jax_dna.energy.rna2.cross_stacking

Cross-stacking energy term for RNA2 model.

Classes

`CrossStackingConfiguration`	Configuration for the cross-stacking energy function.
`CrossStacking`	Cross-stacking energy function for RNA2 model.

Module Contents

class jax_dna.energy.rna2.cross_stacking.CrossStackingConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

dr_low_cross: float | None = None

dr_high_cross: float | None = None

k_cross: float | None = None

r0_cross: float | None = None

dr_c_cross: float | None = None

theta0_cross_1: float | None = None

delta_theta_star_cross_1: float | None = None

a_cross_1: float | None = None

theta0_cross_2: float | None = None

delta_theta_star_cross_2: float | None = None

a_cross_2: float | None = None

theta0_cross_3: float | None = None

delta_theta_star_cross_3: float | None = None

a_cross_3: float | None = None

theta0_cross_7: float | None = None

delta_theta_star_cross_7: float | None = None

a_cross_7: float | None = None

theta0_cross_8: float | None = None

delta_theta_star_cross_8: float | None = None

a_cross_8: float | None = None

b_low_cross: float | None = None

dr_c_low_cross: float | None = None

b_high_cross: float | None = None

dr_c_high_cross: float | None = None

b_cross_1: float | None = None

delta_theta_cross_1_c: float | None = None

b_cross_2: float | None = None

delta_theta_cross_2_c: float | None = None

b_cross_3: float | None = None

delta_theta_cross_3_c: float | None = None

b_cross_7: float | None = None

delta_theta_cross_7_c: float | None = None

b_cross_8: float | None = None

delta_theta_cross_8_c: float | None = None

required_params: tuple[str] = ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',...

init_params() → CrossStackingConfiguration[source]

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class jax_dna.energy.rna2.cross_stacking.CrossStacking[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

Cross-stacking energy function for RNA2 model.

params: CrossStackingConfiguration

pairwise_energies(body_i: jax_dna.energy.rna2.nucleotide.Nucleotide, body_j: jax_dna.energy.rna2.nucleotide.Nucleotide, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) → jax_dna.utils.types.Arr_Unbonded_Neighbors[source]: Computes the cross stacking energy for each unbonded pair.

__call__(body: jax_dna.energy.rna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) → jax_dna.utils.types.Scalar[source]: Calculate the energy of the system.