def read(f, format=None):
"""Read in a molecule from a file, file-like object, or string.
Will also depickle a pickled object.
Note:
Files with ``.bz2`` or ``.gz`` suffixes will be automatically decompressed.
Currently does not support files with more than one record - only returns the first record
Args:
f (str or file-like): Either a path to a file, OR a string with the
file's contents, OR a file-like object
format (str): molecule format (pdb, xyz, sdf, etc.) or pickle format
(recognizes p, pkl, or pickle); guessed from filename if not passed
Returns:
moldesign.Molecule or object: molecule parsed from the file (or python object, for
pickle files)
Raises:
ValueError: if ``f`` isn't recognized as a string, file path, or file-like object
"""
filename = None
# Open a file-like object
if isinstance(f,
basestring) and os.path.exists(f): # it's a path to a file
filename = f
format, compression = _get_format(filename, format)
fileobj = COMPRESSION[compression](filename, mode='r')
elif hasattr(f, 'open'): # we can get a file-like object
fileobj = f.open('r')
elif hasattr(f, 'read'): # it's already file-like
fileobj = f
elif isinstance(f, basestring): # assume it's just a string
if format is None:
raise IOError(
('No file named "%s"; ' % f[:50]) +
'please set the `format` argument if you want to parse the string'
)
fileobj = StringIO.StringIO(f)
else:
raise ValueError(
'Parameter to moldesign.read (%s) not ' % str(f) +
'recognized as string, file path, or file-like object')
if format in READERS:
mol = READERS[format](fileobj)
else: # default to openbabel if there's not an explicit reader for this format
mol = openbabel_interface.read_stream(fileobj, format)
if filename is not None and mol.name not in (None, 'untitled'):
mol.name = filename
mdt.helpers.atom_name_check(mol)
return mol
def read_xyz(f):
tempmol = openbabel_interface.read_stream(f, 'xyz')
for atom in tempmol.atoms:
atom.residue = None
atom.chain = None
return mdt.Molecule(tempmol.atoms)