def test_invalid_readers_in_frag_traj(self):
data = [np.array([[[1, 2], [3, 4]], [0, 1]])]
from pyemma.coordinates.data.fragmented_trajectory_reader import FragmentedTrajectoryReader
reader = FragmentedTrajectoryReader(data)
with self.assertRaises(ValueError) as cm:
save_traj(reader, self.sets, None)
self.assertIn("FeatureReader", cm.exception.args[0])
def test_invalid_maximum_traj_index(self):
frag_traj = [[self.trajfiles[0], self.trajfiles[1]], self.trajfiles[2],
self.trajfiles[2]]
set = [[0, 2], [0, 1], [2, 42]]
from pyemma.coordinates.data.fragmented_trajectory_reader import FragmentedTrajectoryReader
reader = FragmentedTrajectoryReader(frag_traj,
topologyfile=self.pdbfile)
with self.assertRaises(ValueError) as cm:
save_traj(reader, set, None)
self.assertIn("larger than", cm.exception.args[0])
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_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_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_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)
def test_with_fragmented_reader(self):
from pyemma.util.files import TemporaryDirectory
trajlen = 35
# trajectory 0 (first trajectory, is trajfiles[2])
# -> skipped
# trajectory 1 (second trajectory, is {trajfiles[0], trajfiles[1]})
# fragment 1:
# -> frames 0,1,2,10
# fragment 2:
# -> frames 1 (i.e., 36) and 34 (i.e., 69)
# trajectory 2 (third trajectory, is trajfiles[2])
# -> frame 5
ra_indices = np.array([[1, 0], [1, 1], [1, 2], [1, 10],
[1, trajlen + 1], [1, 2 * trajlen - 1], [2, 5]],
dtype=int)
with TemporaryDirectory() as td:
trajfiles = []
xyzs = []
for i in range(3):
tf, xyz, _ = create_traj(start=i * 10, dir=td, length=trajlen)
trajfiles.append(tf)
xyzs.append(xyz)
topfile = get_top()
frag_traj = [
trajfiles[2], [trajfiles[0], trajfiles[1]], trajfiles[2]
]
expected = xyzs[0][np.array([0, 1, 2, 10]), :], xyzs[1][np.array(
[1, 34])], np.array([(xyzs[2][5, :])])
expected = np.vstack(expected)
reader = coor.source(frag_traj, top=topfile)
for cs in range(1, 10):
traj = save_traj(reader, ra_indices, None, chunksize=cs)
np.testing.assert_almost_equal(traj.xyz, expected)
def test_list_input_save_IO(self):
# Test that we're saving to disk alright
save_traj(self.trajfiles, self.sets, self.outfile, top=self.pdbfile)
exist = os.stat(self.outfile)
self.assertTrue(exist, "Could not write to disk")
def test_reader_input_returns_trajectory(self):
self.assertTrue(
isinstance(save_traj(self.reader, self.sets, None), md.Trajectory))
def test_reader_input_save_IO(self):
# Test that we're saving to disk alright
save_traj(self.reader, self.sets, self.outfile)
exist = os.stat(self.outfile)
self.assertTrue(exist, "Could not write to disk")
def test_list_input_returns_trajectory(self):
self.assertTrue(
isinstance(
save_traj(self.trajfiles, self.sets, None, top=self.pdbfile),
md.Trajectory))
def test_reader_input_returns_trajectory_w_image_molecules(self):
self.assertTrue(
isinstance(
save_traj(self.reader, self.sets, None, image_molecules=True),
md.Trajectory))