jax_dna.energy.na1.unbonded_excluded_volume

Unbonded excluded volume energy function for DNA1 model.

Classes

UnbondedExcludedVolumeConfiguration	Configuration for the unbonded excluded volume energy function.
UnbondedExcludedVolume	Unbonded excluded volume energy function for NA1 model.

Module Contents

class jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration

Bases: jax_dna.energy.configuration.BaseConfiguration

Configuration for the unbonded excluded volume energy function.

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

dna_eps_exc: float | None = None

dna_dr_star_base: float | None = None

dna_sigma_base: float | None = None

dna_dr_star_back_base: float | None = None

dna_sigma_back_base: float | None = None

dna_dr_star_base_back: float | None = None

dna_sigma_base_back: float | None = None

dna_dr_star_backbone: float | None = None

dna_sigma_backbone: float | None = None

rna_eps_exc: float | None = None

rna_dr_star_base: float | None = None

rna_sigma_base: float | None = None

rna_dr_star_back_base: float | None = None

rna_sigma_back_base: float | None = None

rna_dr_star_base_back: float | None = None

rna_sigma_base_back: float | None = None

rna_dr_star_backbone: float | None = None

rna_sigma_backbone: float | None = None

drh_eps_exc: float | None = None

drh_dr_star_base: float | None = None

drh_sigma_base: float | None = None

drh_dr_star_back_base: float | None = None

drh_sigma_back_base: float | None = None

drh_dr_star_base_back: float | None = None

drh_sigma_base_back: float | None = None

drh_dr_star_backbone: float | None = None

drh_sigma_backbone: float | None = None

dna_config: jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

rna_config: jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

drh_config: jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_dr_star_back_base',...

init_params() → UnbondedExcludedVolumeConfiguration

Initializes the dependent parameters in configuration.

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

class jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume

Bases: jax_dna.energy.base.BaseEnergyFunction

Unbonded excluded volume energy function for NA1 model.

params: UnbondedExcludedVolumeConfiguration

__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

Calculate the energy of the system.