def __init__(self, filename, mode='r', force_overwrite=True):
self._open = False
self._file = None
self._topology = None
self._positions = None
self._mode = mode
self._last_topology = None
if mode == 'r':
PDBTrajectoryFile._loadNameReplacementTables()
if _is_url(filename):
self._file = urlopen(filename)
if filename.lower().endswith('.gz'):
if six.PY3:
self._file = gzip.GzipFile(fileobj=self._file)
else:
self._file = gzip.GzipFile(fileobj=six.StringIO(
self._file.read()))
if six.PY3:
self._file = six.StringIO(self._file.read().decode('utf-8'))
else:
self._file = open_maybe_zipped(filename, 'r')
self._read_models()
elif mode == 'w':
self._header_written = False
self._footer_written = False
self._file = open_maybe_zipped(filename, 'w', force_overwrite)
else:
raise ValueError("invalid mode: %s" % mode)
self._open = True
def __init__(self, filename, mode='r', force_overwrite=True):
"""Open a xyz file for reading/writing. """
self._is_open = False
self._filename = filename
self._mode = mode
self._frame_index = 0
# track which line we're on. this is not essential, but its useful
# when reporting errors to the user to say what line it occured on.
self._line_counter = 0
if mode == 'r':
self._fh = open_maybe_zipped(filename, 'r')
self._is_open = True
elif mode == 'w':
self._fh = open_maybe_zipped(filename, 'w', force_overwrite)
self._is_open = True
else:
raise ValueError('mode must be one of "r" or "w". '
'you supplied "{0}"'.format(mode))
def __init__(self, filename, mode='r', force_overwrite=True):
"""Open a xyz file for reading/writing. """
self._is_open = False
self._filename = filename
self._mode = mode
self._frame_index = 0
# track which line we're on. this is not essential, but its useful
# when reporting errors to the user to say what line it occured on.
self._line_counter = 0
if mode == 'r':
self._fh = open_maybe_zipped(filename, 'r')
self._is_open = True
elif mode == 'w':
self._fh = open_maybe_zipped(filename, 'w', force_overwrite)
self._is_open = True
else:
raise ValueError('mode must be one of "r" or "w". '
'you supplied "{0}"'.format(mode))
def test_write_bz2(self):
fn = os.path.join(self.tmpdir, 'write.bz2')
with open_maybe_zipped(fn, 'w') as f:
f.write(u'COOKIE')
with bz2.BZ2File(fn, 'r') as f:
eq(f.read().decode('utf-8'), u'COOKIE')
def test_read_bz2(self):
fn = os.path.join(self.tmpdir, 'read.bz2')
with bz2.BZ2File(fn, 'w') as f:
f.write('COOKIE'.encode('utf-8'))
eq(open_maybe_zipped(fn, 'r').read(), u'COOKIE')
def test_write_gz(self):
fn = os.path.join(self.tmpdir, 'write.gz')
with open_maybe_zipped(fn, 'w') as f:
f.write(u'COOKIE')
with gzip.GzipFile(fn, 'r') as f:
eq(f.read().decode('utf-8'), u'COOKIE')
def test_read_gz(self):
fn = os.path.join(self.tmpdir, 'read.gz')
with gzip.GzipFile(fn, 'w') as f:
f.write('COOKIE'.encode('utf-8'))
eq(open_maybe_zipped(fn, 'r').read(), u'COOKIE')
def test_read_gz(tmpdir):
fn = '{}/read.gz'.format(tmpdir)
with gzip.GzipFile(fn, 'w') as f:
f.write('COOKIE'.encode('utf-8'))
eq(open_maybe_zipped(fn, 'r').read(), u'COOKIE')
def test_write_bz2(tmpdir):
fn = '{}/write.bz2'.format(tmpdir)
with open_maybe_zipped(fn, 'w') as f:
f.write(u'COOKIE')
with bz2.BZ2File(fn, 'r') as f:
eq(f.read().decode('utf-8'), u'COOKIE')
def test_read_bz2(tmpdir):
fn = '{}/read.bz2'.format(tmpdir)
with bz2.BZ2File(fn, 'w') as f:
f.write('COOKIE'.encode('utf-8'))
eq(open_maybe_zipped(fn, 'r').read(), u'COOKIE')
def test_write_gz(tmpdir):
fn = '{}/write.gz'.format(tmpdir)
with open_maybe_zipped(fn, 'w') as f:
f.write(u'COOKIE')
with gzip.GzipFile(fn, 'r') as f:
eq(f.read().decode('utf-8'), u'COOKIE')
