jax_dna.energy.na1.fene

FENE energy function for NA1 model.

Classes

`FeneConfiguration`	Configuration for the FENE energy function.
`Fene`	FENE energy function for NA1 model.

Module Contents

class jax_dna.energy.na1.fene.FeneConfiguration[source]

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the FENE energy function.

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

dna_eps_backbone: float | None = None

dna_r0_backbone: float | None = None

dna_delta_backbone: float | None = None

dna_fmax: float | None = None

dna_finf: float | None = None

rna_eps_backbone: float | None = None

rna_r0_backbone: float | None = None

rna_delta_backbone: float | None = None

rna_fmax: float | None = None

rna_finf: float | None = None

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

rna_config: jax_dna.energy.dna1.FeneConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_backbone', 'dna_r0_backbone', 'dna_delta_backbone', 'dna_fmax', 'dna_finf',...

init_params() → FeneConfiguration[source]

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.na1.fene.Fene[source]

Bases: jax_dna.energy.base.BaseEnergyFunction

FENE energy function for NA1 model.

params: FeneConfiguration

__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.