mythos.energy.na1.hydrogen_bonding

Hydrogen bonding energy function for NA1 model.

Classes

HydrogenBondingConfiguration	Configuration for the cross-stacking energy function.
HydrogenBonding	Hydrogen bonding energy function for NA1 model.

Module Contents

class mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_eps_hb: float | None = None

dna_a_hb: float | None = None

dna_dr0_hb: float | None = None

dna_dr_c_hb: float | None = None

dna_dr_low_hb: float | None = None

dna_dr_high_hb: float | None = None

dna_a_hb_1: float | None = None

dna_theta0_hb_1: float | None = None

dna_delta_theta_star_hb_1: float | None = None

dna_a_hb_2: float | None = None

dna_theta0_hb_2: float | None = None

dna_delta_theta_star_hb_2: float | None = None

dna_a_hb_3: float | None = None

dna_theta0_hb_3: float | None = None

dna_delta_theta_star_hb_3: float | None = None

dna_a_hb_4: float | None = None

dna_theta0_hb_4: float | None = None

dna_delta_theta_star_hb_4: float | None = None

dna_a_hb_7: float | None = None

dna_theta0_hb_7: float | None = None

dna_delta_theta_star_hb_7: float | None = None

dna_a_hb_8: float | None = None

dna_theta0_hb_8: float | None = None

dna_delta_theta_star_hb_8: float | None = None

dna_ss_hb_weights: numpy.ndarray | None = None

rna_eps_hb: float | None = None

rna_a_hb: float | None = None

rna_dr0_hb: float | None = None

rna_dr_c_hb: float | None = None

rna_dr_low_hb: float | None = None

rna_dr_high_hb: float | None = None

rna_a_hb_1: float | None = None

rna_theta0_hb_1: float | None = None

rna_delta_theta_star_hb_1: float | None = None

rna_a_hb_2: float | None = None

rna_theta0_hb_2: float | None = None

rna_delta_theta_star_hb_2: float | None = None

rna_a_hb_3: float | None = None

rna_theta0_hb_3: float | None = None

rna_delta_theta_star_hb_3: float | None = None

rna_a_hb_4: float | None = None

rna_theta0_hb_4: float | None = None

rna_delta_theta_star_hb_4: float | None = None

rna_a_hb_7: float | None = None

rna_theta0_hb_7: float | None = None

rna_delta_theta_star_hb_7: float | None = None

rna_a_hb_8: float | None = None

rna_theta0_hb_8: float | None = None

rna_delta_theta_star_hb_8: float | None = None

rna_ss_hb_weights: numpy.ndarray | None = None

drh_eps_hb: float | None = None

drh_a_hb: float | None = None

drh_dr0_hb: float | None = None

drh_dr_c_hb: float | None = None

drh_dr_low_hb: float | None = None

drh_dr_high_hb: float | None = None

drh_a_hb_1: float | None = None

drh_theta0_hb_1: float | None = None

drh_delta_theta_star_hb_1: float | None = None

drh_a_hb_2: float | None = None

drh_theta0_hb_2: float | None = None

drh_delta_theta_star_hb_2: float | None = None

drh_a_hb_3: float | None = None

drh_theta0_hb_3: float | None = None

drh_delta_theta_star_hb_3: float | None = None

drh_a_hb_4: float | None = None

drh_theta0_hb_4: float | None = None

drh_delta_theta_star_hb_4: float | None = None

drh_a_hb_7: float | None = None

drh_theta0_hb_7: float | None = None

drh_delta_theta_star_hb_7: float | None = None

drh_a_hb_8: float | None = None

drh_theta0_hb_8: float | None = None

drh_delta_theta_star_hb_8: float | None = None

drh_ss_hb_weights: numpy.ndarray | None = None

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

pseq_constraints: mythos.input.sequence_constraints.SequenceConstraints | None = None

dna_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

rna_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

drh_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_hb', 'dna_a_hb', 'dna_dr0_hb', 'dna_dr_c_hb', 'dna_dr_low_hb',...

init_params() → HydrogenBondingConfiguration

Initializes the dependent parameters in configuration.

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

class mythos.energy.na1.hydrogen_bonding.HydrogenBonding

Bases: mythos.energy.base.BaseEnergyFunction

Hydrogen bonding energy function for NA1 model.

params: HydrogenBondingConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.