def test_save_SaveTrajs_multipass(self):
# Without the "inmemory" option, i.e. multipass
__ = save_trajs(self.reader, self.sets, outfiles=self.n_pass_files)
sets_frag = []
for i in range(len(self.sets)):
sets_frag.append([])
for traj_ix, frame_ix in self.sets[i]:
sets_frag[-1].append([0, traj_ix * 33 + frame_ix])
save_trajs(self.frag_reader,
[np.array(sets_frag[0]),
np.array(sets_frag[1])],
outfiles=self.frag_pass_files)
# Reload the object to memory
traj_n_pass = single_traj_from_n_files(self.n_pass_files,
top=self.pdbfile)
traj_frag = single_traj_from_n_files(self.frag_pass_files,
top=self.pdbfile)
# Check for diffs
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_n_pass,
self.traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_frag,
self.traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
def test_save_SaveTrajs_IO(self):
# Test that we're saving to disk alright
flist = save_trajs(self.reader, self.sets, prefix=self.subdir)
exist = True
for f in flist:
exist = exist and os.stat(f)
self.assertTrue(exist, "Could not write to disk")
def test_save_SaveTrajs_multipass_with_stride(self):
# With the inmemory option = True
for stride in self.strides[:]:
# Since none of the trajfiles have more than 30 frames, the frames have to be re-drawn for every stride
sets = np.copy(self.sets)
sets[0][:, 1] = np.random.randint(0,
high=30 / stride,
size=np.shape(sets[0])[0])
sets[1][:, 1] = np.random.randint(0,
high=30 / stride,
size=np.shape(sets[1])[0])
__ = save_trajs(self.reader,
sets,
outfiles=self.one_pass_files,
inmemory=False,
stride=stride)
traj_1_pass = single_traj_from_n_files(self.one_pass_files,
top=self.pdbfile)
# Also the reference has to be re-drawn using the stride. For this, we use the re-scale the strided
# frame-indexes to the unstrided value
sets[0][:, 1] *= stride
sets[1][:, 1] *= stride
traj_ref = save_traj_w_md_load_frame(self.reader, sets)
# Check for diffs
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_1_pass,
traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
def test_save_SaveDtrajs_IO(self):
# Test that we're saving to disk alright
flist = save_trajs(self.reader, self.sets, prefix=self.subdir)
exist = True
for f in flist:
exist = exist and os.stat(f)
self.assertTrue(exist, "Could not write to disk")
def test_save_SaveDtrajs_precision(self):
# Test without the "inmemory" option
__ = save_trajs(self.reader, self.sets,
outfiles=self.n_pass_files)
# Test with the inmemory option = True
__ = save_trajs(self.reader, self.sets,
outfiles=self.one_pass_files, inmemory=True)
# Reload the objects to memory
traj_n_pass = single_traj_from_n_files(self.n_pass_files, top=self.pdbfile)
traj_1_pass = single_traj_from_n_files(self.one_pass_files, top=self.pdbfile)
R = np.zeros((2, traj_1_pass.n_frames, 3))
atom_index = 0
# Artificially mess the the coordinates
# traj_1_pass.xyz [0, atom_index, 2] +=1e-5
for ii, traj in enumerate([traj_n_pass, traj_1_pass]):
R[ii, :] = traj.xyz[:, atom_index]
# Compare the R-trajectories among themselves
found_diff = False
first_diff = None
errmsg = ''
for ii, iR in enumerate(R):
# Norm of the difference vector
norm_diff = np.sqrt(((iR - R) ** 2).sum(2))
# Any differences?
if (norm_diff > self.eps).any():
first_diff = np.argwhere(norm_diff > self.eps)[0]
found_diff = True
errmsg = "Delta R_%u at frame %u: [%2.1e, %2.1e]" % (atom_index, first_diff[1],
norm_diff[0, first_diff[1]],
norm_diff[1, first_diff[1]])
errmsg2 = "\nThe position of atom %u differs by > %2.1e for the same frame between trajectories" % (
atom_index, self.eps)
errmsg += errmsg2
break
self.assertFalse(found_diff, errmsg)
def test_save_SaveTrajs_onepass(self):
# With the inmemory option = True
__ = save_trajs(self.reader, self.sets,
outfiles=self.one_pass_files, inmemory=True)
traj_1_pass = single_traj_from_n_files(self.one_pass_files, top=self.pdbfile)
# Check for diffs
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj_1_pass, self.traj_ref, atom=0)
self.assertFalse(found_diff, errmsg)
def test_save_SaveTrajs_multipass(self):
# Without the "inmemory" option, i.e. multipass
__ = save_trajs(self.reader, self.sets,
outfiles=self.n_pass_files)
# Reload the object to memory
traj_n_pass = single_traj_from_n_files(self.n_pass_files, top=self.pdbfile)
# Check for diffs
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj_n_pass, self.traj_ref, atom=0)
self.assertFalse(found_diff, errmsg)
def test_out_of_bound_indexes(self):
# assert ValueError with index info is raised for faulty input
self.sets[0][:,1] *= 100000
with self.assertRaises(ValueError) as raised:
save_trajs(self.reader, self.sets, outfiles=self.one_pass_files)
