jax_dna.energy.na1.hydrogen_bonding =================================== .. py:module:: jax_dna.energy.na1.hydrogen_bonding .. autoapi-nested-parse:: Hydrogen bonding energy function for NA1 model. Classes ------- .. autoapisummary:: jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration jax_dna.energy.na1.hydrogen_bonding.HydrogenBonding Module Contents --------------- .. py:class:: HydrogenBondingConfiguration Bases: :py:obj:`jax_dna.energy.configuration.BaseConfiguration` Configuration for the cross-stacking energy function. .. py:attribute:: nt_type :type: jax_dna.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: dna_eps_hb :type: float | None :value: None .. py:attribute:: dna_a_hb :type: float | None :value: None .. py:attribute:: dna_dr0_hb :type: float | None :value: None .. py:attribute:: dna_dr_c_hb :type: float | None :value: None .. py:attribute:: dna_dr_low_hb :type: float | None :value: None .. py:attribute:: dna_dr_high_hb :type: float | None :value: None .. py:attribute:: dna_a_hb_1 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_1 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_1 :type: float | None :value: None .. py:attribute:: dna_a_hb_2 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_2 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_2 :type: float | None :value: None .. py:attribute:: dna_a_hb_3 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_3 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_3 :type: float | None :value: None .. py:attribute:: dna_a_hb_4 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_4 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_4 :type: float | None :value: None .. py:attribute:: dna_a_hb_7 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_7 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_7 :type: float | None :value: None .. py:attribute:: dna_a_hb_8 :type: float | None :value: None .. py:attribute:: dna_theta0_hb_8 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_hb_8 :type: float | None :value: None .. py:attribute:: dna_ss_hb_weights :type: numpy.ndarray | None .. py:attribute:: rna_eps_hb :type: float | None :value: None .. py:attribute:: rna_a_hb :type: float | None :value: None .. py:attribute:: rna_dr0_hb :type: float | None :value: None .. py:attribute:: rna_dr_c_hb :type: float | None :value: None .. py:attribute:: rna_dr_low_hb :type: float | None :value: None .. py:attribute:: rna_dr_high_hb :type: float | None :value: None .. py:attribute:: rna_a_hb_1 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_1 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_1 :type: float | None :value: None .. py:attribute:: rna_a_hb_2 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_2 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_2 :type: float | None :value: None .. py:attribute:: rna_a_hb_3 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_3 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_3 :type: float | None :value: None .. py:attribute:: rna_a_hb_4 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_4 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_4 :type: float | None :value: None .. py:attribute:: rna_a_hb_7 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_7 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_7 :type: float | None :value: None .. py:attribute:: rna_a_hb_8 :type: float | None :value: None .. py:attribute:: rna_theta0_hb_8 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_hb_8 :type: float | None :value: None .. py:attribute:: rna_ss_hb_weights :type: numpy.ndarray | None .. py:attribute:: drh_eps_hb :type: float | None :value: None .. py:attribute:: drh_a_hb :type: float | None :value: None .. py:attribute:: drh_dr0_hb :type: float | None :value: None .. py:attribute:: drh_dr_c_hb :type: float | None :value: None .. py:attribute:: drh_dr_low_hb :type: float | None :value: None .. py:attribute:: drh_dr_high_hb :type: float | None :value: None .. py:attribute:: drh_a_hb_1 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_1 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_1 :type: float | None :value: None .. py:attribute:: drh_a_hb_2 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_2 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_2 :type: float | None :value: None .. py:attribute:: drh_a_hb_3 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_3 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_3 :type: float | None :value: None .. py:attribute:: drh_a_hb_4 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_4 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_4 :type: float | None :value: None .. py:attribute:: drh_a_hb_7 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_7 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_7 :type: float | None :value: None .. py:attribute:: drh_a_hb_8 :type: float | None :value: None .. py:attribute:: drh_theta0_hb_8 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_hb_8 :type: float | None :value: None .. py:attribute:: drh_ss_hb_weights :type: numpy.ndarray | None .. py:attribute:: dna_config :type: jax_dna.energy.dna1.HydrogenBondingConfiguration | None :value: None .. py:attribute:: rna_config :type: jax_dna.energy.dna1.HydrogenBondingConfiguration | None :value: None .. py:attribute:: drh_config :type: jax_dna.energy.dna1.HydrogenBondingConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_eps_hb', 'dna_a_hb', 'dna_dr0_hb', 'dna_dr_c_hb', 'dna_dr_low_hb',... .. py:method:: init_params() -> HydrogenBondingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: HydrogenBonding Bases: :py:obj:`jax_dna.energy.base.BaseEnergyFunction` Hydrogen bonding energy function for NA1 model. .. py:attribute:: params :type: HydrogenBondingConfiguration .. py:method:: __call__(body: jax_dna.energy.na1.nucleotide.HybridNucleotide, seq: jax_dna.utils.types.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.