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__(*args, **kwargs)

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

Methods

__init__(*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