helixmc.util.writhe_exact

helixmc.util.writhe_exact(dr)

Compute the writhe of the helix using the exact Gauss double integral. O(N^2) complexity.

Parameters:

dr : ndarray, shape (N,3)

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

Returns:

writhe : float

The overall writhe of the helix.

See also

writhe_fuller

Compute the writhe of the helix using the Fuller approximated single integral.

ribbon_twist

Compute the ribbon-twist of a helix.

Notes

Details of the evaluation scheme is dicussed in reference [1] [2].

References

[1]	Rossetto V, Maggs AC (2003) Writhing geometry of open DNA. J. Chem. Phys. 118: 9864-9874.

[2]	Klenin K, Langowski J (2000) Computation of writhe in modeling of supercoiled DNA. Biopolymers 54: 307-317.