def test_read_3(get_fn):
# Test read with n_frames
fn_dtr = get_fn('frame0.dtr')
dtr_traj = DTRTrajectoryFile(fn_dtr)
dtr_traj.seek(1)
xyz, times, cell_lens, cell_angles = dtr_traj.read(n_frames=900)
eq(len(xyz), 500)
def test_read_7():
'test two full read'
reader = DTRTrajectoryFile(fn_dtr)
xyz, times, cell_lens, cell_angles = reader.read()
xyz, times, cell_lens, cell_angles = reader.read()
eq(len(xyz), 0)
eq(len(times), 0)
eq(len(cell_lens), 0)
eq(len(cell_angles), 0)
def test_read_7():
'test two full read'
reader = DTRTrajectoryFile(fn_dtr)
xyz, times, cell_lens, cell_angles = reader.read()
xyz, times, cell_lens, cell_angles = reader.read()
eq(len(xyz), 0)
eq(len(times), 0)
eq(len(cell_lens), 0)
eq(len(cell_angles), 0)
def test_read_6():
"DTRReader: check streaming read followed by reading the 'rest'"
xyz_ref, times_ref, box_lengths_ref, box_angles_ref = DTRTrajectoryFile(fn_dtr).read()
reader = DTRTrajectoryFile(fn_dtr)
for i in range(int(len(xyz_ref)/2)):
xyz, times, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(times_ref[np.newaxis, i], times)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
xyz_rest, times_rest, box_rest, angles_rest = reader.read()
yield lambda: eq(xyz_ref[i+1:], xyz_rest)
yield lambda: eq(times_ref[i+1:], times_rest)
yield lambda: eq(box_lengths_ref[i+1:], box_rest)
yield lambda: eq(box_angles_ref[i+1:], angles_rest)
yield lambda: len(xyz_ref) == i + len(xyz_rest)
def test_read_7(get_fn):
# Test two full reads
fn_dtr = get_fn('frame0.dtr')
reader = DTRTrajectoryFile(fn_dtr)
xyz, times, cell_lens, cell_angles = reader.read()
xyz, times, cell_lens, cell_angles = reader.read()
eq(len(xyz), 0)
eq(len(times), 0)
eq(len(cell_lens), 0)
eq(len(cell_angles), 0)
def test_read():
"""
test the default read and compare against reference trajectory in dcd format
"""
dtr_traj = DTRTrajectoryFile(fn_dtr)
eq(len(dtr_traj), 501)
xyz, times, cell_lens, cell_angles = dtr_traj.read()
xyz2, cell_lens2, cell_angles2 = DCDTrajectoryFile(fn_dcd).read()
eq(xyz, xyz2)
eq(cell_lens, cell_lens2)
eq(cell_angles, cell_angles2)
def test_read():
"""
test the default read and compare against reference trajectory in dcd format
"""
dtr_traj = DTRTrajectoryFile(fn_dtr)
eq(len(dtr_traj), 501)
xyz, times, cell_lens, cell_angles = dtr_traj.read()
xyz2, cell_lens2, cell_angles2 = DCDTrajectoryFile(fn_dcd).read()
eq(xyz, xyz2)
eq(cell_lens, cell_lens2)
eq(cell_angles, cell_angles2)
def test_read_5():
"check streaming read of frames 1 at a time"
xyz_ref, times_ref, box_lengths_ref, box_angles_ref = DTRTrajectoryFile(fn_dtr).read()
reader = DTRTrajectoryFile(fn_dtr)
for i in range(len(xyz_ref)):
xyz, times, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(times_ref[np.newaxis, i], times)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
def test_read(get_fn):
# Test the default read and compare against reference trajectory in dcd format
fn_dtr = get_fn('frame0.dtr')
fn_dcd = get_fn('frame0.dcd')
dtr_traj = DTRTrajectoryFile(fn_dtr)
eq(len(dtr_traj), 501)
xyz, times, cell_lens, cell_angles = dtr_traj.read()
xyz2, cell_lens2, cell_angles2 = DCDTrajectoryFile(fn_dcd).read()
eq(xyz, xyz2)
eq(cell_lens, cell_lens2)
eq(cell_angles, cell_angles2)
def test_read_6(get_fn):
# Check streaming read followed by reading the 'rest'
fn_dtr = get_fn('frame0.dtr')
xyz_ref, times_ref, box_lengths_ref, box_angles_ref = DTRTrajectoryFile(fn_dtr).read()
reader = DTRTrajectoryFile(fn_dtr)
for i in range(len(xyz_ref) // 2):
xyz, times, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(times_ref[np.newaxis, i], times)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
xyz_rest, times_rest, box_rest, angles_rest = reader.read()
i = len(xyz_ref) // 2
assert eq(xyz_ref[i:], xyz_rest)
assert eq(times_ref[i:], times_rest)
assert eq(box_lengths_ref[i:], box_rest)
assert eq(box_angles_ref[i:], angles_rest)
assert len(xyz_ref) == i + len(xyz_rest)
def test_read_3():
"""test read with n_frames"""
dtr_traj = DTRTrajectoryFile(fn_dtr)
dtr_traj.seek(1)
xyz, times, cell_lens, cell_angles = dtr_traj.read(n_frames=900)
eq(len(xyz), 500)
def test_read_closed():
f = DTRTrajectoryFile(fn_dtr)
f.close()
f.read()
def test_read_3():
"""test read with n_frames"""
dtr_traj = DTRTrajectoryFile(fn_dtr)
dtr_traj.seek(1)
xyz, times, cell_lens, cell_angles = dtr_traj.read(n_frames=900)
eq(len(xyz), 500)
def test_read_closed():
f = DTRTrajectoryFile(fn_dtr)
f.close()
f.read()
def test_read_closed(get_fn):
fn_dtr = get_fn('frame0.dtr')
with pytest.raises(IOError):
f = DTRTrajectoryFile(fn_dtr)
f.close()
f.read()
