helixmc.util.ribbon_twist¶

helixmc.util.ribbon_twist(dr, rb_vec, return_val_only=True, twist_center=0.0)¶

Compute the ribbon-twist (supercoiling twist) of a helix.

Parameters:

dr : ndarray, shape (N,3)

Input delta_r vectors (dr[i] = r[i+1] - r[i]).

rb_vec : ndarray, shape (N+1,3)

The ribbon vectors for the helix, equals to frame[:,:,1] in the current setting. Must be normalized vectors.

return_val_only : bool, optional

If True, return one float value for the overall twist of the system. Otherwise return the individual twists for each bp-step. Default set to True.

twist_center : float, optional

Fold the step twists to (center - pi, center + pi], default to 0.

Returns:

twist : float or ndarray of shape (N)

The overall twist or the individual twists of the helix. See the ‘return_val_only’ parameter above.

Raises:

ValueError

If dr.shape[0] != rb_vec.shape[0] + 1.