def test_read_5():
with DCDTrajectoryFile(fn_dcd) as f:
xyz_ref, box_lengths_ref, box_angles_ref = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz, box_lengths, box_angles = f.read(atom_indices=[1, 2, 5])
yield lambda: eq(xyz_ref[:, [1, 2, 5], :], xyz)
def test_seek():
reference = DCDTrajectoryFile(get_fn('frame0.dcd')).read()[0]
with DCDTrajectoryFile(get_fn('frame0.dcd')) 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_read_6():
with DCDTrajectoryFile(fn_dcd) as f:
xyz_ref, box_lengths_ref, box_angles_ref = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz, box_lengths, box_angles = f.read(
atom_indices=slice(None, None, 2))
yield lambda: eq(xyz_ref[:, ::2, :], xyz)
def test_read_2():
"DCDReader: check nframes"
xyz1, box_lengths1, box_angles1 = DCDTrajectoryFile(fn_dcd).read()
xyz2, box_lengths2, box_angles2 = DCDTrajectoryFile(fn_dcd).read(10000)
yield lambda: eq(xyz1, xyz2)
yield lambda: eq(box_lengths1, box_lengths2)
yield lambda: eq(box_angles1, box_angles2)
def test_write_1():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
with DCDTrajectoryFile(temp, 'w') as f:
f.write(xyz)
with DCDTrajectoryFile(temp) as f:
xyz2 = f.read()[0]
eq(xyz, xyz2)
def test_write_0():
with DCDTrajectoryFile(fn_dcd) as f:
xyz = f.read()[0]
with DCDTrajectoryFile(temp, 'w') as f:
f.write(xyz)
with DCDTrajectoryFile(temp) as f:
xyz2 = f.read()[0]
eq(xyz, xyz2)
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_stride():
"Read dcd with stride"
with DCDTrajectoryFile(fn_dcd) as f:
xyz1, box_lengths1, box_angles1 = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz2, box_lengths2, box_angles2 = f.read(stride=2)
yield lambda: eq(xyz1[::2], xyz2)
yield lambda: eq(box_lengths1[::2], box_lengths2)
yield lambda: eq(box_angles1[::2], box_angles2)
def test_read_stride_2():
"Read dcd with stride when n_frames is supplied (different code path)"
with DCDTrajectoryFile(fn_dcd) as f:
xyz1, box_lengths1, box_angles1 = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz2, box_lengths2, box_angles2 = f.read(n_frames=1000, stride=2)
yield lambda: eq(xyz1[::2], xyz2)
yield lambda: eq(box_lengths1[::2], box_lengths2)
yield lambda: eq(box_angles1[::2], box_angles2)
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_3():
"checking"
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((600, 3), dtype=np.float32)
with DCDTrajectoryFile(temp, 'w') as f:
f.write(xyz, box_lengths)
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_tell():
with DCDTrajectoryFile(get_fn('frame0.dcd')) as f:
eq(f.tell(), 0)
f.read(101)
eq(f.tell(), 101)
f.read(3)
eq(f.tell(), 104)
def test_read_1():
with BINPOSTrajectoryFile(fn_binpos, chunk_size_multiplier=0.5) as f:
xyz = f.read()
with DCDTrajectoryFile(fn_dcd) as f:
xyz2 = f.read()[0]
xyz3 = io.loadh(get_fn('frame0.binpos.h5'), 'xyz')
yield lambda: eq(xyz[1:], xyz2)
yield lambda: eq(xyz, xyz3)
def test_ragged_1():
# try first writing no cell angles/lengths, and then adding some
xyz = np.random.randn(100, 5, 3)
cell_lengths = np.random.randn(100, 3)
cell_angles = np.random.randn(100, 3)
with DCDTrajectoryFile(temp, 'w', force_overwrite=True) as f:
f.write(xyz)
assert_raises(ValueError,
lambda: f.write(xyz, cell_lengths, cell_angles))
def test_ragged_2():
# try first writing no cell angles/lengths, and then adding some
xyz = np.random.randn(100, 5, 3)
time = np.random.randn(100)
cell_lengths = np.random.randn(100, 3)
cell_angles = np.random.randn(100, 3)
#from mdtraj.formats import HDF5TrajectoryFile
with DCDTrajectoryFile(temp, 'w', force_overwrite=True) as f:
f.write(xyz, cell_lengths, cell_angles)
assert_raises(ValueError, lambda: f.write(xyz))
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_do_overwrite():
with open(temp, 'w') as f:
f.write('a')
with DCDTrajectoryFile(temp, 'w', force_overwrite=False) as f:
f.write(np.random.randn(10, 5, 3))
def test_write_4():
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')
for i in range(len(xyz)):
f.write(xyz[i], box_lengths[i], box_angles[i])
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_write_closed():
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
def setUp(self):
super(TestDCDRead, self).setUp()
with DCDTrajectoryFile(self.fn, 'w') as f:
f.write(xyz=self.xyz)
def test(self):
"Test the read speed of the DCD code (10000 frames, 100 atoms)"
with DCDTrajectoryFile(self.fn) as f:
f.read()
def test_write_closed():
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10,3,3))
def test(self):
"Test the write speed of the DCD code (10000 frames, 100 atoms)"
with DCDTrajectoryFile(self.fn, 'w') as f:
f.write(xyz=self.xyz)
def test_read():
xyz, box_lengths, box_angles = DCDTrajectoryFile(fn_dcd).read()
xyz2 = io.loadh(get_fn('frame0.dcd.h5'), 'xyz')
eq(xyz, xyz2)