def run(self, scope, storage):
"""Save trajectory quantities."""
filename = self.arguments['filename']
box = scope['box']
box = garnett.trajectory.Box(Lx=box[0],
Ly=box[1],
Lz=box[2],
xy=box[3],
xz=box[4],
yz=box[5])
positions = scope['position']
if 'orientation' in scope:
orientations = scope['orientation']
else:
orientations = np.tile([(1, 0, 0, 0)], (len(positions), 1))
types = scope['type']
if 'type_names' not in scope:
type_names = [chr(ord('A') + t) for t in sorted(set(types))]
else:
type_names = scope['type_names']
the_frame = FakeFrame(box, positions, orientations, type_names, types,
None, None, len(positions))
mode = ('w' if any(filename.endswith(suf)
for suf in ['.pos', '.cif']) else 'wb')
with storage.open(self.arguments['filename'],
mode=mode,
on_filesystem=True) as f:
garnett.write([the_frame], f.name)
def make_gsd(job):
try:
with garnett.read(job.fn('dump.pos')) as traj:
garnett.write(traj, job.fn('dump.gsd'))
except garnett.errors.ParserError as e:
print(e)
job.doc.failed = True
def test_write_pos(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
tmp_name = os.path.join(tmp_dir, 'test.pos')
garnett.write(traj, tmp_name)
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name) as traj2:
self.assertEqual(len(traj), len(traj2))
def test_write_format(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
# No suffix is given to the temp file, so no format is detected
tmp_name = os.path.join(tmp_dir, 'test')
garnett.write(traj, tmp_name, fmt='pos')
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name, fmt='pos') as traj2:
self.assertEqual(len(traj), len(traj2))
def test_write_io(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
tmp_name = os.path.join(tmp_dir, 'test_io.gsd')
with open(tmp_name, 'wb') as gsdfile:
garnett.write(traj, gsdfile)
# Read back the file and check if it is the same as the original
with garnett.read(tmp_name) as traj2:
self.assertEqual(len(traj), len(traj2))
def test_default(self):
with TemporaryDirectory() as tmp_dir:
gsdfile = os.path.join(tmp_dir, 'testfile.gsd')
posfile = os.path.join(tmp_dir, 'testfile.pos')
with open(gsdfile, "wb") as f:
f.write(base64.b64decode(garnett.samples.GSD_BASE64))
with garnett.read(gsdfile) as traj:
with self.assertRaises(AttributeError):
traj[-1].shapedef
garnett.write(traj, posfile)
with garnett.read(posfile) as traj:
for frame in traj:
for name in frame.shapedef.keys():
self.assertEqual(frame.shapedef[name],
DEFAULT_SHAPE_DEFINITION)
def main(args):
with garnett.read(args.infile) as traj:
traj_centered = garnett.trajectory.Trajectory(
(center(frame) for frame in traj))
garnett.write(traj_centered, args.outfile)
return 0
def write(traj, *args, **kwargs):
trajectory = [getattr(frame, '_garnett_frame', frame) for frame in traj]
garnett.write(trajectory, *args, **kwargs)
def main(args):
with garnett.read(args.infile) as traj:
garnett.write(traj, args.outfile)
return 0
def test_write_unsupported(self):
with self.create_tmp_and_traj() as (tmp_dir, traj):
# No suffix is given to the temp file, so no format is detected
tmp_name = os.path.join(tmp_dir, 'test')
with self.assertRaises(NotImplementedError):
garnett.write(traj, tmp_name)
