jax_dna.energy.na1.coaxial_stacking

Coaxial stacking energy term for NA1 model.

Classes

CoaxialStackingConfiguration	Configuration for the cross-stacking energy function.
CoaxialStacking	Coaxial stacking energy function for NA1 model.

Module Contents

class jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration

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_coax: float | None = None

dna_dr_high_coax: float | None = None

dna_k_coax: float | None = None

dna_dr0_coax: float | None = None

dna_dr_c_coax: float | None = None

dna_theta0_coax_4: float | None = None

dna_delta_theta_star_coax_4: float | None = None

dna_a_coax_4: float | None = None

dna_theta0_coax_1: float | None = None

dna_delta_theta_star_coax_1: float | None = None

dna_a_coax_1: float | None = None

dna_theta0_coax_5: float | None = None

dna_delta_theta_star_coax_5: float | None = None

dna_a_coax_5: float | None = None

dna_theta0_coax_6: float | None = None

dna_delta_theta_star_coax_6: float | None = None

dna_a_coax_6: float | None = None

dna_a_coax_1_f6: float | None = None

dna_b_coax_1_f6: float | None = None

rna_dr_low_coax: float | None = None

rna_dr_high_coax: float | None = None

rna_k_coax: float | None = None

rna_dr0_coax: float | None = None

rna_dr_c_coax: float | None = None

rna_theta0_coax_4: float | None = None

rna_delta_theta_star_coax_4: float | None = None

rna_a_coax_4: float | None = None

rna_theta0_coax_1: float | None = None

rna_delta_theta_star_coax_1: float | None = None

rna_a_coax_1: float | None = None

rna_theta0_coax_5: float | None = None

rna_delta_theta_star_coax_5: float | None = None

rna_a_coax_5: float | None = None

rna_theta0_coax_6: float | None = None

rna_delta_theta_star_coax_6: float | None = None

rna_a_coax_6: float | None = None

rna_cos_phi3_star_coax: float | None = None

rna_a_coax_3p: float | None = None

rna_cos_phi4_star_coax: float | None = None

rna_a_coax_4p: float | None = None

drh_dr_low_coax: float | None = None

drh_dr_high_coax: float | None = None

drh_k_coax: float | None = None

drh_dr0_coax: float | None = None

drh_dr_c_coax: float | None = None

drh_theta0_coax_4: float | None = None

drh_delta_theta_star_coax_4: float | None = None

drh_a_coax_4: float | None = None

drh_theta0_coax_1: float | None = None

drh_delta_theta_star_coax_1: float | None = None

drh_a_coax_1: float | None = None

drh_theta0_coax_5: float | None = None

drh_delta_theta_star_coax_5: float | None = None

drh_a_coax_5: float | None = None

drh_theta0_coax_6: float | None = None

drh_delta_theta_star_coax_6: float | None = None

drh_a_coax_6: float | None = None

drh_cos_phi3_star_coax: float | None = None

drh_a_coax_3p: float | None = None

drh_cos_phi4_star_coax: float | None = None

drh_a_coax_4p: float | None = None

dna_config: jax_dna.energy.dna2.CoaxialStackingConfiguration | None = None

rna_config: jax_dna.energy.dna1.CoaxialStackingConfiguration | None = None

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

required_params: tuple[str] = ('nt_type', 'dna_dr_low_coax', 'dna_dr_high_coax', 'dna_k_coax', 'dna_dr0_coax',...

init_params() → CoaxialStackingConfiguration

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.na1.coaxial_stacking.CoaxialStacking

Bases: jax_dna.energy.base.BaseEnergyFunction

Coaxial stacking energy function for NA1 model.

params: CoaxialStackingConfiguration

__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.