def test_write_coordinates_reshape():
coordinates = np.random.randn(10,3)
with LH5TrajectoryFile(temp, 'w') as f:
f.write(coordinates)
with LH5TrajectoryFile(temp) as f:
eq(f.read(), coordinates.reshape(1,10,3), decimal=3)
def test_topology():
top = md.load(get_fn('native.pdb')).topology
with LH5TrajectoryFile(temp, 'w') as f:
f.topology = top
with LH5TrajectoryFile(temp) as f:
assert f.topology == top
def test_write_multiple():
coordinates = np.random.randn(4, 10, 3)
with LH5TrajectoryFile(temp, 'w') as f:
f.write(coordinates)
f.write(coordinates)
with LH5TrajectoryFile(temp) as f:
eq(f.read(), np.vstack((coordinates, coordinates)), decimal=3)
def test_read_slice_0():
coordinates = np.random.randn(4, 10,3)
with LH5TrajectoryFile(temp, 'w') as f:
f.write(coordinates)
with LH5TrajectoryFile(temp) as f:
eq(f.read(n_frames=2), coordinates[:2], decimal=3)
eq(f.read(n_frames=2), coordinates[2:4], decimal=3)
with LH5TrajectoryFile(temp) as f:
eq(f.read(stride=2), coordinates[::2], decimal=3)
with LH5TrajectoryFile(temp) as f:
eq(f.read(stride=2, atom_indices=np.array([0,1])), coordinates[::2, [0,1], :], decimal=3)
def test_write_coordinates():
coordinates = np.random.randn(4, 10,3)
with LH5TrajectoryFile(temp, 'w') as f:
f.write(coordinates)
with LH5TrajectoryFile(temp) as f:
eq(f.read(), coordinates, decimal=3)
with LH5TrajectoryFile(temp) as f:
f.seek(2)
eq(f.read(), coordinates[2:], decimal=3)
f.seek(0)
eq(f.read(), coordinates[0:], decimal=3)
f.seek(-1, 2)
eq(f.read(), coordinates[3:], decimal=3)
def test_do_overwrite_1():
with open(temp, 'w') as f:
f.write('a')
with pytest.raises(IOError):
with LH5TrajectoryFile(temp, 'w', force_overwrite=False) as f:
f.write(np.random.randn(10, 5, 3))
def test_do_overwrite_0():
with open(temp, 'w') as f:
f.write('a')
with LH5TrajectoryFile(temp, 'w', force_overwrite=True) as f:
f.write(np.random.randn(10,5,3))