Trajectory.superpose(reference, frame=0, atom_indices=None, ref_atom_indices=None, parallel=True)

Superpose each conformation in this trajectory upon a reference


reference : md.Trajectory

Align self to a particular frame in reference

frame : int

The index of the conformation in reference to align to.

atom_indices : array_like, or None

The indices of the atoms to superpose. If not supplied, all atoms will be used.

ref_atom_indices : array_like, or None

Use these atoms on the reference structure. If not supplied, the same atom indices will be used for this trajectory and the reference one.

parallel : bool

Use OpenMP to run the superposition in parallel over multiple cores