mythos.energy.dna2.stacking

Stacking energy function for DNA1 model.

Classes

Stacking energy function for DNA2 model.

Module Contents

class mythos.energy.dna2.stacking.Stacking[source]

Bases: mythos.energy.dna1.Stacking

Stacking energy function for DNA2 model.

params: mythos.energy.dna1.StackingConfiguration

pairwise_energies(body: mythos.energy.dna2.nucleotide.Nucleotide, 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.dna2.nucleotide.Nucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.