mythos.energy.dna1.hydrogen_bonding

Hydrogen bonding energy function for DNA1 model.

Attributes

HB_WEIGHTS_SA

Classes

`HydrogenBondingConfiguration`	Configuration for the hydrogen bonding energy function.
`HydrogenBonding`	Hydrogen bonding energy function for DNA1 model.

Module Contents

mythos.energy.dna1.hydrogen_bonding.HB_WEIGHTS_SA

class mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the hydrogen bonding energy function.

eps_hb: float | None = None

a_hb: float | None = None

dr0_hb: float | None = None

dr_c_hb: float | None = None

dr_low_hb: float | None = None

dr_high_hb: float | None = None

a_hb_1: float | None = None

theta0_hb_1: float | None = None

delta_theta_star_hb_1: float | None = None

a_hb_2: float | None = None

theta0_hb_2: float | None = None

delta_theta_star_hb_2: float | None = None

a_hb_3: float | None = None

theta0_hb_3: float | None = None

delta_theta_star_hb_3: float | None = None

a_hb_4: float | None = None

theta0_hb_4: float | None = None

delta_theta_star_hb_4: float | None = None

a_hb_7: float | None = None

theta0_hb_7: float | None = None

delta_theta_star_hb_7: float | None = None

a_hb_8: float | None = None

theta0_hb_8: float | None = None

delta_theta_star_hb_8: float | None = None

ss_hb_weights: numpy.ndarray | None = None

b_low_hb: float | None = None

dr_c_low_hb: float | None = None

b_high_hb: float | None = None

dr_c_high_hb: float | None = None

b_hb_1: float | None = None

delta_theta_hb_1_c: float | None = None

b_hb_2: float | None = None

delta_theta_hb_2_c: float | None = None

b_hb_3: float | None = None

delta_theta_hb_3_c: float | None = None

b_hb_4: float | None = None

delta_theta_hb_4_c: float | None = None

b_hb_7: float | None = None

delta_theta_hb_7_c: float | None = None

b_hb_8: float | None = None

delta_theta_hb_8_c: float | None = None

eps_hb_weights: numpy.ndarray | None = None

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

pseq_constraints: mythos.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',...

dependent_params: tuple[str] = ('b_low_hb', 'dr_c_low_hb', 'b_high_hb', 'dr_c_high_hb', 'b_hb_1', 'delta_theta_hb_1_c',...

init_params() → HydrogenBondingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna1.hydrogen_bonding.HydrogenBonding[source]

Bases: mythos.energy.base.BaseEnergyFunction

Hydrogen bonding energy function for DNA1 model.

params: HydrogenBondingConfiguration

compute_v_hb(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the sequence-independent energy for each unbonded pair.

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

pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, seq: mythos.utils.types.Discrete_Sequence, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the hydrogen bonding energy for each unbonded pair.

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