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: | filename : str
mode : {‘r’, ‘w’}
force_overwrite : bool
|
---|---|
Other Parameters: | |
min_chunk_size : int, default=100
chunk_size_multiplier, int, default=1.5
|
See also
Examples
>>> # load up the data from a trr
>>> with XTCTrajectoryFile('traj.trr') as f:
>>> xyz, time, step, box, lambdas = f.read()
x.__init__(...) initializes x; see help(type(x)) for signature
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 |
Attributes
distance_unit | |
offsets | get byte offsets from current xtc file |
Close the TRR file
get byte offsets from current xtc file See Also ——– set_offsets
Read data from a TRR file
Parameters: | n_frames : int, None
stride : int, optional
atom_indices : array_like, optional
|
---|---|
Returns: | xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32
time : np.ndarray, shape=(n_frames), dtype=np.float32
step : np.ndarray, shape=(n_frames), dtype=np.int32
box : np.ndarray, shape=(n_frames, 3, 3), dtype=np.float32
lambd : np.ndarray, shape=(n_frames), dtype=np.float32
|
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.
Read a trajectory from an XTC file
Parameters: | topology : Topology
n_frames : int, None
stride : int, optional
atom_indices : array_like, optional
|
---|---|
Returns: | trajectory : Trajectory
|
See also
Move to a new file position
Parameters: | offset : int
whence : {0, 1, 2}
|
---|
Current file position
Returns: | offset : int
|
---|
Write data to a TRR file
Parameters: | xyz : np.ndarray, dtype=np.float32, shape=(n_frames, n_atoms, 3)
time : np.ndarray, dtype=float32, shape=(n_frames), optional
step : np.ndarray, dtype=int32, shape=(n_frames), optional
box : np.ndarray, dtype=float32, shape=(n_frames, 3, 3), optional
lambd : np.ndarray, dtype=np.float32, shape=(n_frames), optional
|
---|