jax_dna.energy.dna2.stacking

Stacking energy function for DNA1 model.

Classes

Stacking

Stacking energy function for DNA2 model.

Module Contents

class jax_dna.energy.dna2.stacking.Stacking[source]

Bases: jax_dna.energy.dna1.Stacking

Stacking energy function for DNA2 model.

params: jax_dna.energy.dna1.StackingConfiguration
pairwise_energies(body: jax_dna.energy.dna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2) → jax_dna.utils.types.Arr_Bonded_Neighbors[source]

Computes the stacking energy for each bonded pair.

__call__(body: jax_dna.energy.dna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) → jax_dna.utils.types.Scalar[source]

Calculate the energy of the system.