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
