def setUp(self):
self.eps = 1e-10
path = pkg_resources.resource_filename(__name__, 'data') + os.path.sep
self.pdbfile = os.path.join(path, 'bpti_ca.pdb')
self.trajfiles = [os.path.join(path, 'bpti_001-033.xtc'),
os.path.join(path, 'bpti_034-066.xtc'),
os.path.join(path, 'bpti_067-100.xtc')
]
# Create random sets of files and frames to be retrieved from trajfiles
n_members_set1 = 10
n_members_set2 = 20
set_1 = np.vstack((np.random.permutation([0, 2] * n_members_set1)[:n_members_set1],
np.random.randint(32, size=n_members_set1))).T
set_2 = np.vstack((np.random.permutation([0, 2] * n_members_set2)[:n_members_set2],
np.random.randint(32, size=n_members_set2))).T
self.sets = [set_1, set_2]
self.subdir = tempfile.mkdtemp(suffix='save_trajs_test/')
# Instantiate the reader
self.reader = coor.source(self.trajfiles, top=self.pdbfile)
self.reader.chunksize = 30
self.n_pass_files = [self.subdir + 'n_pass.set_%06u.xtc' % ii for ii in range(len(self.sets))]
self.one_pass_files = [self.subdir + '1_pass.set_%06u.xtc' % ii for ii in range(len(self.sets))]
self.traj_ref = save_traj_w_md_load_frame(self.reader, self.sets)
self.strides = [2, 3, 5]
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_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_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)
