def __init__(self, filename):
"""
Args:
filename - cif file name. bzipped or gzipped cifs are fine too.
"""
if isinstance(filename, basestring):
with file_open_zip_aware(filename, "r") as f:
self._cif = CifFile.ReadCif(f)
else:
self._cif = CifFile.ReadCif(filename)
def save_data(self, filename):
"""
Save the assimilated data to a file.
Args:
filename:
filename to save the assimilated data to. Note that if the
filename ends with gz or bz2, the relevant gzip or bz2
compression will be applied.
"""
with file_open_zip_aware(filename, "w") as f:
json.dump(list(self._data), f)
def load_data(self, filename):
"""
Load assimilated data from a file
"""
with file_open_zip_aware(filename, "r") as f:
self._data = json.load(f)
excluded_bonding_elements = args.exclude_bonding[0].split(',') if args.exclude_bonding else []
file_format = args.format
filename = args.input_file[0]
s = None
if filename.endswith(".cif"):
file_format = "cif"
elif filename.startswith("POSCAR"):
file_format = "poscar"
elif re.search('\.json', filename):
file_format = 'mpjson'
if file_format == 'poscar':
p = Poscar.from_file(filename)
s = p.struct
elif file_format == 'cif':
r = CifParser(filename)
s = r.get_structures(False)[0]
else:
d = json.load(file_open_zip_aware(filename))
ts = TransformedStructure.from_dict(d)
s = ts.final_structure
if s:
vis = StructureVis(excluded_bonding_elements=excluded_bonding_elements)
vis.set_structure(s)
vis.show()