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_write_2(tmpdir):
fn = '{}/x.dcd'.format(tmpdir)
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(fn, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(fn)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
assert eq(xyz, xyz2)
assert eq(box_lengths, box_lengths2)
assert eq(box_angles, box_angles2)
def test_write_2(tmpdir):
fn = '{}/x.dcd'.format(tmpdir)
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(fn, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(fn)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
assert eq(xyz, xyz2)
assert eq(box_lengths, box_lengths2)
assert eq(box_angles, box_angles2)
def test_write_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
def test_write_closed():
f = DCDTrajectoryFile(fn_dcd, "w")
f.close()
f.write(np.random.randn(10, 3, 3))
def test_write_closed():
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
class Dcd(TrjHandler):
'''
Read and write cell and positions from/to DCD file.
Velocities, step and time are ignored.
Currently mstools use mdtraj to support DCD file.
Therefore, appending is not supported.
'''
def __init__(self, file, mode='r'):
super().__init__()
try:
from mdtraj.formats import DCDTrajectoryFile
except:
raise ImportError('Currently mstools use mdtraj to parse DCD format. Cannot import mdtraj')
if mode == 'r':
self._dcd = DCDTrajectoryFile(file, mode='r')
elif mode == 'w':
self._dcd = DCDTrajectoryFile(file, mode='w')
else:
raise Exception('Appending not supported for DCD')
def close(self):
try:
self._dcd.close()
except:
pass
def get_info(self):
self.n_frame = len(self._dcd)
if self.n_frame == 0:
raise Exception('Empty DCD file')
positions, lengths, angles = self._dcd.read(1)
_, self.n_atom, _ = positions.shape
return self.n_atom, self.n_frame
def read_frame(self, i_frame, frame):
self._dcd.seek(i_frame)
positions, box_lengths, box_angles = self._dcd.read(1)
angle = box_angles[0]
angle[np.abs(angle - 90) < 1E-4] = 90 # in case precision issue
frame.positions = positions[0] / 10 # convert A to nm
frame.cell.set_box([box_lengths[0] / 10, angle]) # convert A to nm
def write_frame(self, frame, subset=None, **kwargs):
'''
Write a frame into the opened DCD file
Parameters
----------
frame : Frame
subset : list of int, optional
kwargs : dict
Ignored
'''
if subset is None:
positions = frame.positions
else:
positions = frame.positions[subset]
self._dcd.write(positions * 10, frame.cell.lengths * 10, frame.cell.angles) # convert nm to A
def test_write_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
