mdtraj.formats.DCDTrajectoryFile

class mdtraj.formats.DCDTrajectoryFile

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:

filename : string

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_overwrite : bool

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
>>> xyzf.read()            # read all of the remaining frames
>>> f.close()
>>> # read all of the data with automatic closing of the file
>>> with DCDTrajectoryFile('mytrajectory.dcd') 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))
__init__()

x.__init__(...) initializes x; see help(type(x)) for signature

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

Attributes

distance_unit
close()

Close the DCD file handle

read(n_frames=None, stride=None, atom_indices=None)

Read the data from a DCD file

Parameters:

n_frames : int, optional

If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file.

stride : np.ndarray, optional

Read only every stride-th frame.

atom_indices : array_like, optional

If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.

Returns:

xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=float32

The xyz coordinates of each atom in each frame. By convention, the coordinates in the dcd file are stored in units of angstroms.

cell_lengths : np.ndarray, shape=(n_frames, 3), dtype=float32

The length of the box in each frame. cell_lengths[i,0] is the length of the A axis (in frame i), and cell_lengths[i,1] and cell_lengths[i,2] are the B and C axis respectively. By convention, the cell lengths in the dcd file are stored in units of angstroms.

cell_angles : np.ndarray, shape=(n_frames, 3), dtype=float32

Organized analogously to cell_lengths. Gives the alpha, beta and gamma angles respectively in entries cell_angles[i,0], cell_angles[i,1], cell_angles[i,2]. By convention, the cell angles in the dcd file are stored in units of degrees.

read_as_traj(topology, n_frames=None, stride=None, atom_indices=None)

Read a trajectory from an XTC file

Parameters:

topology : Topology

The system topology

n_frames : int, optional

If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file.

stride : np.ndarray, optional

Read only every stride-th frame.

atom_indices : array_like, optional

If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.

Returns:

trajectory : Trajectory

A trajectory object containing the loaded portion of the file.

seek(offset, whence=0)

Move to a new file position

Parameters:

offset : int

A number of frames.

whence : {0, 1, 2}

0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported

tell()

Current file position

Returns:

offset : int

The current frame in the file.

write(xyz, cell_lengths=None, cell_angles=None)

Write one or more frames of data to the DCD file

Parameters:

xyz : np.ndarray, shape=(n_frames, n_atoms, 3)

The cartesian coordinates of the atoms to write. By convention for this trajectory format, the lengths should be in units of angstroms.

cell_lengths : np.ndarray, shape=(n_frames, 3), dtype=float32, optional

The length of the periodic box in each frame, in each direction, a, b, c. By convention for this trajectory format, the lengths should be in units of angstroms.

cell_angles : np.ndarray, shape=(n_frames, 3), dtype=float32, optional

Organized analogously to cell_lengths. Gives the alpha, beta and gamma angles respectively. By convention for this trajectory format, the angles should be in units of degrees.

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