mdtraj.Trajectory.superpose¶

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

Superpose each conformation in this trajectory upon a reference

Parameters

referencemd.Trajectory: Align self to a particular frame in reference
frameint: The index of the conformation in reference to align to.
atom_indicesarray_like, or None: The indices of the atoms to superpose. If not supplied, all atoms will be used.
ref_atom_indicesarray_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.
parallelbool: Use OpenMP to run the superposition in parallel over multiple cores

Returns