mythos.energy.dna1.stacking

Stacking energy function for DNA1 model.

Attributes

STACK_WEIGHTS_SA

Classes

`StackingConfiguration`	Configuration for the stacking energy function.
`Stacking`	Stacking energy function for DNA1 model.

Module Contents

mythos.energy.dna1.stacking.STACK_WEIGHTS_SA

class mythos.energy.dna1.stacking.StackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

eps_stack_base: float | None = None

eps_stack_kt_coeff: float | None = None

dr_low_stack: float | None = None

dr_high_stack: float | None = None

a_stack: float | None = None

dr0_stack: float | None = None

dr_c_stack: float | None = None

theta0_stack_4: float | None = None

delta_theta_star_stack_4: float | None = None

a_stack_4: float | None = None

theta0_stack_5: float | None = None

delta_theta_star_stack_5: float | None = None

a_stack_5: float | None = None

theta0_stack_6: float | None = None

delta_theta_star_stack_6: float | None = None

a_stack_6: float | None = None

neg_cos_phi1_star_stack: float | None = None

a_stack_1: float | None = None

neg_cos_phi2_star_stack: float | None = None

a_stack_2: float | None = None

pseq: mythos.utils.types.Probabilistic_Sequence | None = None

pseq_constraints: mythos.input.sequence_constraints.SequenceConstraints | None = None

kt: float | None = None

ss_stack_weights: numpy.ndarray | None = None

b_low_stack: float | None = None

dr_c_low_stack: float | None = None

b_high_stack: float | None = None

dr_c_high_stack: float | None = None

b_stack_4: float | None = None

delta_theta_stack_4_c: float | None = None

b_stack_5: float | None = None

delta_theta_stack_5_c: float | None = None

b_stack_6: float | None = None

delta_theta_stack_6_c: float | None = None

b_neg_cos_phi1_stack: float | None = None

neg_cos_phi1_c_stack: float | None = None

b_neg_cos_phi2_stack: float | None = None

neg_cos_phi2_c_stack: float | None = None

eps_stack: float | None = None

required_params: tuple[str] = ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...

dependent_params: tuple[str] = ('b_low_stack', 'dr_c_low_stack', 'b_high_stack', 'dr_c_high_stack', 'b_stack_4',...

init_params() → StackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.stacking.Stacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Stacking energy function for DNA1 model.

params: StackingConfiguration

compute_v_stack(stack_sites: mythos.utils.types.Arr_Nucleotide_3, back_sites: mythos.utils.types.Arr_Nucleotide_3, base_normals: mythos.utils.types.Arr_Nucleotide_3, cross_prods: mythos.utils.types.Arr_Nucleotide_3, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the sequence-independent energy for each bonded pair.

pseq_weights(i: int, j: int, seq: mythos.utils.types.Probabilistic_Sequence) → float[source]: Computes the probabilistic sequence-dependent weight for a bonded pair.

pairwise_energies(body: mythos.energy.base.BaseNucleotide, seq: mythos.utils.types.Discrete_Sequence, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the stacking energy for each bonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.