def create_crystal_symmetry(sg, cell):
space_group = None if sg is None else sgtbx.space_group_info(sg).group()
unit_cell = uctbx.infer_unit_cell_from_symmetry(cell, space_group)
xs = crystal.symmetry(unit_cell, space_group=space_group)
return xs
"Unit cell parameters not found in the cif file")
unit_cell = None
elif (ic == 0):
try:
vals = [float_from_string(s) for s in items]
except ValueError:
raise CifBuilderError("Invalid unit cell parameters are given")
try:
unit_cell = uctbx.unit_cell(vals)
except RuntimeError, e:
if "cctbx Error: Unit cell" in str(e):
raise CifBuilderError(e)
else:
raise
elif (space_group is not None):
unit_cell = uctbx.infer_unit_cell_from_symmetry(
[float_from_string(s) for s in items if s is not None], space_group)
else:
raise CifBuilderError(
"Not all unit cell parameters are given in the cif file")
if unit_cell is not None and space_group is not None:
if not space_group.is_compatible_unit_cell(unit_cell):
# try primitive setting
space_group_input = space_group
space_group = space_group.info().primitive_setting().group()
if not space_group.is_compatible_unit_cell(unit_cell):
raise CifBuilderError(
"Space group is incompatible with unit cell parameters:\n" + \
" Space group: %s\n" %space_group_input.info() + \
" Unit cell: %s" %unit_cell)
self.crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group=space_group)
unit_cell = None
elif (ic == 0):
try:
vals = [float_from_string(s) for s in items]
except ValueError:
raise CifBuilderError("Invalid unit cell parameters are given")
try:
unit_cell = uctbx.unit_cell(vals)
except RuntimeError, e:
if "cctbx Error: Unit cell" in str(e):
raise CifBuilderError(e)
else:
raise
elif (space_group is not None):
unit_cell = uctbx.infer_unit_cell_from_symmetry(
[float_from_string(s) for s in items if s is not None],
space_group)
else:
raise CifBuilderError(
"Not all unit cell parameters are given in the cif file")
if (unit_cell is not None and space_group is not None
and not space_group.is_compatible_unit_cell(unit_cell)):
raise CifBuilderError(
"Space group is incompatible with unit cell parameters")
self.crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group=space_group)
class crystal_structure_builder(crystal_symmetry_builder):
def __init__(self, cif_block):
# XXX To do: interpret _atom_site_refinement_flags
def create_crystal_symmetry(sg, cell):
space_group = None if sg is None else sgtbx.space_group_info(sg).group()
unit_cell = uctbx.infer_unit_cell_from_symmetry(cell, space_group)
xs = crystal.symmetry(unit_cell, space_group=space_group)
return xs
def __init__(self, cif_block, strict=False):
# The order of priority for determining space group is:
# sym_ops, hall symbol, H-M symbol, space group number
self.cif_block = cif_block
sym_ops = self.get_cif_item('_space_group_symop_operation_xyz')
sym_op_ids = self.get_cif_item('_space_group_symop_id')
space_group = None
if sym_ops is not None:
if isinstance(sym_ops, string_types):
sym_ops = flex.std_string([sym_ops])
if sym_op_ids is not None:
if isinstance(sym_op_ids, string_types):
sym_op_ids = flex.std_string([sym_op_ids])
assert len(sym_op_ids) == len(sym_ops)
self.sym_ops = {}
space_group = sgtbx.space_group()
if isinstance(sym_ops, string_types): sym_ops = [sym_ops]
for i, op in enumerate(sym_ops):
try:
s = sgtbx.rt_mx(op)
except RuntimeError as e:
str_e = str(e)
if "Parse error: " in str_e:
raise CifBuilderError(
"Error interpreting symmetry operator: %s" %
(str_e.split("Parse error: ")[-1]))
else:
raise
if sym_op_ids is None:
sym_op_id = i + 1
else:
try:
sym_op_id = int(sym_op_ids[i])
except ValueError as e:
raise CifBuilderError(
"Error interpreting symmetry operator id: %s" %
(str(e)))
self.sym_ops[sym_op_id] = s
space_group.expand_smx(s)
else:
hall_symbol = self.get_cif_item('_space_group_name_Hall')
hm_symbol = self.get_cif_item('_space_group_name_H-M_alt')
sg_number = self.get_cif_item('_space_group_IT_number')
if space_group is None and hall_symbol not in (None, '?'):
try:
space_group = sgtbx.space_group(hall_symbol)
except Exception:
pass
if space_group is None and hm_symbol not in (None, '?'):
try:
space_group = sgtbx.space_group_info(
symbol=hm_symbol).group()
except Exception:
pass
if space_group is not None and sg_number not in (None, '?'):
try:
space_group = sgtbx.space_group_info(
number=sg_number).group()
except Exception:
pass
if (space_group is None and strict):
raise CifBuilderError(
"No symmetry instructions could be extracted from the cif block"
)
items = [self.get_cif_item("_cell_length_" + s) for s in "abc"]
for i, item in enumerate(items):
if isinstance(item, flex.std_string):
raise CifBuilderError(
"Data item _cell_length_%s cannot be declared in a looped list"
% ("abc"[i]))
for s in ["alpha", "beta", "gamma"]:
item = self.get_cif_item("_cell_angle_" + s)
if isinstance(item, flex.std_string):
raise CifBuilderError(
"Data item _cell_angle_%s cannot be declared in a looped list"
% s)
if (item == "?"):
item = "90" # enumeration default for angles is 90 degrees
items.append(item)
ic = items.count(None)
if (ic == 6):
if (strict):
raise CifBuilderError(
"Unit cell parameters not found in the cif file")
unit_cell = None
elif (ic == 0):
try:
vals = [float_from_string(s) for s in items]
except ValueError:
raise CifBuilderError("Invalid unit cell parameters are given")
try:
unit_cell = uctbx.unit_cell(vals)
except RuntimeError as e:
if "cctbx Error: Unit cell" in str(e):
raise CifBuilderError(e)
else:
raise
elif (space_group is not None):
unit_cell = uctbx.infer_unit_cell_from_symmetry(
[float_from_string(s) for s in items if s is not None],
space_group)
else:
raise CifBuilderError(
"Not all unit cell parameters are given in the cif file")
if unit_cell is not None and space_group is not None:
if not space_group.is_compatible_unit_cell(unit_cell):
# try primitive setting
space_group_input = space_group
space_group = space_group.info().primitive_setting().group()
if not space_group.is_compatible_unit_cell(unit_cell):
raise CifBuilderError(
"Space group is incompatible with unit cell parameters:\n" + \
" Space group: %s\n" %space_group_input.info() + \
" Unit cell: %s" %unit_cell)
self.crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group=space_group)
def unit_cell(self):
self._unit_cell = uctbx.infer_unit_cell_from_symmetry(
self.unit_cell_parameters, self.space_group())
if (self._unit_cell is None):
raise RuntimeError, "Cannot interpret unit cell parameters."
return self._unit_cell
def unit_cell(self):
self._unit_cell = uctbx.infer_unit_cell_from_symmetry(
self.unit_cell_parameters, self.space_group())
if (self._unit_cell is None):
raise RuntimeError, "Cannot interpret unit cell parameters."
return self._unit_cell