def test_iter(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
fa = traj[:]
iter_me(traj, traj.n_frames)
iter_me(fa, traj.n_frames)
iter_me(traj(), traj.n_frames)
iter_me(fa(), traj.n_frames)
iter_me(traj(mask='@CA'), traj.n_frames)
iter_me(fa(mask='@CA'), traj.n_frames)
iter_me([traj, fa], 2 * traj.n_frames)
iter_me((traj, fa), 2 * traj.n_frames)
iter_me((traj, (fa[0], )), traj.n_frames + 1)
for frame in iterframe_master(traj[0]):
assert frame.n_atoms == traj.top.n_atoms
i = 0
for frame in iterframe_master([traj, traj[:1]]):
i += 1
assert frame.n_atoms == traj.top.n_atoms
assert i == traj.n_frames + 1
i = 0
for frame in iterframe_master(traj.iterchunk()):
i += 1
assert isinstance(frame, Frame)
assert i == traj.n_frames
i = 0
for frame in iterframe_master([
traj.iterchunk(),
]):
i += 1
assert isinstance(frame, Frame)
assert i == traj.n_frames
# raise if wrong type
def test_raise():
for frame in pt.iterframe_master([0, 3]):
pass
with pytest.raises(TypeError):
test_raise()
def test_iter_with_a_list_of_frame_and_trajectory_and_FrameIterator(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
ref = traj[0]
for idx, frame in enumerate(iterframe_master([traj[0], traj])):
assert isinstance(frame, Frame), 'must a a Frame'
assert idx == traj.n_frames
# FrameIterator: traj()
for idx, frame in enumerate(iterframe_master([traj[0], traj()])):
assert isinstance(frame, Frame), 'must a a Frame'
assert idx == traj.n_frames
# FrameIterator: traj()
fi = traj.iterframe(frame_indices=[0, 3])
for idx, frame in enumerate(iterframe_master([traj[0], fi])):
assert isinstance(frame, Frame), 'must a a Frame'
def test_append_trajectory(self):
# test append
traj = pt.Trajectory()
t = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj.top = t.top
# append single Frame
traj.append(t[0])
assert traj.n_frames == 1
# append xyz
traj.append(t.xyz[:])
assert traj.n_frames == t.n_frames + 1
# append TrajectoryIterator
traj.append(t)
assert traj.n_frames == t.n_frames * 2 + 1
# append frame_iter
traj.append(t.iterframe())
assert traj.n_frames == t.n_frames * 3 + 1
# append pt.iterframe_master
traj.append(pt.iterframe_master(t))
assert traj.n_frames == t.n_frames * 4 + 1
# append itself
NFrames = traj.n_frames
traj.append(traj)
assert traj.n_frames == NFrames * 2
# append itself frame_iter
traj.append(traj.iterframe(stop=2))
assert traj.n_frames == NFrames * 2 + 2
# append pt.iterframe_master for itself
NFrames = traj.n_frames
traj.append(pt.iterframe_master(traj))
assert traj.n_frames == NFrames * 2
# append pt.iterframe_master for itself + other
n0 = traj.n_frames
n1 = t.n_frames
traj.append(pt.iterframe_master([traj, t]))
assert traj.n_frames == 2 * n0 + n1
def test_append_trajectory(self):
# test append
traj = pt.Trajectory()
t = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
traj.top = t.top
# append single Frame
traj.append(t[0])
assert traj.n_frames == 1
# append xyz
traj.append(t.xyz[:])
assert traj.n_frames == t.n_frames + 1
# append TrajectoryIterator
traj.append(t)
assert traj.n_frames == t.n_frames * 2 + 1
# append frame_iter
traj.append(t.iterframe())
assert traj.n_frames == t.n_frames * 3 + 1
# append pt.iterframe_master
traj.append(pt.iterframe_master(t))
assert traj.n_frames == t.n_frames * 4 + 1
# append itself
NFrames = traj.n_frames
traj.append(traj)
assert traj.n_frames == NFrames * 2
# append itself frame_iter
traj.append(traj.iterframe(stop=2))
assert traj.n_frames == NFrames * 2 + 2
# append pt.iterframe_master for itself
NFrames = traj.n_frames
traj.append(pt.iterframe_master(traj))
assert traj.n_frames == NFrames * 2
# append pt.iterframe_master for itself + other
n0 = traj.n_frames
n1 = t.n_frames
traj.append(pt.iterframe_master([traj, t]))
assert traj.n_frames == 2 * n0 + n1
def test_assert(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = Trajectory.from_iterable(iterframe_master(traj), top=traj.top)
for f0, f1 in zip(fa, traj):
aa_eq(f0.xyz, f1.xyz)
def test_raise():
for frame in pt.iterframe_master([0, 3]):
pass
def iter_me(obj, n_frames):
it = iterframe_master(obj)
for idx, frame in enumerate(it):
pass
assert idx + 1 == n_frames
