def read_zeolite(binary_filepath: str,
parent_zeolite: PerfectZeolite,
json_filepath: Optional[str] = None) -> Zeolite:
if json_filepath:
with open(json_filepath, 'r') as f:
attr_dict = json.load(f)
additions_map = attr_dict['additions_maps']
else:
additions_map = None
z = Zeolite(read(binary_filepath))
z.register_with_parent(parent_zeolite, additions_map)
return z
def read_zeolites(file_path: str,
str_ext: str = '.traj',
zipped: bool = True,
glob_cmd: Optional[str] = None) -> Dict[str, PerfectZeolite]:
"""
Read the zeolites from a .zeo file or folder or folder
:param file_path: path to .zeo file with or without .zeo extension or path to unzipped zeo folder
:type file_path: str
:param str_ext: type of files in .zeo zip file
:type str_ext: str
:param glob_cmd: regular expression to select from folder structure
:type glob_cmd: str
:return: Dictionary of Zeotypes loaded from the files
:rtype: Dict[str, PerfectZeolite]
"""
if zipped:
if '.' not in file_path:
file_path = file_path + '.zeo'
folder_path = unpack_zeo_file(file_path)
else:
folder_path = file_path
zeotype_dict = {}
folder_list = glob.glob(os.path.join(folder_path, '*/'))
# read parent zeolite
try:
parent_folder = [
folder for folder in folder_list if Path(folder).stem == 'parent'
][0]
except IndexError as e:
raise FileExistsError(
'parent folder not found in specified directory') from e
# get parent zeolite binary file
# use regex binary command
if glob_cmd:
binary_glob_cmd = glob_cmd
else:
binary_glob_cmd = '*' + str_ext
binary_filepath = glob.glob(os.path.join(parent_folder,
binary_glob_cmd))[0]
json_filepath = glob.glob(os.path.join(parent_folder, '*.json'))[0]
index_mapper_filepath = glob.glob(
os.path.join(folder_path, 'index_mapper.json'))[0]
parent_zeolite = read_parent_zeolite(binary_filepath, json_filepath,
index_mapper_filepath)
zeotype_dict['parent'] = parent_zeolite
for folder in folder_list:
if folder == parent_folder:
continue
name = Path(folder).stem
json_path = os.path.join(folder, name + '.json')
binary_path = os.path.join(folder, name + str_ext)
with open(json_path, 'r') as f:
my_zeotype = Zeolite(read(binary_path))
attr_dict = json.load(f)
my_zeotype.name = name
additions_map = attr_dict['additions_map']
my_zeotype.register_with_parent(parent_zeolite, additions_map)
zeotype_dict[name] = my_zeotype
if zipped:
delete_folder(folder_path)
return zeotype_dict