mythos.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 mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the unbonded 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_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: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None
rna_config: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None
drh_config: mythos.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[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume[source]

Bases: mythos.energy.base.BaseEnergyFunction

Unbonded excluded volume energy function for NA1 model.

params: UnbondedExcludedVolumeConfiguration
compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar[source]

Compute the energy of the system given the nucleotide.