mdtraj.load_trr

mdtraj.load_trr(filename, top=None, stride=None, atom_indices=None, frame=None)

Load a Gromacs TRR file from disk.

The .trr format is a cross-platform compressed binary trajectory format produced by the gromacs software that stores atomic coordinates, box vectors, and time information.

Parameters:
  • filename (str) – Filename of TRR trajectory file.

  • top ({str, Trajectory, Topology}) – The TRR format does not contain topology information. Pass in either the path to a pdb file, a trajectory, or a topology to supply this information.

  • stride (int, default=None) – Only read every stride-th frame

  • atom_indices (array_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 requires an extra copy, but will save memory.

  • frame (int, optional) – Use this option to load only a single frame from a trajectory on disk. If frame is None, the default, the entire trajectory will be loaded. If supplied, stride will be ignored.

Examples

>>> import mdtraj as md                                        
>>> traj = md.load_trr('output.trr', top='topology.pdb')       
>>> print traj                                                 
<mdtraj.Trajectory with 500 frames, 423 atoms at 0x110740a90>  
Returns:

trajectory – The resulting trajectory, as an md.Trajectory object.

Return type:

md.Trajectory

See also

mdtraj.TRRTrajectoryFile

Low level interface to TRR files