mythos.energy.na1.bonded_excluded_volume

Bonded excluded volume energy for DNA1 model.

Classes

BondedExcludedVolumeConfiguration	Configuration for the bonded excluded volume energy function.
BondedExcludedVolume	Bonded excluded volume energy function for NA1 model.

Module Contents

class mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the bonded excluded volume energy function.

nt_type: mythos.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_sigma_back_base: float | None = None

dna_sigma_base_back: float | None = None

dna_dr_star_back_base: float | None = None

dna_dr_star_base_back: float | None = None

rna_eps_exc: float | None = None

rna_dr_star_base: float | None = None

rna_sigma_base: float | None = None

rna_sigma_back_base: float | None = None

rna_sigma_base_back: float | None = None

rna_dr_star_back_base: float | None = None

rna_dr_star_base_back: float | None = None

dna_config: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None = None

rna_config: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None = None

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

init_params() → BondedExcludedVolumeConfiguration

Initializes the dependent parameters in configuration.

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

class mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolume

Bases: mythos.energy.base.BaseEnergyFunction

Bonded excluded volume energy function for NA1 model.

params: BondedExcludedVolumeConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.