mythos.energy.dna1.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 DNA1 model.

Module Contents

class mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the unbonded excluded volume energy function.

eps_exc: float | None = None
dr_star_base: float | None = None
sigma_base: float | None = None
dr_star_back_base: float | None = None
sigma_back_base: float | None = None
dr_star_base_back: float | None = None
sigma_base_back: float | None = None
dr_star_backbone: float | None = None
sigma_backbone: float | None = None
b_base: float | None = None
dr_c_base: float | None = None
b_back_base: float | None = None
dr_c_back_base: float | None = None
b_base_back: float | None = None
dr_c_base_back: float | None = None
b_backbone: float | None = None
dr_c_backbone: float | None = None
required_params: tuple[str] = ('eps_exc', 'dr_star_base', 'sigma_base', 'dr_star_back_base', 'sigma_back_base',...
dependent_params: tuple[str] = ('b_base', 'dr_c_base', 'b_back_base', 'dr_c_back_base', 'b_base_back', 'dr_c_base_back',...
init_params() → UnbondedExcludedVolumeConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume[source]

Bases: mythos.energy.base.BaseEnergyFunction

Unbonded excluded volume energy function for DNA1 model.

params: UnbondedExcludedVolumeConfiguration
pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]

Computes the excluded volume energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]

Compute the energy of the system given the nucleotide.