def test_read_write():
xyz = np.around(10 * np.random.randn(100, 11, 3), decimals=3)
with XYZTrajectoryFile(temp, mode='w') as f:
f.write(xyz)
with XYZTrajectoryFile(temp) as f:
xyz2 = f.read()
eq(xyz, xyz2)
def test_multiread(get_fn):
reference = md.load(get_fn('frame0.xyz'), top=get_fn('native.pdb'))
with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
xyz0 = f.read(n_frames=1)
xyz1 = f.read(n_frames=1)
eq(reference.xyz[0], xyz0[0] / 10)
eq(reference.xyz[1], xyz1[0] / 10)
def test_seek(get_fn):
reference = md.load(get_fn('frame0.xyz'), top=get_fn('native.pdb'))
with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
f.seek(1)
eq(1, f.tell())
xyz1 = f.read(n_frames=1)
eq(reference.xyz[1], xyz1[0] / 10)
f.seek(10)
eq(10, f.tell())
xyz10 = f.read(n_frames=1)
eq(reference.xyz[10], xyz10[0] / 10)
eq(11, f.tell())
f.seek(-8, 1)
xyz3 = f.read(n_frames=1)
eq(reference.xyz[3], xyz3[0] / 10)
f.seek(4, 1)
xyz8 = f.read(n_frames=1)
eq(reference.xyz[8], xyz8[0] / 10)
def test_read_0(get_fn):
with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
xyz = f.read()
with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
xyz3 = f.read(stride=3)
eq(xyz[::3], xyz3)