jax_dna.energy.na1.cross_stacking

Cross-stacking energy term for NA1 model.

Classes

CrossStackingConfiguration	Configuration for the cross-stacking energy function.
CrossStacking	Cross-stacking energy function for NA1 model.

Module Contents

class jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

nt_type: jax_dna.utils.types.Arr_Nucleotide | None = None

dna_dr_low_cross: float | None = None

dna_dr_high_cross: float | None = None

dna_k_cross: float | None = None

dna_r0_cross: float | None = None

dna_dr_c_cross: float | None = None

dna_theta0_cross_1: float | None = None

dna_delta_theta_star_cross_1: float | None = None

dna_a_cross_1: float | None = None

dna_theta0_cross_2: float | None = None

dna_delta_theta_star_cross_2: float | None = None

dna_a_cross_2: float | None = None

dna_theta0_cross_3: float | None = None

dna_delta_theta_star_cross_3: float | None = None

dna_a_cross_3: float | None = None

dna_theta0_cross_4: float | None = None

dna_delta_theta_star_cross_4: float | None = None

dna_a_cross_4: float | None = None

dna_theta0_cross_7: float | None = None

dna_delta_theta_star_cross_7: float | None = None

dna_a_cross_7: float | None = None

dna_theta0_cross_8: float | None = None

dna_delta_theta_star_cross_8: float | None = None

dna_a_cross_8: float | None = None

rna_dr_low_cross: float | None = None

rna_dr_high_cross: float | None = None

rna_k_cross: float | None = None

rna_r0_cross: float | None = None

rna_dr_c_cross: float | None = None

rna_theta0_cross_1: float | None = None

rna_delta_theta_star_cross_1: float | None = None

rna_a_cross_1: float | None = None

rna_theta0_cross_2: float | None = None

rna_delta_theta_star_cross_2: float | None = None

rna_a_cross_2: float | None = None

rna_theta0_cross_3: float | None = None

rna_delta_theta_star_cross_3: float | None = None

rna_a_cross_3: float | None = None

rna_theta0_cross_7: float | None = None

rna_delta_theta_star_cross_7: float | None = None

rna_a_cross_7: float | None = None

rna_theta0_cross_8: float | None = None

rna_delta_theta_star_cross_8: float | None = None

rna_a_cross_8: float | None = None

drh_dr_low_cross: float | None = None

drh_dr_high_cross: float | None = None

drh_k_cross: float | None = None

drh_r0_cross: float | None = None

drh_dr_c_cross: float | None = None

drh_theta0_cross_1: float | None = None

drh_delta_theta_star_cross_1: float | None = None

drh_a_cross_1: float | None = None

drh_theta0_cross_2: float | None = None

drh_delta_theta_star_cross_2: float | None = None

drh_a_cross_2: float | None = None

drh_theta0_cross_3: float | None = None

drh_delta_theta_star_cross_3: float | None = None

drh_a_cross_3: float | None = None

drh_theta0_cross_4: float | None = None

drh_delta_theta_star_cross_4: float | None = None

drh_a_cross_4: float | None = None

drh_theta0_cross_7: float | None = None

drh_delta_theta_star_cross_7: float | None = None

drh_a_cross_7: float | None = None

drh_theta0_cross_8: float | None = None

drh_delta_theta_star_cross_8: float | None = None

drh_a_cross_8: float | None = None

dna_config: jax_dna.energy.dna1.CrossStackingConfiguration | None = None

rna_config: jax_dna.energy.rna2.CrossStackingConfiguration | None = None

drh_config: jax_dna.energy.dna1.CrossStackingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_dr_low_cross', 'dna_dr_high_cross', 'dna_k_cross', 'dna_r0_cross',...

init_params() → CrossStackingConfiguration

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.na1.cross_stacking.CrossStacking

Bases: jax_dna.energy.base.BaseEnergyFunction

Cross-stacking energy function for NA1 model.

params: CrossStackingConfiguration

__call__(body: jax_dna.energy.na1.nucleotide.HybridNucleotide, 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

Calculate the energy of the system.