def test_trajs_larger_than_frame_index(self):
""" file list is larger than largest traj file """
from pyemma.coordinates.tests.util import create_traj, get_top
files = [create_traj(length=10)[0] for _ in range(20)]
inds = np.vstack((np.arange(20), np.arange(20))).T
with self.assertRaises(ValueError) as cm:
_frames_from_file(files, top=get_top(), frames=inds)
import re
matches = re.match(".*10\).*is larger than trajectory length.*\= 10",
cm.exception.args[0])
assert matches
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_pass_reader(self):
from pyemma.coordinates import source
reader = source(self.trajfiles, top=self.pdbfile)
reader.in_memory = True
inds = np.vstack((np.random.randint(0, 1), np.random.randint(0,
100))).T
traj_test = _frames_from_file(reader.filenames,
self.pdbfile,
inds,
reader=reader)
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_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_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)
def test_returns_trajectory(self):
assert isinstance(
_frames_from_file(self.trajfiles, self.pdbfile, self.frames),
md.Trajectory)
