mythos.energy.dna1.cross_stacking

Cross-stacking energy term for DNA1 model.

Classes

CrossStackingConfiguration	Configuration for the cross-stacking energy function.
CrossStacking	Cross-stacking energy function for DNA1 model.

Module Contents

class mythos.energy.dna1.cross_stacking.CrossStackingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

dr_low_cross: float | None = None

dr_high_cross: float | None = None

k_cross: float | None = None

r0_cross: float | None = None

dr_c_cross: float | None = None

theta0_cross_1: float | None = None

delta_theta_star_cross_1: float | None = None

a_cross_1: float | None = None

theta0_cross_2: float | None = None

delta_theta_star_cross_2: float | None = None

a_cross_2: float | None = None

theta0_cross_3: float | None = None

delta_theta_star_cross_3: float | None = None

a_cross_3: float | None = None

theta0_cross_4: float | None = None

delta_theta_star_cross_4: float | None = None

a_cross_4: float | None = None

theta0_cross_7: float | None = None

delta_theta_star_cross_7: float | None = None

a_cross_7: float | None = None

theta0_cross_8: float | None = None

delta_theta_star_cross_8: float | None = None

a_cross_8: float | None = None

b_low_cross: float | None = None

dr_c_low_cross: float | None = None

b_high_cross: float | None = None

dr_c_high_cross: float | None = None

b_cross_1: float | None = None

delta_theta_cross_1_c: float | None = None

b_cross_2: float | None = None

delta_theta_cross_2_c: float | None = None

b_cross_3: float | None = None

delta_theta_cross_3_c: float | None = None

b_cross_4: float | None = None

delta_theta_cross_4_c: float | None = None

b_cross_7: float | None = None

delta_theta_cross_7_c: float | None = None

b_cross_8: float | None = None

delta_theta_cross_8_c: float | None = None

required_params: tuple[str] = ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',...

dependent_params: tuple[str] = ('b_low_cross', 'dr_c_low_cross', 'b_high_cross', 'dr_c_high_cross', 'b_cross_1',...

init_params() → CrossStackingConfiguration

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.cross_stacking.CrossStacking

Bases: mythos.energy.base.BaseEnergyFunction

Cross-stacking energy function for DNA1 model.

params: CrossStackingConfiguration

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_Unbonded_Neighbors

Computes the cross stacking energy for each unbonded pair.

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

Compute the energy of the system given the nucleotide.