mythos.energy.dna1.fene

FENE energy function for DNA1 model.

Classes

`FeneConfiguration`	Configuration for the FENE energy function.
`Fene`	FENE energy function for DNA1 model.

Module Contents

class mythos.energy.dna1.fene.FeneConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the FENE energy function.

eps_backbone: float | None = None

r0_backbone: float | None = None

delta_backbone: float | None = None

fmax: float | None = None

finf: float | None = None

required_params: tuple[str] = ('eps_backbone', 'r0_backbone', 'delta_backbone', 'fmax', 'finf')

init_params() → FeneConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.fene.Fene[source]

Bases: mythos.energy.base.BaseEnergyFunction

FENE energy function for DNA1 model.

params: FeneConfiguration

pairwise_energies(body: mythos.energy.base.BaseNucleotide, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the FENE energy for each bonded pair.

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