jax_dna.energy.na1.cross_stacking ================================= .. py:module:: jax_dna.energy.na1.cross_stacking .. autoapi-nested-parse:: Cross-stacking energy term for NA1 model. Classes ------- .. autoapisummary:: jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration jax_dna.energy.na1.cross_stacking.CrossStacking Module Contents --------------- .. py:class:: CrossStackingConfiguration 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_dr_low_cross :type: float | None :value: None .. py:attribute:: dna_dr_high_cross :type: float | None :value: None .. py:attribute:: dna_k_cross :type: float | None :value: None .. py:attribute:: dna_r0_cross :type: float | None :value: None .. py:attribute:: dna_dr_c_cross :type: float | None :value: None .. py:attribute:: dna_theta0_cross_1 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_1 :type: float | None :value: None .. py:attribute:: dna_a_cross_1 :type: float | None :value: None .. py:attribute:: dna_theta0_cross_2 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_2 :type: float | None :value: None .. py:attribute:: dna_a_cross_2 :type: float | None :value: None .. py:attribute:: dna_theta0_cross_3 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_3 :type: float | None :value: None .. py:attribute:: dna_a_cross_3 :type: float | None :value: None .. py:attribute:: dna_theta0_cross_4 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_4 :type: float | None :value: None .. py:attribute:: dna_a_cross_4 :type: float | None :value: None .. py:attribute:: dna_theta0_cross_7 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_7 :type: float | None :value: None .. py:attribute:: dna_a_cross_7 :type: float | None :value: None .. py:attribute:: dna_theta0_cross_8 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_cross_8 :type: float | None :value: None .. py:attribute:: dna_a_cross_8 :type: float | None :value: None .. py:attribute:: rna_dr_low_cross :type: float | None :value: None .. py:attribute:: rna_dr_high_cross :type: float | None :value: None .. py:attribute:: rna_k_cross :type: float | None :value: None .. py:attribute:: rna_r0_cross :type: float | None :value: None .. py:attribute:: rna_dr_c_cross :type: float | None :value: None .. py:attribute:: rna_theta0_cross_1 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_cross_1 :type: float | None :value: None .. py:attribute:: rna_a_cross_1 :type: float | None :value: None .. py:attribute:: rna_theta0_cross_2 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_cross_2 :type: float | None :value: None .. py:attribute:: rna_a_cross_2 :type: float | None :value: None .. py:attribute:: rna_theta0_cross_3 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_cross_3 :type: float | None :value: None .. py:attribute:: rna_a_cross_3 :type: float | None :value: None .. py:attribute:: rna_theta0_cross_7 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_cross_7 :type: float | None :value: None .. py:attribute:: rna_a_cross_7 :type: float | None :value: None .. py:attribute:: rna_theta0_cross_8 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_cross_8 :type: float | None :value: None .. py:attribute:: rna_a_cross_8 :type: float | None :value: None .. py:attribute:: drh_dr_low_cross :type: float | None :value: None .. py:attribute:: drh_dr_high_cross :type: float | None :value: None .. py:attribute:: drh_k_cross :type: float | None :value: None .. py:attribute:: drh_r0_cross :type: float | None :value: None .. py:attribute:: drh_dr_c_cross :type: float | None :value: None .. py:attribute:: drh_theta0_cross_1 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_1 :type: float | None :value: None .. py:attribute:: drh_a_cross_1 :type: float | None :value: None .. py:attribute:: drh_theta0_cross_2 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_2 :type: float | None :value: None .. py:attribute:: drh_a_cross_2 :type: float | None :value: None .. py:attribute:: drh_theta0_cross_3 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_3 :type: float | None :value: None .. py:attribute:: drh_a_cross_3 :type: float | None :value: None .. py:attribute:: drh_theta0_cross_4 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_4 :type: float | None :value: None .. py:attribute:: drh_a_cross_4 :type: float | None :value: None .. py:attribute:: drh_theta0_cross_7 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_7 :type: float | None :value: None .. py:attribute:: drh_a_cross_7 :type: float | None :value: None .. py:attribute:: drh_theta0_cross_8 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_cross_8 :type: float | None :value: None .. py:attribute:: drh_a_cross_8 :type: float | None :value: None .. py:attribute:: dna_config :type: jax_dna.energy.dna1.CrossStackingConfiguration | None :value: None .. py:attribute:: rna_config :type: jax_dna.energy.rna2.CrossStackingConfiguration | None :value: None .. py:attribute:: drh_config :type: jax_dna.energy.dna1.CrossStackingConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_dr_low_cross', 'dna_dr_high_cross', 'dna_k_cross', 'dna_r0_cross',... .. py:method:: init_params() -> CrossStackingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: CrossStacking Bases: :py:obj:`jax_dna.energy.base.BaseEnergyFunction` Cross-stacking energy function for NA1 model. .. py:attribute:: params :type: CrossStackingConfiguration .. 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.