jax_dna.energy.na1.debye

Debye-huckel function for NA2 model.

Classes

`DebyeConfiguration`	Configuration for the debye-huckel energy function.
`Debye`	Debye-huckel energy function for NA1 model.

Module Contents

class jax_dna.energy.na1.debye.DebyeConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the debye-huckel energy function.

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

is_end: jax_dna.utils.types.Arr_Nucleotide_Int | None = None

half_charged_ends: bool | None = None

kt: float | None = None

salt_conc: float | None = None

dna_q_eff: float | None = None

dna_lambda_factor: float | None = None

dna_prefactor_coeff: float | None = None

rna_q_eff: float | None = None

rna_lambda_factor: float | None = None

rna_prefactor_coeff: float | None = None

drh_q_eff: float | None = None

drh_lambda_factor: float | None = None

drh_prefactor_coeff: float | None = None

dna_config: jax_dna.energy.dna2.DebyeConfiguration | None = None

rna_config: jax_dna.energy.dna2.DebyeConfiguration | None = None

drh_config: jax_dna.energy.dna2.DebyeConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'is_end', 'half_charged_ends', 'kt', 'salt_conc', 'dna_q_eff', 'dna_lambda_factor',...

init_params() → DebyeConfiguration[source]

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.na1.debye.Debye[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

Debye-huckel energy function for NA1 model.

params: DebyeConfiguration

__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[source]: Calculate the energy of the system.