def test_iterload_comprehensive(tmpdir):
trajin, tn = fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")
# frame_slice
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 0))
aa_eq(traj_tz2_ortho.xyz, t0.xyz)
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 2))
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride
t0 = pt.iterload(trajin, tn, stride=2)
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, ignore frame_slice
t0 = pt.iterload(trajin, tn, stride=2, frame_slice=(0, -1, 3))
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, load two files
t0 = pt.iterload([trajin, trajin], tn, stride=2)
xyz_2 = np.vstack((traj_tz2_ortho.xyz[::2], traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, load two files, ignore frame_slice
t0 = pt.iterload([trajin, trajin],
tn,
stride=2,
frame_slice=[(0, -1, 5), (0, -1, 2)])
xyz_2 = np.vstack((traj_tz2_ortho.xyz[::2], traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, 4 trajs
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3)
# add frame_slice
t1 = pt.iterload(filenames, tn, frame_slice=[
(0, -1, 3),
] * 4)
xyz_expected = np.vstack(
[pt.iterload(fname, tn)[::3].xyz for fname in filenames])
aa_eq(xyz_expected, t0.xyz)
aa_eq(xyz_expected, t1.xyz)
# stride, 4 trajs, ignore frame_slice
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3, frame_slice=(0 - 1, 4))
xyz_expected = np.vstack(
[pt.iterload(fname, tn)[::3].xyz for fname in filenames])
aa_eq(xyz_expected, t0.xyz)
# filename with space
with tmpdir.as_cwd():
traj = pt.datafiles.load_tz2()
fname = "abc\ xyz.nc"
traj.save(fname)
traj2 = pt.iterload(fname, traj.top)
assert traj2.n_frames == traj.n_frames
def test_iterload_comprehensive(self):
fn, tn = ("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# frame_slice
t0 = pt.iterload(fn, tn, frame_slice=(0, -1, 0))
aa_eq(self.traj_tz2_ortho.xyz, t0.xyz)
t0 = pt.iterload(fn, tn, frame_slice=(0, -1, 2))
aa_eq(self.traj_tz2_ortho.xyz[::2], t0.xyz)
# stride
t0 = pt.iterload(fn, tn, stride=2)
aa_eq(self.traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, ignore frame_slice
t0 = pt.iterload(fn, tn, stride=2, frame_slice=(0, -1, 3))
aa_eq(self.traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, load two files
t0 = pt.iterload([fn, fn], tn, stride=2)
xyz_2 = np.vstack(
(self.traj_tz2_ortho.xyz[::2], self.traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, load two files, ignore frame_slice
t0 = pt.iterload([fn, fn],
tn,
stride=2,
frame_slice=[(0, -1, 5), (0, -1, 2)])
xyz_2 = np.vstack(
(self.traj_tz2_ortho.xyz[::2], self.traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, 4 trajs
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3)
# add frame_slice
t1 = pt.iterload(filenames, tn, frame_slice=[
(0, -1, 3),
] * 4)
xyz_expected = np.vstack(
[pt.iterload(fn, tn)[::3].xyz for fn in filenames])
aa_eq(xyz_expected, t0.xyz)
aa_eq(xyz_expected, t1.xyz)
# stride, 4 trajs, ignore frame_slice
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3, frame_slice=(0 - 1, 4))
xyz_expected = np.vstack(
[pt.iterload(fn, tn)[::3].xyz for fn in filenames])
aa_eq(xyz_expected, t0.xyz)