def test_comprehensive(self):
traj = pt.iterload("data/Test_RemdTraj/rem.nc.000",
"data/Test_RemdTraj/ala2.99sb.mbondi2.parm7")
# temperature
aa_eq(traj.temperatures, [300., 630.5, 630.5, 630.5, 630.5, 630.5,
630.5, 630.5, 492.2, 384.3])
# iterframe (already in doctest), just throwing raise to increase coverage score
self.assertRaises(ValueError, lambda: traj.iterframe(rmsfit='crazy'))
# raise
# memory error if load larger than 1GB for xyz
traj = pt.datafiles.load_tz2_ortho()
for _ in range(11):
traj._load(traj.filelist)
self.assertRaises(MemoryError, lambda: traj.xyz)
# can not find filename
self.assertRaises(ValueError, lambda: traj._load(None))
# has filename but does not have Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=None))
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000"))
# empty Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=pt.Topology()))
# weird Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=pt.Frame))
def test_traj_topology(self):
traj = pt.TrajectoryIterator()
assert traj.top.is_empty() == True
traj.top = pt.load_topology(fn('Tc5b.top'))
assert traj.top.is_empty() == False
traj._load(fn('Tc5b.x'))
# use toplogy
traj = pt.TrajectoryIterator()
assert traj.topology.is_empty() == True
traj.topology = pt.load_topology(fn('Tc5b.top'))
assert traj.topology.is_empty() == False
traj._load(fn('Tc5b.x'))
def test_traj_topology(self):
traj = pt.TrajectoryIterator()
assert traj.top.is_empty() == True
traj.top = pt.load_topology("./data/Tc5b.top")
assert traj.top.is_empty() == False
traj._load("./data/Tc5b.x")
# use toplogy
traj = pt.TrajectoryIterator()
assert traj.topology.is_empty() == True
traj.topology = pt.load_topology("./data/Tc5b.top")
assert traj.topology.is_empty() == False
traj._load("./data/Tc5b.x")
def test_indexing(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = pt.TrajectoryIterator()
traj2.top = pt.load_topology(fn('Tc5b.top'))
traj2._load(fn('Tc5b.x'))
farray = traj2[[0, 9, 1]]
assert farray.n_frames == 3
assert traj2[0].atom(0) == farray[0].atom(0)
assert traj2[9].atom(0) == farray[1].atom(0)
assert traj2[1].atom(0) == farray[2].atom(0)
arr = np.asarray(traj2[0]._buffer1d[:])
frame0 = traj2[0]
arr0 = np.asarray(frame0._buffer1d[:])
mat0 = np.asmatrix(arr0).reshape(304, 3)
mat0[:, 0] = np.asmatrix(list(range(304))).reshape(304, 1)
assert frame0[0, 0] == 0.
assert frame0[1, 0] == 1.
assert frame0[2, 0] == 2.
# raise if size = 0
traj3 = pt.Trajectory()
assert traj3.n_frames == 0, 'empty Trajectory, n_frames must be 0'
self.assertRaises(IndexError, lambda: traj3[0])
self.assertRaises(IndexError, lambda: traj3.__setitem__(0, traj[3]))
def test_comprehensive(self):
traj = pt.iterload(fn('Test_RemdTraj/rem.nc.000'),
fn('Test_RemdTraj/ala2.99sb.mbondi2.parm7'))
# temperature
aa_eq(traj.temperatures, [
300., 630.5, 630.5, 630.5, 630.5, 630.5, 630.5, 630.5, 492.2, 384.3
])
# iterframe (already in doctest), just throwing raise to increase coverage score
self.assertRaises(ValueError, lambda: traj.iterframe(rmsfit='crazy'))
# raise
# memory error if load larger than 1GB for xyz
traj = pt.datafiles.load_tz2_ortho()
for _ in range(2):
traj._load(traj.filelist)
with patch('pytraj.trajectory.trajectory_iterator.TrajectoryIterator._estimated_GB') as \
mem:
def mock_get(*args, **kwargs):
return 10000000
mem.__get__ = mock_get
self.assertRaises(MemoryError, lambda: traj.xyz)
# can not find filename
self.assertRaises(ValueError, lambda: traj._load(None))
# has filename but does not have Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=None))
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000')))
# empty Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=pt.Topology()))
# weird Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=pt.Frame))
def test_iter_basic(self):
traj = pt.TrajectoryIterator()
traj.top = pt.load_topology(fn('Tc5b.top'))
traj._load(fn('Tc5b.x'))
for frame in traj:
pass
def test_iter_basic(self):
traj = pt.TrajectoryIterator()
traj.top = pt.load_topology("./data/Tc5b.top")
traj._load("./data/Tc5b.x")
for frame in traj:
pass
