def test_write_1():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
with BINPOSTrajectoryFile(temp, 'w') as f:
f.write(xyz)
xyz2 = BINPOSTrajectoryFile(temp).read()
eq(xyz, xyz2)
def test_seek():
reference = BINPOSTrajectoryFile(get_fn('frame0.binpos')).read()
with BINPOSTrajectoryFile(get_fn('frame0.binpos')) as f:
xyz = f.read(1)[0]
eq(xyz, reference[0])
eq(f.tell(), 1)
xyz = f.read(1)[0]
eq(xyz, reference[1])
eq(f.tell(), 2)
f.seek(0)
eq(f.tell(), 0)
xyz = f.read(1)[0]
eq(f.tell(), 1)
eq(xyz, reference[0])
f.seek(5)
eq(f.read(1)[0], reference[5])
eq(f.tell(), 6)
f.seek(-5, 1)
eq(f.tell(), 1)
xyz = f.read(1)[0]
eq(xyz, reference[1])
f.seek(0, 2)
eq(f.tell(), len(reference))
def test_write_1(tmpdir):
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
fn = '{}/x.binpos'.format(tmpdir)
with BINPOSTrajectoryFile(fn, 'w') as f:
f.write(xyz)
xyz2 = BINPOSTrajectoryFile(fn).read()
assert eq(xyz, xyz2)
def test_read_atom_indices_slice(get_fn):
"Read a binpos with atom_indices as a slice"
fn_binpos = get_fn('frame0.binpos')
with BINPOSTrajectoryFile(fn_binpos) as f:
xyz = f.read(atom_indices=slice(0, 10, None))
xyz2 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
assert eq(xyz, xyz2[:, 0:10, :])
def test_read_atom_indices(get_fn):
"Read a binpos with atom_indices as a list"
fn_binpos = get_fn('frame0.binpos')
with BINPOSTrajectoryFile(fn_binpos) as f:
xyz = f.read(atom_indices=[0, 1, 2])
xyz2 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
assert eq(xyz, xyz2[:, [0, 1, 2], :])
def test_read_stride_2(get_fn):
# Read a binpos with stride=3 when n_frames is supplied (different code path)
fn_binpos = get_fn('frame0.binpos')
with BINPOSTrajectoryFile(fn_binpos) as f:
xyz = f.read(n_frames=1000, stride=3)
xyz2 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
assert eq(xyz, xyz2[::3])
def test_read_stride(get_fn):
# Read a binpos with stride=3
fn_binpos = get_fn('frame0.binpos')
with BINPOSTrajectoryFile(fn_binpos) as f:
xyz = f.read(stride=3)
xyz2 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
assert eq(xyz, xyz2[::3])
def test_read_1():
with BINPOSTrajectoryFile(fn_binpos, chunk_size_multiplier=0.5) as f:
xyz = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz2 = f.read()[0]
xyz3 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
yield lambda: eq(xyz[1:], xyz2)
yield lambda: eq(xyz, xyz3)
def test_tell():
with BINPOSTrajectoryFile(get_fn('frame0.binpos')) as f:
eq(f.tell(), 0)
f.read(101)
eq(f.tell(), 101)
f.read(3)
eq(f.tell(), 104)
def test_read_2(get_fn):
fn_binpos = get_fn('frame0.binpos')
fn_dcd = get_fn('frame0.dcd')
with BINPOSTrajectoryFile(fn_binpos, chunk_size_multiplier=10) as f:
xyz = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz2 = f.read()[0]
xyz3 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
assert eq(xyz[1:], xyz2)
assert eq(xyz, xyz3)
def test_read_stride():
"Read a binpos with stride=3"
with BINPOSTrajectoryFile(fn_binpos) as f:
xyz = f.read(stride=3)
xyz2 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
yield lambda: eq(xyz, xyz2[::3])