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