from __future__ import absolute_import, division, print_function
from six.moves import zip
def examples():
  # Generate space groups (in matrix/vector form) based on spacegroup number
  # (names are *not* a pain)
  # See also: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1sgtbx_1_1space__group__symbols.html#_details
  from cctbx import sgtbx
  for s in sgtbx.space_group_info(symbol="I41/amd").group():
    print(s) # in "xyz" notation
    print(s.r().as_rational().mathematica_form(), \
          s.t().as_rational().transpose().mathematica_form())
  print()

  # now with a space group number
  space_group_info = sgtbx.space_group_info(number=123)
  space_group_info.show_summary()
  print()

  # Generate conditions for allowed reflections etc
  from cctbx import crystal
  from cctbx import miller
  crystal_symmetry = crystal.symmetry(
    unit_cell=(10,10,13,90,90,90),
    space_group_info=space_group_info)
  miller_set = miller.build_set(
    crystal_symmetry=crystal_symmetry,
    anomalous_flag=False,
    d_min=4)
  # change the space group in order to get a few systematic absences
  miller_set = miller_set.customized_copy(
    space_group_info=sgtbx.space_group_info(symbol="I41/amd"))
  sys_absent_flags = miller_set.sys_absent_flags()
  for h,f in zip(sys_absent_flags.indices(), sys_absent_flags.data()):
    print(h, f)
  print()
  # try also (from the command line): libtbx.help cctbx.miller

  # Generate point group of space group in matrix form
  point_group = miller_set.space_group().build_derived_point_group()
  point_group_info = sgtbx.space_group_info(group=point_group)
  point_group_info.show_summary()
  for s in point_group:
    print(s)
  print()

  # Generate point-group matrices for given coordinate
  # first we have to define what we consider as special position
  special_position_settings = crystal.special_position_settings(
    crystal_symmetry=miller_set,
    min_distance_sym_equiv=0.5) # <<<<< here
  site_symmetry = special_position_settings.site_symmetry(
    site=(0,0.48,0))
  print("special position operator:", site_symmetry.special_op_simplified())
  print("distance to original site:", site_symmetry.distance_moved())
  print("point group of the special position:")
  for s in site_symmetry.matrices():
    print(s)
  print()
  # See also: http://cci.lbl.gov/~rwgk/my_papers/iucr/au0265_reprint.pdf

  # Access database for form factors
  from cctbx.eltbx import xray_scattering
  si_form_factor = xray_scattering.it1992("Si")
  gaussians = si_form_factor.fetch()
  for stol in [0, 0.01, 0.02, 0.5]:
    print(stol, gaussians.at_stol(stol))
  print()

  # anomalous scattering factors: Sasaki tables
  from cctbx.eltbx import sasaki
  si_table = sasaki.table("Si")
  for wavelength in [0.5, 0.8, 0.9]:
    data = si_table.at_angstrom(wavelength)
    print(wavelength, data.fp(), data.fdp())
  print()

  # anomalous scattering factors: Henke tables
  from cctbx.eltbx import henke
  si_table = henke.table("Si")
  for wavelength in [0.5, 0.8, 0.9]:
    data = si_table.at_angstrom(wavelength)
    print(wavelength, data.fp(), data.fdp())
  print()
  print("OK")

if (__name__ == "__main__"):
  examples()