sep='_')

The symmetry code for the given rt_mx in the given space group as required by the CIF:

http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html

With the default full_code=False, if the translation term is zero, just the index of the symmetry operation is returned.

direct_space_asu()

group()

is_allowed_origin_shift(shift, tolerance)

Determine whether the specified fractional coordinate shift is allowed under the space group rules.

Parameters:

• shift – tuple specifying fractional coordinate shift

• tolerance – tolerance for coordinate shifts outside the allowed range

Returns:

Python boolean

is_reference_setting()

number_of_continuous_allowed_origin_shifts()

primitive_setting()

reciprocal_space_asu()

reference_setting()

reflection_intensity_equivalent_groups(anomalous_flag=True)

show_summary(f=None, prefix='Space group: ')

structure_seminvariants()

subtract_continuous_allowed_origin_shifts(translation_frac)

symbol_and_number()

type(tidy_cb_op=True, r_den=None, t_den=None)

wyckoff_table()

class cctbx.sgtbx.special_op_simplified(terms)

Bases: slots_getstate_setstate

shelx_fvar_encoding(fvars, site, p_tolerance=1e-05)

terms

class cctbx.sgtbx.special_op_simplified_term(i_vars, multipliers, constant)

Bases: slots_getstate_setstate

constant

i_vars

is_identity()

multipliers

cctbx.sgtbx.special_op_simplifier(special_op)

class cctbx.sgtbx.symmetry_equivalent_pair_interactions(site_symmetry_ops_i, site_symmetry_ops_j, i_seq_eq_j_seq, rt_mx_ji)

Bases: slots_getstate_setstate

get()

is_equivalent(rt_mx_ji)

registry

site_symmetry_ops_j

cctbx.sgtbx.vec3_rat_from_str(s)