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:

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

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

Parameters:

filename : str

String filename 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.

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.

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.

Returns:

trajectory : md.Trajectory

The resulting trajectory, as an md.Trajectory object.