mdtraj.Trajectory.superpose

Trajectory.superpose(self, 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
self