def test_getitem_bool_TypeError(cls, GMX_REF_FILEPATH):
slx = cls([True, False, True])
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
with pytest.raises(TypeError):
for ts in tng[slx]:
ts.step
def test_getitem_bool(arr, cls, GMX_REF_DATA, GMX_REF_FILEPATH):
slx = cls(arr)
ref = np.arange(GMX_REF_DATA.length)[slx]
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for ref_ts, ts in zip(ref, tng[slx]):
assert ref_ts == ts.step
def test_double_iteration(GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for i, frame in enumerate(tng):
assert i == frame.step
for i, frame in enumerate(tng):
assert i == frame.step
def test_sliced_iteration(slice_idx, GMX_REF_DATA, GMX_REF_FILEPATH):
start, stop, step = slice_idx
ref_steps = np.arange(0, GMX_REF_DATA.length)[start:stop:step]
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for ref_ts, ts in zip(ref_steps, tng[start:stop:step]):
assert ref_ts == ts.step
def test_first_positions(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
first_frame = tng.read().positions
assert np.array_equal(GMX_REF_DATA.first_frame, first_frame)
def test_natoms(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
assert GMX_REF_DATA.natoms == tng.n_atoms
def test_load_bad_file(CORRUPT_FILEPATH):
with pytest.raises(IOError):
with pytng.TNGFile(CORRUPT_FILEPATH) as tng:
tng.read()
def test_getitem_int(idx, GMX_REF_DATA, GMX_REF_FILEPATH):
indices = np.arange(GMX_REF_DATA.length)
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
ts = tng[idx]
assert ts.step == indices[idx]
def test_getitem_multipl_ints(slx, cls, GMX_REF_DATA, GMX_REF_FILEPATH):
slx = cls(slx)
indices = np.arange(GMX_REF_DATA.length)
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for ref_step, ts in zip(indices[slx], tng[slx]):
assert ref_step == ts.step
def test_iter(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for i, ts in enumerate(tng):
assert i == ts.step
def test_len(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
assert GMX_REF_DATA.length == tng.n_frames
assert GMX_REF_DATA.length == len(tng)
def test_load_missing_file(MISSING_FILEPATH):
with pytest.raises(IOError):
with pytng.TNGFile(MISSING_FILEPATH) as tng:
tng.read()
def test_box(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
frame = tng.read()
assert np.array_equal(GMX_REF_DATA.box, frame.box)
def test_time(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
for ref_time, ts in zip(GMX_REF_DATA.time, tng):
assert ref_time == ts.time
def test_seek_IOError(idx, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH, 'r') as tng:
with pytest.raises(IndexError):
tng[idx]
def test_last_positions(GMX_REF_DATA, GMX_REF_FILEPATH):
with pytng.TNGFile(GMX_REF_FILEPATH) as tng:
tng.seek(tng.n_frames - 1)
last_frame = tng.read().positions
assert np.array_equal(GMX_REF_DATA.last_frame, last_frame)