mythos.energy.dna2.interactions

DNA2 interactions.

These functions are based on the oxDNA2 model paper found here: https://arxiv.org/abs/1504.00821

Functions

`debye`(→ mythos.utils.types.ARR_OR_SCALAR)	Debye-huckel potential.
`coaxial_stacking`(→ mythos.utils.types.Scalar)	Coaxial stacking energy.

Module Contents

mythos.energy.dna2.interactions.debye(r: mythos.utils.types.ARR_OR_SCALAR, kappa: mythos.utils.types.Scalar, prefactor: mythos.utils.types.Scalar, smoothing_coeff: mythos.utils.types.Scalar, r_cut: mythos.utils.types.Scalar, r_high: mythos.utils.types.Scalar) → mythos.utils.types.ARR_OR_SCALAR[source]: Debye-huckel potential.

mythos.energy.dna2.interactions.coaxial_stacking(dr_stack: mythos.utils.types.ARR_OR_SCALAR, theta4: mythos.utils.types.ARR_OR_SCALAR, theta1: mythos.utils.types.ARR_OR_SCALAR, theta5: mythos.utils.types.ARR_OR_SCALAR, theta6: mythos.utils.types.ARR_OR_SCALAR, dr_low_coax: mythos.utils.types.Scalar, dr_high_coax: mythos.utils.types.Scalar, dr_c_low_coax: mythos.utils.types.Scalar, dr_c_high_coax: mythos.utils.types.Scalar, k_coax: mythos.utils.types.Scalar, dr0_coax: mythos.utils.types.Scalar, dr_c_coax: mythos.utils.types.Scalar, b_low_coax: mythos.utils.types.Scalar, b_high_coax: mythos.utils.types.Scalar, theta0_coax_4: mythos.utils.types.Scalar, delta_theta_star_coax_4: mythos.utils.types.Scalar, delta_theta_coax_4_c: mythos.utils.types.Scalar, a_coax_4: mythos.utils.types.Scalar, b_coax_4: mythos.utils.types.Scalar, theta0_coax_1: mythos.utils.types.Scalar, delta_theta_star_coax_1: mythos.utils.types.Scalar, delta_theta_coax_1_c: mythos.utils.types.Scalar, a_coax_1: mythos.utils.types.Scalar, b_coax_1: mythos.utils.types.Scalar, a_coax_1_f6: mythos.utils.types.Scalar, b_coax_1_f6: mythos.utils.types.Scalar, theta0_coax_5: mythos.utils.types.Scalar, delta_theta_star_coax_5: mythos.utils.types.Scalar, delta_theta_coax_5_c: mythos.utils.types.Scalar, a_coax_5: mythos.utils.types.Scalar, b_coax_5: mythos.utils.types.Scalar, theta0_coax_6: mythos.utils.types.Scalar, delta_theta_star_coax_6: mythos.utils.types.Scalar, delta_theta_coax_6_c: mythos.utils.types.Scalar, a_coax_6: mythos.utils.types.Scalar, b_coax_6: mythos.utils.types.Scalar) → mythos.utils.types.Scalar[source]: Coaxial stacking energy.