jax_dna.energy.dna1.expected_stacking

Stacking energy function for DNA1 model.

Classes

ExpectedStackingConfiguration	Configuration for the expected stacking energy function.
ExpectedStacking	Expected stacking energy function for DNA1 model.

Module Contents

class jax_dna.energy.dna1.expected_stacking.ExpectedStackingConfiguration

Bases: jax_dna.energy.dna1.stacking.StackingConfiguration

Configuration for the expected stacking energy function.

sequence_constraints: jax_dna.input.sequence_constraints.SequenceConstraints | None = None

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

class jax_dna.energy.dna1.expected_stacking.ExpectedStacking

Bases: jax_dna.energy.dna1.stacking.Stacking

Expected stacking energy function for DNA1 model.

params: ExpectedStackingConfiguration

weight(i: int, j: int, seq: jax_dna.utils.types.Probabilistic_Sequence) → float

Computes the sequence-dependent weight for a bonded pair.

__call__(body: jax_dna.energy.base.BaseNucleotide, seq: jax_dna.utils.types.Probabilistic_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

Calculate the energy of the system.