mdtraj.formats.TRRTrajectoryFile¶

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

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

The conventional units in the TRR 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_multiplier, int, 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_trr: High-level wrapper that returns a md.Trajectory

Examples

>>> # load up the data from a trr
>>> with TRRTrajectoryFile('traj.trr') as f:
>>>    xyz, time, step, box, lambdas = f.read()

Attributes

distance_unit
offsets: get byte offsets from current xtc file

Methods

`close`()	Close the TRR file
`read`([n_frames, stride, atom_indices])	Read data from a TRR 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, lambd])	Write data to a TRR file

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

Methods

`__init__`(self, /, \args, \\*kwargs)	Initialize self.
`close`()	Close the TRR file
`read`([n_frames, stride, atom_indices])	Read data from a TRR 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, lambd])	Write data to a TRR file

Attributes

`distance_unit`
`offsets`	get byte offsets from current xtc file See Also ——– set_offsets

close()¶: Close the TRR file

offsets¶: get byte offsets from current xtc file See Also ——– set_offsets

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

Read data from a TRR 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.
lambdnp.ndarray, shape=(n_frames), dtype=np.float32: The alchemical lambda value of each frame.

Notes

The TRR format DOES support saving velocities and forces, but those fields are not read (or written) by the current implementation of this wrapper. However, this functionality is accessible in the internal TRRTrajectoryFile._read()/._write() methods.

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

Read a trajectory from an XTC file

Parameters

topologyTopology: The system topology
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

trajectoryTrajectory: A trajectory object containing the loaded portion of the file.