def read_frame_from_file(self, file_name, frame_num):
# note: this only needs to return the file pointers -- but should
# only do so once that frame has been written!
basename = os.path.basename(file_name)
# basename should be in the format [0-9]+\.trr (as set by the
# trajectory_filename method)
# file_number = int(basename.split('.')[0])
try:
xyz, vel, box = self.read_frame_data(file_name, frame_num)
except (IndexError, OSError, IOError) as e:
# this means that no such frame exists yet, so we return None
# IndexError in older version, OSError more recently (specific
# MDTraj error)
logger.debug("Expected exception caught: " + str(e))
close_file_descriptors(basename)
return None
except RuntimeError as e:
# TODO: matches "TRR read error"
logger.debug("Received partial frame for %s %d", file_name,
frame_num + 1)
return 'partial'
else:
logger.debug("Creating snapshot")
snapshot = ExternalMDSnapshot(file_name=file_name,
file_position=frame_num,
engine=self)
return snapshot
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([np.asarray(snapshot.box_vectors)], dtype=np.float32)
lambd = np.asarray([0.0], dtype=np.float32)
vel = np.asarray([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)