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