mythos.energy.dna1.coaxial_stacking

Coaxial stacking energy function for DNA1 model.

Classes

`CoaxialStackingConfiguration`	Configuration for the coaxial stacking energy function.
`CoaxialStacking`	Coaxial stacking energy function for DNA1 model.

Module Contents

class mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the coaxial stacking energy function.

dr_low_coax: float | None = None

dr_high_coax: float | None = None

k_coax: float | None = None

dr0_coax: float | None = None

dr_c_coax: float | None = None

theta0_coax_4: float | None = None

delta_theta_star_coax_4: float | None = None

a_coax_4: float | None = None

theta0_coax_1: float | None = None

delta_theta_star_coax_1: float | None = None

a_coax_1: float | None = None

theta0_coax_5: float | None = None

delta_theta_star_coax_5: float | None = None

a_coax_5: float | None = None

theta0_coax_6: float | None = None

delta_theta_star_coax_6: float | None = None

a_coax_6: float | None = None

cos_phi3_star_coax: float | None = None

a_coax_3p: float | None = None

cos_phi4_star_coax: float | None = None

a_coax_4p: float | None = None

b_low_coax: float | None = None

dr_c_low_coax: float | None = None

b_high_coax: float | None = None

dr_c_high_coax: float | None = None

b_coax_4: float | None = None

delta_theta_coax_4_c: float | None = None

b_coax_1: float | None = None

delta_theta_coax_1_c: float | None = None

b_coax_5: float | None = None

delta_theta_coax_5_c: float | None = None

b_coax_6: float | None = None

delta_theta_coax_6_c: float | None = None

b_cos_phi3_coax: float | None = None

cos_phi3_c_coax: float | None = None

b_cos_phi4_coax: float | None = None

cos_phi4_c_coax: float | None = None

required_params: tuple[str] = ('dr_low_coax', 'dr_high_coax', 'k_coax', 'dr0_coax', 'dr_c_coax', 'theta0_coax_4',...

dependent_params: tuple[str] = ('b_low_coax', 'dr_c_low_coax', 'b_high_coax', 'dr_c_high_coax', 'b_coax_4',...

init_params() → CoaxialStackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.coaxial_stacking.CoaxialStacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Coaxial stacking energy function for DNA1 model.

params: CoaxialStackingConfiguration

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[source]: Computes the coaxial stacking 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.