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