mdtraj.formats.XTCTrajectoryFile¶

class mdtraj.formats.XTCTrajectoryFile(filenamee, mode='r', force_overwrite=True, **kwargs)¶

Interface for reading and writing to a GROMACS XTC file. This is a file-like objec that supports both reading and writing. It also supports the context manager ptorocol, so you can use it with the python ‘with’ statement.

The conventional units in the XTC file are nanometers and picoseconds. The format only supports saving coordinates, the time, the md step, and the unit cell parametrs (box vectors)

Parameters

filenamestr: The filename to open. A path to a file on disk.
mode{‘r’, ‘w’}: The mode in which to open the file, either ‘r’ for read or ‘w’ for write.
force_overwritebool: If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

Other Parameters

min_chunk_sizeint, default=100: In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. This parameter is the minimum size of the buffer to allocate.
chunk_size_multiplierint, default=1.5: In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. We can guess this information based on the size of the file on disk, but it’s not perfect. This parameter inflates the guess by a multiplicative factor.

See also

mdtraj.load_xtc: High-level wrapper that returns a md.Trajectory

Examples

>>> # read the data from from an XTC file
>>> with XTCTrajectoryFile('traj.xtc') as f:
>>>    xyz, time, step, box = f.read()

>>> # write some random coordinates to an XTC file
>>> with XTCTrajectoryFile('output.xtc', 'w') as f:
>>>     f.write(np.random.randn(10,1,3))

Attributes

distance_unit
offsets: get byte offsets from current xtc file

Methods

`close`()	Close the XTC file handle
`read`([n_frames, stride, atom_indices])	Read data from an XTC 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[, time, step, box])	Write data to an XTC file

flush

__init__(self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(self, /, \args, \\*kwargs)	Initialize self.
`close`()	Close the XTC file handle
`flush`()
`read`([n_frames, stride, atom_indices])	Read data from an XTC 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[, time, step, box])	Write data to an XTC file

Attributes

`distance_unit`
`offsets`	get byte offsets from current xtc file

close()¶: Close the XTC file handle

offsets¶: get byte offsets from current xtc file

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

Read data from an XTC file

Parameters

n_framesint, None: The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded.
strideint, optional: Read only every stride-th frame.
atom_indicesarray_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

xyznp.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32: The cartesian coordinates, in nanometers
timenp.ndarray, shape=(n_frames), dtype=np.float32: The simulation time, in picoseconds, corresponding to each frame
stepnp.ndarray, shape=(n_frames), dtype=np.int32: The step in the simulation corresponding to each frame
boxnp.ndarray, shape=(n_frames, 3, 3), dtype=np.float32: The box vectors in each frame.
status: int: either _EXDROK or _EXDRENDOFFILE