def getCoordsets(self, indices=None):
"""Returns coordinate sets at given *indices*. *indices* may be an
integer, a list of integers or ``None``. ``None`` returns all
coordinate sets."""
if self._closed:
raise ValueError('I/O operation on closed file')
if (self._indices is None and
(indices is None or indices == slice(None))):
nfi = self._nfi
self.reset()
n_floats = self._n_floats + self._unitcell * 14
n_atoms = self._n_atoms
n_csets = self._n_csets
data = np.fromfile(self._file, self._dtype,
n_floats * n_csets)
if len(data) > n_floats * n_csets:
n_csets = len(data)/n_floats
data = data[:n_csets]
LOGGER.warning('DCD is corrupt, {0:d} out of {1:d} frames '
'were parsed.'.format(n_csets, self._n_csets))
data = data.reshape((n_csets, n_floats))
if self._unitcell:
data = data[:, 14:]
data = data.reshape((n_csets, 3, n_atoms+2))
data = data[:, :, 1:-1]
data = data.transpose(0, 2, 1)
self.goto(nfi)
if self._astype is not None and self._astype != data.dtype:
data = data.astype(self._astype)
return data
else:
return TrajFile.getCoordsets(self, indices)
def __init__(self, filename, mode='r', **kwargs):
TrajFile.__init__(self, filename, mode)
self._astype = kwargs.get('astype', None)
if self._mode != 'w':
self._parseHeader()
def __init__(self, filename, mode='r'):
TrajFile.__init__(self, filename, mode)
if self._mode != 'w':
self._parseHeader()