mythos.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 mythos.energy.dna2.debye.DebyeConfiguration[source]

Bases: mythos.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

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', '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 mythos.energy.dna2.debye.Debye[source]

Bases: mythos.energy.base.BaseEnergyFunction

Debye-huckel energy function for DNA2 model.

params: DebyeConfiguration

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

__post_init__(topology: mythos.input.topology.Topology | None) → None[source]

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

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.