jax_dna.energy.rna2.stacking

Stacking energy function for RNA2 model.

Classes

`StackingConfiguration`	Configuration for the stacking energy function.
`Stacking`	Stacking energy function for DNA1 model.

Module Contents

class jax_dna.energy.rna2.stacking.StackingConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

eps_stack_base: float | None = None

eps_stack_kt_coeff: float | None = None

dr_low_stack: float | None = None

dr_high_stack: float | None = None

a_stack: float | None = None

dr0_stack: float | None = None

dr_c_stack: float | None = None

theta0_stack_5: float | None = None

delta_theta_star_stack_5: float | None = None

a_stack_5: float | None = None

theta0_stack_6: float | None = None

delta_theta_star_stack_6: float | None = None

a_stack_6: float | None = None

theta0_stack_9: float | None = None

delta_theta_star_stack_9: float | None = None

a_stack_9: float | None = None

theta0_stack_10: float | None = None

delta_theta_star_stack_10: float | None = None

a_stack_10: float | None = None

neg_cos_phi1_star_stack: float | None = None

a_stack_1: float | None = None

neg_cos_phi2_star_stack: float | None = None

a_stack_2: float | None = None

kt: float | None = None

ss_stack_weights: numpy.ndarray | None

b_low_stack: float | None = None

dr_c_low_stack: float | None = None

b_high_stack: float | None = None

dr_c_high_stack: float | None = None

b_stack_5: float | None = None

delta_theta_stack_5_c: float | None = None

b_stack_6: float | None = None

delta_theta_stack_6_c: float | None = None

b_stack_9: float | None = None

delta_theta_stack_9_c: float | None = None

b_stack_10: float | None = None

delta_theta_stack_10_c: float | None = None

b_neg_cos_phi1_stack: float | None = None

neg_cos_phi1_c_stack: float | None = None

b_neg_cos_phi2_stack: float | None = None

neg_cos_phi2_c_stack: float | None = None

eps_stack: float | None = None

required_params: tuple[str] = ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...

init_params() → StackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.rna2.stacking.Stacking[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

Stacking energy function for DNA1 model.

params: StackingConfiguration

compute_v_stack(body: jax_dna.energy.rna2.nucleotide.Nucleotide, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2) → jax_dna.utils.types.Arr_Bonded_Neighbors[source]: Computes the sequence-independent energy for each bonded pair.

pairwise_energies(body: jax_dna.energy.rna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2) → jax_dna.utils.types.Arr_Bonded_Neighbors[source]: Computes the stacking energy for each bonded pair.

__call__(body: jax_dna.energy.rna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_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.