mdtraj.formats.DCDTrajectoryFile

class mdtraj.formats.DCDTrajectoryFile(filename, mode='r', force_overwrite=True)

Interface for reading and writing to a CHARMM/NAMD DCD file. This is a file-like object, that both reading or writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.

The conventional units in the DCD file are angstroms and degrees. The format supports saving coordinates and unit cell parameters (lengths and angles)

Parameters

filenamestring

Path to the file to open

mode{‘r’, ‘w’}

Mode in which to open the file. ‘r’ is for reading, and ‘w’ is for writing.

force_overwritebool

In mode=’w’, how do you want to behave if a file by the name of filename already exists? if force_overwrite=True, it will be overwritten.

See also

mdtraj.load_dcd

High-level wrapper that returns a md.Trajectory

Examples

>>> # read a single frame, and then read the remaining frames
>>> f = DCDTrajectoryFile('mytrajectory.dcd', 'r')
>>> f.read(n_frames=1)  # read a single frame from the file
>>> xyz.read()            # read all of the remaining frames
>>> f.close()

>>> # read all of the data with automatic closing of the file
>>> with DCDTrajectoryFile('mytrajectory.dcd', 'r') as f:
>>>    xyz, cell_lengths, cell_angles = f.read()

>>> # write some xyz coordinates to a new file
>>> with DCDTrajectoryFile('mytrajectory2.dcd', 'w') as f:
>>>     f.write(np.random.randn(10,3,3))

>>> # write frames one at a time
>>> with DCDTrajectoryFile('mytrajectory2.dcd', 'w') as f:
>>>     n_frames, n_atoms = 5, 10
>>>     for i in range(n_frames):
>>>         f.write(np.random.randn(n_atoms, 3))

Attributes

distance_unit

Methods

close	Close the DCD file handle
read([n_frames, stride, atom_indices])	Read the data from a DCD file
read_as_traj(topology[, n_frames, stride, …])	Read a trajectory from an XTC file
seek(offset[, whence])	Move to a new file position
tell	Current file position
write(xyz[, cell_lengths, cell_angles])	Write one or more frames of data to the DCD file

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(*args, **kwargs)	Initialize self.
close	Close the DCD file handle
read([n_frames, stride, atom_indices])	Read the data from a DCD file
read_as_traj(topology[, n_frames, stride, …])	Read a trajectory from an XTC file
seek(offset[, whence])	Move to a new file position
tell	Current file position
write(xyz[, cell_lengths, cell_angles])	Write one or more frames of data to the DCD file

Attributes

distance_unit