def test_read_4():
"DCDReader: check streaming read followed by reading the 'rest'"
xyz_ref, box_lengths_ref, box_angles_ref = DCDTrajectoryFile(fn_dcd).read()
reader = DCDTrajectoryFile(fn_dcd)
for i in range(int(len(xyz_ref)/2)):
xyz, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
xyz_rest, box_rest, angles_rest = reader.read()
yield lambda: eq(xyz_ref[i+1:], xyz_rest)
yield lambda: eq(box_lengths_ref[i+1:], box_rest)
yield lambda: eq(box_angles_ref[i+1:], angles_rest)
yield lambda: len(xyz_ref) == i + len(xyz_rest)
def test_read_4():
"DCDReader: check streaming read followed by reading the 'rest'"
xyz_ref, box_lengths_ref, box_angles_ref = DCDTrajectoryFile(fn_dcd).read()
reader = DCDTrajectoryFile(fn_dcd)
for i in range(int(len(xyz_ref) / 2)):
xyz, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
xyz_rest, box_rest, angles_rest = reader.read()
yield lambda: eq(xyz_ref[i + 1:], xyz_rest)
yield lambda: eq(box_lengths_ref[i + 1:], box_rest)
yield lambda: eq(box_angles_ref[i + 1:], angles_rest)
yield lambda: len(xyz_ref) == i + len(xyz_rest)
def test_read_3():
"DCDReader: check streaming read of frames 1 at a time"
xyz_ref, box_lengths_ref, box_angles_ref = DCDTrajectoryFile(fn_dcd).read()
reader = DCDTrajectoryFile(fn_dcd)
for i in range(len(xyz_ref)):
xyz, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
def test_read_3():
"DCDReader: check streaming read of frames 1 at a time"
xyz_ref, box_lengths_ref, box_angles_ref = DCDTrajectoryFile(fn_dcd).read()
reader = DCDTrajectoryFile(fn_dcd)
for i in range(len(xyz_ref)):
xyz, box_lenths, box_angles = reader.read(1)
eq(xyz_ref[np.newaxis, i], xyz)
eq(box_lengths_ref[np.newaxis, i], box_lenths)
eq(box_angles_ref[np.newaxis, i], box_angles)
def test_write_2():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0,0] = 10.0
f = DCDTrajectoryFile(temp, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(temp)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
yield lambda: eq(xyz, xyz2)
yield lambda: eq(box_lengths, box_lengths2)
yield lambda: eq(box_angles, box_angles2)
def test_write_2():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0, 0] = 10.0
f = DCDTrajectoryFile(temp, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(temp)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
yield lambda: eq(xyz, xyz2)
yield lambda: eq(box_lengths, box_lengths2)
yield lambda: eq(box_angles, box_angles2)
def test_read_closed():
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()
def test_read_closed():
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()