jax_dna.energy.dna1.expected_hydrogen_bonding

Expected hydrogen bonding energy function for DNA1 model.

Classes

ExpectedHydrogenBondingConfiguration

Configuration for the expected hydrogen bonding energy function.

ExpectedHydrogenBonding

Expected hydrogen bonding energy function for DNA1 model.

Module Contents

class jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBondingConfiguration[source]

Bases: jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration

Configuration for the expected hydrogen bonding energy function.

sequence_constraints: jax_dna.input.sequence_constraints.SequenceConstraints | None = None
required_params: tuple[str] = ('eps_hb', 'a_hb', 'dr0_hb', 'dr_c_hb', 'dr_low_hb', 'dr_high_hb', 'a_hb_1', 'theta0_hb_1',...
class jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBonding[source]

Bases: jax_dna.energy.dna1.hydrogen_bonding.HydrogenBonding

Expected hydrogen bonding energy function for DNA1 model.

params: ExpectedHydrogenBondingConfiguration
weight(i: int, j: int, seq: jax_dna.utils.types.Probabilistic_Sequence) → float[source]

Computes the sequence-dependent weight for an unbonded 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[source]

Calculate the energy of the system.