jax_dna.energy.dna2.debye

Debye-huckel function for DNA2 model.

Classes

`DebyeConfiguration`	Configuration for the debye-huckel energy function.
`Debye`	Debye-huckel energy function for DNA2 model.

Module Contents

class jax_dna.energy.dna2.debye.DebyeConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the debye-huckel energy function.

q_eff: float | None = None

lambda_factor: float | None = None

prefactor_coeff: float | None = None

kt: float | None = None

salt_conc: float | None = None

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

half_charged_ends: bool | None = None

lambda_: float | None = None

kappa: float | None = None

r_high: float | None = None

prefactor: float | None = None

smoothing_coeff: float | None = None

r_cut: float | None = None

required_params: tuple[str] = ('q_eff', 'lambda_factor', 'prefactor_coeff', 'kt', 'salt_conc', 'is_end', 'half_charged_ends')

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.dna2.debye.Debye[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

Debye-huckel energy function for DNA2 model.

params: DebyeConfiguration

pairwise_energies(body_i: jax_dna.energy.base.BaseNucleotide, body_j: jax_dna.energy.base.BaseNucleotide, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) → jax_dna.utils.types.Arr_Bonded_Neighbors[source]: Computes the debye-huckel energy for each unbonded pair.

__call__(body: jax_dna.energy.base.BaseNucleotide, 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.