def __init__(self, structure_file, file_type=None):
PDBIO.__init__(self)
dirname, filename_without_extension, file_type2 = ssbio.utils.split_folder_and_path(
structure_file)
self.structure_file = structure_file
# Unzip the file if it is zipped
if file_type == '.gz':
unzipped = ssbio.utils.gunzip_file(structure_file, outdir=dirname)
dirname, filename_without_extension, file_type2 = ssbio.utils.split_folder_and_path(
unzipped)
if not file_type:
file_type = file_type2
else:
if '.' not in file_type:
file_type = '.{}'.format(file_type)
if file_type in ['.pdb', '.ent', '.mmcif', '.cif', '.mmtf']:
# Load the structure
if file_type.lower() == '.pdb' or file_type.lower() == '.ent':
structure = pdbp.get_structure(id='ssbio_pdb',
file=structure_file)
if file_type.lower() == '.mmcif' or file_type.lower() == '.cif':
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = cifp.get_structure(structure_id='ssbio_cif',
filename=structure_file)
if file_type.lower() == '.mmtf':
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = mmtfp.get_structure(file_path=structure_file)
log.debug('{}: parsed 3D coordinates of structure'.format(
op.basename(structure_file)))
else:
raise ValueError('{}: unsupported file type'.format(file_type))
# If there are multiple models (NMR), use the first model as the representative structure
# if len(structure) > 1:
# self.first_model = structure[0]
# structure = structure[0]
# self.set_structure(structure)
# log.debug('{}: using first model'.format(structure_file))
# elif len(structure) == 0:
# log.error('{}: no models in structure!'.format(structure_file))
# else:
self.set_structure(structure)
self.first_model = structure[0]
def __init__(self, structure_file, file_type=None):
PDBIO.__init__(self)
dirname, filename_without_extension, file_type2 = ssbio.utils.split_folder_and_path(
structure_file)
self.structure_file = structure_file
# Unzip the file if it is zipped
if file_type == '.gz':
unzipped = ssbio.utils.gunzip_file(structure_file, outdir=dirname)
dirname, filename_without_extension, file_type2 = ssbio.utils.split_folder_and_path(
unzipped)
if not file_type:
file_type = file_type2
else:
if '.' not in file_type:
file_type = '.{}'.format(file_type)
if file_type.lower() in ['.pdb', '.ent', '.mmcif', '.cif', '.mmtf']:
# Load the structure
if file_type.lower() == '.pdb' or file_type.lower() == '.ent':
structure = pdbp.get_structure(id='ssbio_pdb',
file=structure_file)
if file_type.lower() == '.mmcif' or file_type.lower() == '.cif':
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = cifp.get_structure(structure_id='ssbio_cif',
filename=structure_file)
if file_type.lower() == '.mmtf':
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
structure = mmtfp.get_structure(file_path=structure_file)
log.debug('{}: parsed 3D coordinates of structure'.format(
op.basename(structure_file)))
else:
raise ValueError('{}: unsupported file type'.format(file_type))
self.set_structure(structure)
try:
self.first_model = structure[0]
except KeyError:
raise KeyError(
'{}: no models contained in structure! Please check structure file contents.'
.format(structure_file))