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

class cctbx.sgtbx.direct_space_asu.direct_space_asu(hall_symbol, cuts=[])

Bases: object

add_buffer(unit_cell, thickness=None, relative_thickness=None)

add_plane(normal_direction, point=None)

add_planes(normal_directions, point=None, both_directions=False)

box_max(shape_vertices=None)

box_min(shape_vertices=None)

change_basis(cb_op)

define_metric(unit_cell)

extract_all_cuts()

in_which_cuts(point)

is_inside(point, shape_only=False)

Check if a given point in direct space is inside the asymmetric unit. The coordinates of the point are expected to be factional coordinates. To use cartesian coordinates you can use something like: asu.is_inside(unit_cell.fractionalize(site_cart)).

Parameters:

shape_only (boolean) – If set to ‘True’ ??? #XXX what exactly is this option for?

Returns:

True if point is inside the asymmetric unit

Return type:

boolean

shape_only()

shape_vertices()

show_comprehensive_summary(f=None)

show_summary(f=None)