def test_0(self):
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
frame0 = traj[0]
assert frame0._buffer2d[0, 0] == frame0[0, 0]
assert frame0._buffer2d[0, 1] == frame0[0, 1]
assert frame0._buffer2d[0, 2] == frame0[0, 2]
assert frame0._buffer2d[1, 0] == frame0[1, 0]
assert frame0._buffer2d[19, 0] == frame0[19, 0]
frame0._buffer2d[19, 0] = 1000.
# make sure changing _buffer2d will update frame0.xyz too
assert frame0._buffer2d[19, 0] == frame0[19, 0]
arr0 = np.asarray(frame0._buffer2d)
arr0[19] = [200, 300, 400.]
assert frame0._buffer2d[19, 0] == frame0[19, 0] == arr0[19, 0]
frame1 = frame0.copy()
frame1.strip(traj.top("!@CA"))
_f = pt.Frame(frame0, traj.top("@CA"))
CA_2 = _f[2, :]
aa_eq(CA_2, frame1[2, :])
assert frame0._buffer1d.shape == (912, )
assert frame0._buffer2d.shape == (304, 3)
assert frame0._buffer1d.is_c_contig() == True
frame0._buffer2d[1:3, 0] = array('d', [1., 2.])
aa_eq(frame0[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
aa_eq(frame0._buffer2d[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
def test_force(self):
frame = pt.Frame(304)
force = np.zeros(304 * 3) + 1.
assert frame.force is None
frame.force = force
assert frame.force.shape == (304, 3)
frame.force = None
assert frame.force is None
def test_velocity(self):
frame = pt.Frame(304)
velocity = np.zeros(304 * 3) + 1.
assert frame.velocity is None
frame.velocity = velocity
assert frame.velocity.shape == (304, 3)
frame.velocity = None
assert frame.velocity is None
def get_frame_with_force(traj, forces=frcs):
frame0 = pt.Frame()
crdinfo = dict(has_force=True)
frame0._allocate_force_and_velocity(traj.top, crdinfo)
for frame, frc in zip(traj, frcs):
frame0.xyz[:] = frame.xyz
frame0.force[:] = frc
yield frame0
def test_velocity_and_force_allocation(self):
frame = pt.Frame()
top = pt.tools.make_fake_topology(100)
assert frame.n_atoms == 0
assert not frame.has_force()
assert not frame.has_velocity()
crdinfo = dict(has_force=True, has_velocity=True)
frame._allocate_force_and_velocity(top, crdinfo)
assert frame.n_atoms == 100
assert frame.has_force()
assert frame.has_velocity()
def shape_mismatch2():
fa[0] = pt.Frame()
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
for xyz0 in traj.xyz:
frame = pt.Frame(traj.n_atoms, xyz0, _as_ptr=True)
aa_eq(frame.xyz, xyz0)
def test_0(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
for xyz0 in traj.xyz:
frame = pt.Frame(traj.n_atoms, xyz0, _as_ptr=True)
aa_eq(frame.xyz, xyz0)