mdtraj.compute_directors¶

mdtraj.
compute_directors
(traj, indices='chains')¶ Compute the characteristic vector describing the orientation of each group
In this definition, the long molecular axis is found from the inertia tensor, \(I_{ab}\), and is taken to be the eigenvector associated with the smallest eigenvalue of \(I_{ab}\).
See [1] for brief summary and discussion on other methods to obtain the director.
 Parameters
 trajTrajectory
Trajectory to compute orientation of.
 indices{‘chains’, ‘residues’, list of lists}, optional, default=’chains’
The group to consider. Users can pass their own indices as a list of lists with the “shape” (n_compounds, len(each_compound)). Recognized string keywords are ‘chains’ and ‘residues’.
 Returns
 directorsnp.ndarray, shape=(traj.n_frames, len(indices), 3), dtype=float64
Characteristic vectors describing the trajectory for each frame.
Notes
Since there is no preferred orientation of the director, the director \(n\) has the same meaning as \(n\). Therefore, care should be taken to ensure the director is pointing in the direction you think it is, e.g., by contraining it to a hemisphere that makes physical sense.
References