mdtraj.load_xyz¶

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

Load a xyz trajectory file.

While there is no universal standard for this format, this plugin adheres to the same format as the VMD plugin:

Most notably, units are in angstroms and anything past the ‘z’ field is ignored.

Parameters

filenamepath-like: Path of xyz trajectory file.
top{str, Trajectory, Topology}: The xyz format does not contain topology information. Pass in either the path to a pdb file, a trajectory, or a topology to supply this information.
strideint, default=None: Only read every stride-th frame
atom_indicesarray_like, optional: If not none, then read only a subset of the atoms coordinates from the file.
frameint, 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.

Returns

trajectorymd.Trajectory: The resulting trajectory, as an md.Trajectory object.