def read_frame_data(self, filename, frame_num):
"""
Returns pos, vel, box or raises error
"""
# if self._last_filename != filename:
# try:
# self._file.close()
# except AttributeError:
# pass # first time thru, self._file is None
# self._file = TRRTrajectoryFile(filename)
# f = self._file
# do we need to reopen the TRR each time to avoid problems with the
# fiel length changing?
trr = TRRTrajectoryFile(filename)
f = trr
logger.debug("Reading file %s frame %d (of %d)", filename, frame_num,
len(f))
# logger.debug("File length: %d", len(f))
try:
f.seek(offset=frame_num)
data = f._read(n_frames=1, atom_indices=None, get_velocities=True)
finally:
trr.close()
return data[0][0], data[5][0], data[3][0]
def write_frame_to_file(self, filename, snapshot, mode='w'):
if os.path.isfile(filename):
# stop if we already have this file; could also happen because
# of a weird behavior in a mover. You must remove the files if
# you don't want them.
raise RuntimeError("File " + str(filename) + " exists. " +
"Preventing overwrite.")
# type control before passing things to Cython code
xyz = np.asarray([snapshot.xyz], dtype=np.float32)
time = np.asarray([0.0], dtype=np.float32)
step = np.asarray([0], dtype=np.int32)
box = np.asarray([snapshot.box_vectors], dtype=np.float32)
lambd = np.asarray([0.0], dtype=np.float32)
vel = np.asarray([snapshot.velocities], dtype=np.float32)
try:
trr = TRRTrajectoryFile(filename, mode)
trr._write(xyz, time, step, box, lambd, vel)
finally:
trr.close()
close_file_descriptors(filename)
