def test_seek():
reference = XTCTrajectoryFile(get_fn('frame0.xtc')).read()[0]
with XTCTrajectoryFile(get_fn('frame0.xtc')) as f:
eq(f.tell(), 0)
eq(f.read(1)[0][0], reference[0])
eq(f.tell(), 1)
xyz = f.read(1)[0][0]
eq(xyz, reference[1])
eq(f.tell(), 2)
f.seek(0)
eq(f.tell(), 0)
xyz = f.read(1)[0][0]
eq(f.tell(), 1)
eq(xyz, reference[0])
f.seek(5)
eq(f.read(1)[0][0], reference[5])
eq(f.tell(), 6)
f.seek(-5, 1)
eq(f.tell(), 1)
eq(f.read(1)[0][0], reference[1])
def test_xtc_write_wierd_0():
x0 = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)
x1 = np.asarray(np.random.randn(100, 9, 3), dtype=np.float32)
with XTCTrajectoryFile(temp, 'w') as f:
f.write(x0)
f.write(x1)
xr = XTCTrajectoryFile(temp).read()[0]
print(xr.shape)
def test_write_0():
with XTCTrajectoryFile(fn_xtc) as f:
xyz = f.read()[0]
f = XTCTrajectoryFile(temp, 'w')
f.write(xyz)
f.close()
with XTCTrajectoryFile(temp) as f:
xyz2, time2, step2, box2 = f.read()
eq(xyz, xyz2)
def test_write_1():
xyz = np.asarray(np.around(np.random.randn(100, 10, 3), 3),
dtype=np.float32)
time = np.asarray(np.random.randn(100), dtype=np.float32)
step = np.arange(100)
box = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)
with XTCTrajectoryFile(temp, 'w') as f:
f.write(xyz, time=time, step=step, box=box)
with XTCTrajectoryFile(temp) as f:
xyz2, time2, step2, box2 = f.read()
eq(xyz, xyz2)
eq(time, time2)
eq(step, step2)
eq(box, box2)
def test_read_atomindices_2():
iofile = io.loadh(get_fn('frame0.xtc.h5'), deferred=False)
with XTCTrajectoryFile(fn_xtc) as f:
xyz, time, step, box = f.read(atom_indices=slice(None, None, 2))
yield lambda: eq(xyz, iofile['xyz'][:, ::2])
yield lambda: eq(step, iofile['step'])
yield lambda: eq(box, iofile['box'])
yield lambda: eq(time, iofile['time'])
def test_read_chunk1():
with XTCTrajectoryFile(fn_xtc, 'r', chunk_size_multiplier=0.5) as f:
xyz, time, step, box = f.read()
iofile = io.loadh(get_fn('frame0.xtc.h5'), deferred=False)
yield lambda: eq(xyz, iofile['xyz'])
yield lambda: eq(step, iofile['step'])
yield lambda: eq(box, iofile['box'])
yield lambda: eq(time, iofile['time'])
def test_ragged_1():
# try first writing no box vectors,, and then adding some
xyz = np.random.randn(100, 5, 3)
time = np.random.randn(100)
box = np.random.randn(100, 3, 3)
with XTCTrajectoryFile(temp, 'w', force_overwrite=True) as f:
f.write(xyz)
assert_raises(ValueError, lambda: f.write(xyz, time, box))
def test_tell():
with XTCTrajectoryFile(get_fn('frame0.xtc')) as f:
eq(f.tell(), 0)
f.read(101)
eq(f.tell(), 101)
f.read(3)
eq(f.tell(), 104)
def test_read_stride_2():
"read xtc with stride with n_frames"
iofile = io.loadh(get_fn('frame0.xtc.h5'), deferred=False)
with XTCTrajectoryFile(fn_xtc) as f:
xyz, time, step, box = f.read(n_frames=1000, stride=3)
yield lambda: eq(xyz, iofile['xyz'][::3])
yield lambda: eq(step, iofile['step'][::3])
yield lambda: eq(box, iofile['box'][::3])
yield lambda: eq(time, iofile['time'][::3])
def test_ragged_2():
# try first writing no box vectors, and then adding some
xyz = np.random.randn(100, 5, 3)
time = np.random.randn(100)
box = np.random.randn(100, 3, 3)
#from mdtraj.formats import HDF5TrajectoryFile
with XTCTrajectoryFile(temp, 'w', force_overwrite=True) as f:
f.write(xyz, time=time, box=box)
assert_raises(ValueError, lambda: f.write(xyz))
def test_write_0():
with XTCTrajectoryFile(fn_xtc) as f:
xyz = f.read()[0]
f = XTCTrajectoryFile(temp, 'w')
f.write(xyz)
f.close()
with XTCTrajectoryFile(temp) as f:
xyz2, time2, step2, box2 = f.read()
eq(xyz, xyz2)
def setUp(self):
super(TestXTCRead, self).setUp()
with XTCTrajectoryFile(self.fn, 'w') as f:
f.write(xyz=self.xyz)
def test_read_error_1():
XTCTrajectoryFile('/tmp/sdfsdfsdf')
def test_read_error_0():
xyz = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)
with XTCTrajectoryFile(temp, 'w') as f:
f.read(xyz)
def test_write_error_0():
xyz = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)
with XTCTrajectoryFile(temp, 'r') as f:
f.write(xyz)
def test(self):
"Test the read speed of the XTC code (10000 frames, 100 atoms)"
with XTCTrajectoryFile(self.fn) as f:
f.read()
def test_read_error_2():
XTCTrajectoryFile(get_fn('frame0.dcd')).read()
def test(self):
"Test the write speed of the XTC code (10000 frames, 100 atoms)"
with XTCTrajectoryFile(self.fn, 'w') as f:
f.write(xyz=self.xyz)