mdtraj.load_lh5

mdtraj.load_lh5(filename, top=None, stride=None, atom_indices=None, frame=None)[source]

Load an deprecated MSMBuilder2 LH5 trajectory file.

Parameters:
  • filename (path-like) – filename of AMBER NetCDF file.

  • top ({path-like, Trajectory, Topology}) – The NetCDF 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.

See also

mdtraj.LH5TrajectoryFile

Low level interface to LH5 files