jax_dna.energy.na1.stacking

Stacking energy function for DNA1 model.

Classes

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

Module Contents

class jax_dna.energy.na1.stacking.StackingConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

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

kt: float | None = None

dna_eps_stack_base: float | None = None

dna_eps_stack_kt_coeff: float | None = None

dna_dr_low_stack: float | None = None

dna_dr_high_stack: float | None = None

dna_a_stack: float | None = None

dna_dr0_stack: float | None = None

dna_dr_c_stack: float | None = None

dna_theta0_stack_4: float | None = None

dna_delta_theta_star_stack_4: float | None = None

dna_a_stack_4: float | None = None

dna_theta0_stack_5: float | None = None

dna_delta_theta_star_stack_5: float | None = None

dna_a_stack_5: float | None = None

dna_theta0_stack_6: float | None = None

dna_delta_theta_star_stack_6: float | None = None

dna_a_stack_6: float | None = None

dna_neg_cos_phi1_star_stack: float | None = None

dna_a_stack_1: float | None = None

dna_neg_cos_phi2_star_stack: float | None = None

dna_a_stack_2: float | None = None

dna_ss_stack_weights: numpy.ndarray | None

rna_eps_stack_base: float | None = None

rna_eps_stack_kt_coeff: float | None = None

rna_dr_low_stack: float | None = None

rna_dr_high_stack: float | None = None

rna_a_stack: float | None = None

rna_dr0_stack: float | None = None

rna_dr_c_stack: float | None = None

rna_theta0_stack_5: float | None = None

rna_delta_theta_star_stack_5: float | None = None

rna_a_stack_5: float | None = None

rna_theta0_stack_6: float | None = None

rna_delta_theta_star_stack_6: float | None = None

rna_a_stack_6: float | None = None

rna_theta0_stack_9: float | None = None

rna_delta_theta_star_stack_9: float | None = None

rna_a_stack_9: float | None = None

rna_theta0_stack_10: float | None = None

rna_delta_theta_star_stack_10: float | None = None

rna_a_stack_10: float | None = None

rna_neg_cos_phi1_star_stack: float | None = None

rna_a_stack_1: float | None = None

rna_neg_cos_phi2_star_stack: float | None = None

rna_a_stack_2: float | None = None

rna_ss_stack_weights: numpy.ndarray | None

dna_config: jax_dna.energy.dna1.StackingConfiguration | None = None

rna_config: jax_dna.energy.rna2.StackingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'kt', 'dna_eps_stack_base', 'dna_eps_stack_kt_coeff', 'dna_dr_low_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.na1.stacking.Stacking[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

Stacking energy function for DNA1 model.

params: StackingConfiguration

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