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
filenamestr

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.

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.

See also

mdtraj.XYZTrajectoryFile

Low level interface to xyz files