jax_dna.energy.dna1.base_smoothing_functions

Smoothing functions for the base functions in DNA1 model.

functional forms from oxDNA paper https://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719/files/mdcac62bc9133143fc05070ed20048c50 # Section 2.4.1

Functions

_solve_f1_b(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter b in the f1 smoothing function.
_solve_f1_xc_star(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter xc_star in the f1 smoothing function.
get_f1_smoothing_params(...)	Get the smoothing parameters for the f1 smoothing function.
_solve_f2_b(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter b in the f2 smoothing function.
_solve_f2_xc_star(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter xc_star in the f2 smoothing function.
get_f2_smoothing_params(...)	Get the smoothing parameters for the f2 smoothing function.
_solve_f3_b(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter b in the f3 smoothing function.
_solve_f3_xc(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter xc in the f3 smoothing function.
get_f3_smoothing_params(...)	Get the smoothing parameters for the f3 smoothing function.
_solve_f4_b(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter b in the f4 smoothing function.
_solve_f4_xc(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter xc in the f4 smoothing function.
get_f4_smoothing_params(...)	Get the smoothing parameters for the f4 smoothing function.
_solve_f5_b(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter b in the f5 smoothing function.
_solve_f5_xc(→ jax_dna.utils.types.Scalar)	Solve for the smoothing parameter xc in the f5 smoothing function.
get_f5_smoothing_params(...)	Get the smoothing parameters for the f5 smoothing function.

Module Contents

jax_dna.energy.dna1.base_smoothing_functions._solve_f1_b(x: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter b in the f1 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f1_xc_star(x: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter xc_star in the f1 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions.get_f1_smoothing_params(x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar, x_low: jax_dna.utils.types.Scalar, x_high: jax_dna.utils.types.Scalar) → tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

Get the smoothing parameters for the f1 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f2_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter b in the f2 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f2_xc_star(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter xc_star in the f2 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions.get_f2_smoothing_params(x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar, x_low: jax_dna.utils.types.Scalar, x_high: jax_dna.utils.types.Scalar) → tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

Get the smoothing parameters for the f2 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f3_b(x: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter b in the f3 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f3_xc(x: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter xc in the f3 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions.get_f3_smoothing_params(r_star: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) → tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

Get the smoothing parameters for the f3 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f4_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter b in the f4 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f4_xc(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter xc in the f4 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions.get_f4_smoothing_params(a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, delta_x_star: jax_dna.utils.types.Scalar) → tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

Get the smoothing parameters for the f4 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f5_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter b in the f5 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions._solve_f5_xc(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) → jax_dna.utils.types.Scalar

Solve for the smoothing parameter xc in the f5 smoothing function.

jax_dna.energy.dna1.base_smoothing_functions.get_f5_smoothing_params(a: jax_dna.utils.types.Scalar, x_star: jax_dna.utils.types.Scalar) → tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

Get the smoothing parameters for the f5 smoothing function.