Python get_standard_label Examples

Example #1

def exercise_basic():
    std_labels = xray_scattering.standard_labels_list()
    assert len(std_labels) == 217
    assert std_labels[:5] == ["H", "D", "T", "Hiso", "He"]
    assert std_labels[-1] == "Pu6+"
    for l in std_labels:
        assert xray_scattering.get_standard_label(label=l,
                                                  exact=True,
                                                  optional=False) == l
    assert xray_scattering.get_standard_label(label="na+") == "Na1+"
    assert xray_scattering.get_standard_label(label="na+") == "Na1+"
    assert xray_scattering.get_standard_label(label="o-") == "O1-"
    assert xray_scattering.get_standard_label(label="SI4+A") == "Si4+"
    assert xray_scattering.get_standard_label(label="SI1+") == "Si"
    assert xray_scattering.get_standard_label(
        label="SI1+", exact=True, optional=True) is None
    try:
        xray_scattering.get_standard_label(label="SI1+",
                                           exact=True,
                                           optional=False)
    except ValueError as e:
        assert str(e) == 'Unknown scattering type label: "SI1+"'
    else:
        raise Exception_expected
    #
    from cctbx.eltbx import tiny_pse
    for sl in std_labels:
        e, c = xray_scattering.get_element_and_charge_symbols(
            scattering_type=sl)
        assert e == "T" or tiny_pse.table(e, True).symbol() == e
        if (c != ""):
            assert len(c) == 2
            assert "123456789".find(c[0]) >= 0
            assert c[1] in ["+", "-"]

Example #2

File: tst_xray_scattering.py Project: cctbx/cctbx-playground

def exercise_basic():
  std_labels = xray_scattering.standard_labels_list()
  assert len(std_labels) == 217
  assert std_labels[:5] == ["H", "D", "T", "Hiso", "He"]
  assert std_labels[-1] == "Pu6+"
  for l in std_labels:
    assert xray_scattering.get_standard_label(
      label=l, exact=True, optional=False) == l
  assert xray_scattering.get_standard_label(label="na+") == "Na1+"
  assert xray_scattering.get_standard_label(label="na+") == "Na1+"
  assert xray_scattering.get_standard_label(label="o-") == "O1-"
  assert xray_scattering.get_standard_label(label="SI4+A") == "Si4+"
  assert xray_scattering.get_standard_label(label="SI1+") == "Si"
  assert xray_scattering.get_standard_label(label="SI1+",
    exact=True, optional=True) is None
  try:
    xray_scattering.get_standard_label(label="SI1+",
      exact=True, optional=False)
  except ValueError, e:
    assert str(e) == 'Unknown scattering type label: "SI1+"'

Example #3

File: tst_xray_scattering.py Project: zhuligs/cctbx_project

def exercise_basic():
    std_labels = xray_scattering.standard_labels_list()
    assert len(std_labels) == 217
    assert std_labels[:5] == ["H", "D", "T", "Hiso", "He"]
    assert std_labels[-1] == "Pu6+"
    for l in std_labels:
        assert xray_scattering.get_standard_label(label=l,
                                                  exact=True,
                                                  optional=False) == l
    assert xray_scattering.get_standard_label(label="na+") == "Na1+"
    assert xray_scattering.get_standard_label(label="na+") == "Na1+"
    assert xray_scattering.get_standard_label(label="o-") == "O1-"
    assert xray_scattering.get_standard_label(label="SI4+A") == "Si4+"
    assert xray_scattering.get_standard_label(label="SI1+") == "Si"
    assert xray_scattering.get_standard_label(
        label="SI1+", exact=True, optional=True) is None
    try:
        xray_scattering.get_standard_label(label="SI1+",
                                           exact=True,
                                           optional=False)
    except ValueError, e:
        assert str(e) == 'Unknown scattering type label: "SI1+"'

Example #4

File: e_scattering.py Project: cctbx/cctbx-playground

def __get_cache():
  global __cache
  if (__cache is None):
    from cctbx.eltbx.xray_scattering import get_standard_label
    from libtbx.containers import OrderedDict
    __cache = OrderedDict()
    assert len(ito_vol_c_2011_table_4_3_2_2) == 98
    for line in ito_vol_c_2011_table_4_3_2_2:
      flds = line.split()
      assert len(flds) == 12
      std_lbl = get_standard_label(flds[0], exact=True)
      assert flds[0] == std_lbl
      assert std_lbl not in __cache
      assert flds[1] == str(len(__cache)+1)
      def vals(i,j): return [float(s) for s in flds[i:j]]
      array_of_a = vals(2,7)
      array_of_b = vals(7,12)
      __cache[std_lbl] = gaussian(array_of_a, array_of_b)
  return __cache

Example #5

def __get_cache():
  global __cache
  if (__cache is None):
    from cctbx.eltbx.xray_scattering import get_standard_label
    from libtbx.containers import OrderedDict
    __cache = OrderedDict()
    assert len(ito_vol_c_2011_table_4_3_2_2) == 98
    for line in ito_vol_c_2011_table_4_3_2_2:
      flds = line.split()
      assert len(flds) == 12
      std_lbl = get_standard_label(flds[0], exact=True)
      assert flds[0] == std_lbl
      assert std_lbl not in __cache
      assert flds[1] == str(len(__cache)+1)
      def vals(i,j): return [float(s) for s in flds[i:j]]
      array_of_a = vals(2,7)
      array_of_b = vals(7,12)
      __cache[std_lbl] = gaussian(array_of_a, array_of_b)
  return __cache

Example #6

def ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian(label, exact=False):
    from cctbx.eltbx import xray_scattering
    std_lbl = xray_scattering.get_standard_label(label=label, exact=exact)
    return __get_cache().get(std_lbl)

Example #7

File: e_scattering.py Project: cctbx/cctbx-playground

def ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian(label, exact=False):
  from cctbx.eltbx import xray_scattering
  std_lbl = xray_scattering.get_standard_label(label=label, exact=exact)
  return __get_cache().get(std_lbl)