def __init__(self,
file_object=None,
file_path=None,
cif_model=None,
data_structure_builder=None,
data_block_name=None,
base_array_info=None,
style="classic",
**kwds):
assert file_object is None or cif_model is None
if data_structure_builder is None:
data_structure_builders = (builders.miller_array_builder,
builders.crystal_structure_builder)
else:
assert data_structure_builder in (
builders.miller_array_builder,
builders.crystal_structure_builder)
data_structure_builders = (data_structure_builder, )
self.xray_structures = OrderedDict()
self.miller_arrays = OrderedDict()
self.original_arrays = OrderedDict()
if cif_model is None:
cif_model = reader(file_path=file_path,
file_object=file_object).model()
if not len(cif_model):
raise Sorry("No data block found in CIF")
if data_block_name is not None and not data_block_name in cif_model:
if (file_path is None):
msg = 'Unknown CIF data block name: "%s"' % data_block_name
else:
msg = 'Unknown CIF data block name "%s" in file: "%s"' % (
data_block_name, file_path)
raise RuntimeError(msg)
errors = []
wavelengths = {}
for key, block in cif_model.items():
if data_block_name is not None and key != data_block_name: continue
for builder in data_structure_builders:
if builder == builders.crystal_structure_builder:
if '_atom_site_fract_x' in block or '_atom_site_Cartn_x' in block:
self.xray_structures.setdefault(
key,
builder(block).structure)
elif builder == builders.miller_array_builder:
block_wavelengths = builders.get_wavelengths(block)
if (block_wavelengths is not None):
wavelengths = block_wavelengths
if base_array_info is not None:
base_array_info = base_array_info.customized_copy(
labels=[key])
if ('_refln_index_h' in block or '_refln.index_h' in block
or '_diffrn_refln' in block):
b = builder(block,
base_array_info=base_array_info,
wavelengths=wavelengths,
style=style)
self.miller_arrays.setdefault(key, b.arrays())
self.original_arrays.setdefault(key, b.origarrays())
def __init__(self,
file_object=None,
file_path=None,
cif_model=None,
data_structure_builder=None,
data_block_name=None,
base_array_info=None,
**kwds):
assert file_object is None or cif_model is None
if data_structure_builder is None:
data_structure_builders = (
builders.miller_array_builder, builders.crystal_structure_builder)
else:
assert data_structure_builder in (
builders.miller_array_builder, builders.crystal_structure_builder)
data_structure_builders = (data_structure_builder,)
self.xray_structures = OrderedDict()
self.miller_arrays = OrderedDict()
if cif_model is None:
cif_model = reader(file_path=file_path, file_object=file_object).model()
if not len(cif_model):
raise Sorry("No data block found in CIF")
if data_block_name is not None and not data_block_name in cif_model:
if (file_path is None):
msg = 'Unknown CIF data block name: "%s"' % data_block_name
else:
msg = 'Unknown CIF data block name "%s" in file: "%s"' % (
data_block_name, file_path)
raise RuntimeError(msg)
errors = []
wavelengths = {}
for key, block in cif_model.items():
if data_block_name is not None and key != data_block_name: continue
for builder in data_structure_builders:
if builder == builders.crystal_structure_builder:
if '_atom_site_fract_x' in block or '_atom_site_Cartn_x' in block:
self.xray_structures.setdefault(key, builder(block).structure)
elif builder == builders.miller_array_builder:
block_wavelengths = builders.get_wavelengths(block)
if (block_wavelengths is not None) :
wavelengths = block_wavelengths
if base_array_info is not None:
base_array_info = base_array_info.customized_copy(labels=[key])
if ( '_refln_index_h' in block or '_refln.index_h' in block or
'_diffrn_refln' in block
):
self.miller_arrays.setdefault(
key, builder(block, base_array_info=base_array_info,
wavelengths=wavelengths).arrays())