def test_read_1(get_fn):
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz, _ = f.read()
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz3, _ = f.read(stride=3)
eq(xyz[::3], xyz3)
def test_read_0(get_fn):
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz, box = f.read()
assert box is None
with MDCRDTrajectoryFile(get_fn('frame0.mdcrdbox'), n_atoms=22) as f:
xyz2, box = f.read()
eq(box.shape, (1002, 3))
eq(xyz, xyz2)
def test_atom_indices_0(get_fn):
atom_indices = np.arange(10)
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz0, box0 = f.read(n_frames=1)
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz1, box1 = f.read(n_frames=1, atom_indices=atom_indices)
eq(xyz0[:, atom_indices], xyz1)
def test_read_write_0():
xyz = 10 * np.random.randn(100, 11, 3)
with MDCRDTrajectoryFile(temp, mode='w') as f:
f.write(xyz)
with MDCRDTrajectoryFile(temp, n_atoms=11) as f:
xyz2, _ = f.read()
eq(_, None)
eq(xyz, xyz2, decimal=3)
def test_read_write_1():
xyz = 10 * np.random.randn(100, 11, 3)
box = np.random.randn(100, 3)
with MDCRDTrajectoryFile(temp, mode='w') as f:
f.write(xyz, box)
with MDCRDTrajectoryFile(temp, n_atoms=11) as f:
xyz2, box2 = f.read()
eq(box, box2, decimal=3)
eq(xyz, xyz2, decimal=3)
def test_multiread(get_fn):
reference = md.load(get_fn('frame0.mdcrd'), top=get_fn('native.pdb'))
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
xyz0, box0 = f.read(n_frames=1)
xyz1, box1 = 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.mdcrd'), top=get_fn('native.pdb'))
with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
f.seek(1)
eq(1, f.tell())
xyz1, box1 = f.read(n_frames=1)
eq(reference.xyz[1], xyz1[0] / 10)
f.seek(10)
eq(10, f.tell())
xyz10, box10 = f.read(n_frames=1)
eq(reference.xyz[10], xyz10[0] / 10)
eq(11, f.tell())
f.seek(-8, 1)
xyz3, box3 = f.read(n_frames=1)
eq(reference.xyz[3], xyz3[0] / 10)
f.seek(4, 1)
xyz8, box8 = f.read(n_frames=1)
eq(reference.xyz[8], xyz8[0] / 10)