mdtraj.Trajectory.superpose

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

Superpose each conformation in this trajectory upon a reference

Parameters:
  • 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

Return type:

self