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_gets_the_right_frames_with_stride_with_copy(self):
for stride in [2, 3, 5, 6, 10, 15]:
# Make sure we don't overshoot the number of available frames (100)
frames = randint(0, high=floor(100 / stride), size=self.n_frames)
traj_test = _frames_from_file(self.trajfiles,
self.pdbfile,
frames,
chunksize=self.chunksize,
stride=stride,
verbose=False,
copy_not_join=True)
traj_ref = md.load(self.trajfiles, top=self.pdbfile,
stride=stride)[frames]
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_test,
traj_ref,
atom=0,
mess=False)
self.assertFalse(found_diff, errmsg)
assert allclose(traj_test.time, traj_ref.time)
assert allclose(traj_test.unitcell_lengths,
traj_ref.unitcell_lengths)
assert allclose(traj_test.unitcell_angles,
traj_ref.unitcell_angles)
def test_reader_input_save_correct_frames_with_stride_in_memory(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])
traj = save_traj(self.reader,
sets,
None,
stride=stride,
verbose=False)
# 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,
traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
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_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_list_input_save_correct_frames_mem(self):
# Keep object in memory
traj = save_traj(self.trajfiles, self.sets, None, top=self.pdbfile)
# Check for diffs
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj,
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_with_fragmented_reader(self):
# intenionally group bpti dataset to a fake fragmented traj
frag_traj = [[self.trajfiles[0], self.trajfiles[1]], self.trajfiles[2]]
reader = coor.source(frag_traj, top=self.pdbfile)
traj = save_traj(reader, self.sets, None)
traj_ref = save_traj_w_md_load_frame(self.reader, self.sets)
# Check for diffs
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj,
traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
def test_gets_the_right_frames_no_stride_with_chunk(self):
traj_test = _frames_from_file(self.trajfiles,
self.pdbfile,
self.frames,
chunksize=self.chunksize,
verbose=False)
traj_ref = md.load(self.trajfiles, top=self.pdbfile)[self.frames]
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj_test,
traj_ref,
atom=0,
mess=False)
self.assertFalse(found_diff, errmsg)
def test_list_input_save_correct_frames_disk(self):
save_traj(self.trajfiles, self.sets, self.outfile, top=self.pdbfile)
# Reload the object to memory
traj = md.load(self.outfile, top=self.pdbfile)
# Check for diffs
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj,
self.traj_ref,
atom=0)
self.assertFalse(found_diff, errmsg)
def test_gets_the_right_frames_no_stride_no_chunk(self):
# I am calling this "no_chunk" because chunksize = int(1e3) will force frames_from_file to load one single chunk
traj_test = _frames_from_file(self.trajfiles,
self.pdbfile,
self.frames,
chunksize=int(1e3),
verbose=False)
traj_ref = md.load(self.trajfiles, top=self.pdbfile)[self.frames]
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj_test,
traj_ref,
atom=0,
mess=False)
self.assertFalse(found_diff, errmsg)
def test_with_fragmented_reader_chunksize_0(self):
# intentionally group bpti dataset to a fake fragmented traj
frag_traj = [[self.trajfiles[0], self.trajfiles[1]], self.trajfiles[2],
self.trajfiles[2]]
reader = coor.source(frag_traj, top=self.pdbfile, chunk_size=0)
assert reader.chunksize == 0
traj = save_traj(reader, self.sets, None)
traj_ref = save_traj_w_md_load_frame(self.reader, self.sets)
# Check for diffs
(found_diff, errmsg) = compare_coords_md_trajectory_objects(traj,
traj_ref,
atom=0)
np.testing.assert_equal(traj.xyz, traj_ref.xyz)
self.assertFalse(found_diff, errmsg)
def test_gets_the_right_frames_with_stride_no_chunk(self):
# I am calling this "no_chunk" because chunksize = int(1e3) will force frames_from_file to load one single chunk
for stride in [2, 5, 10]:
# Make sure we don't overshoot the number of available frames (100)
frames = randint(0, high=floor(100 / stride), size=self.n_frames)
traj_test = _frames_from_file(self.trajfiles,
self.pdbfile,
frames,
stride=stride,
verbose=False)
traj_ref = md.load(self.trajfiles, top=self.pdbfile,
stride=stride)[frames]
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_test,
traj_ref,
atom=0,
mess=False)
self.assertFalse(found_diff, errmsg)
def test_gets_the_right_frames_with_stride_with_chunk_mdTopology_input(
self):
for stride in [2, 3, 5, 6, 10, 15]:
# Make sure we don't overshoot the number of available frames (100)
frames = randint(0, high=floor(100 / stride), size=self.n_frames)
traj_test = _frames_from_file(self.trajfiles,
self.mdTrajectory.top,
frames,
chunksize=self.chunksize,
stride=stride,
verbose=False)
traj_ref = md.load(self.trajfiles, top=self.pdbfile,
stride=stride)[frames]
(found_diff,
errmsg) = compare_coords_md_trajectory_objects(traj_test,
traj_ref,
atom=0,
mess=False)
self.assertFalse(found_diff, errmsg)
