mythos.energy.na1.coaxial_stacking ================================== .. py:module:: mythos.energy.na1.coaxial_stacking .. autoapi-nested-parse:: Coaxial stacking energy term for NA1 model. Classes ------- .. autoapisummary:: mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration mythos.energy.na1.coaxial_stacking.CoaxialStacking Module Contents --------------- .. py:class:: CoaxialStackingConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the cross-stacking energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: dna_dr_low_coax :type: float | None :value: None .. py:attribute:: dna_dr_high_coax :type: float | None :value: None .. py:attribute:: dna_k_coax :type: float | None :value: None .. py:attribute:: dna_dr0_coax :type: float | None :value: None .. py:attribute:: dna_dr_c_coax :type: float | None :value: None .. py:attribute:: dna_theta0_coax_4 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_coax_4 :type: float | None :value: None .. py:attribute:: dna_a_coax_4 :type: float | None :value: None .. py:attribute:: dna_theta0_coax_1 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_coax_1 :type: float | None :value: None .. py:attribute:: dna_a_coax_1 :type: float | None :value: None .. py:attribute:: dna_theta0_coax_5 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_coax_5 :type: float | None :value: None .. py:attribute:: dna_a_coax_5 :type: float | None :value: None .. py:attribute:: dna_theta0_coax_6 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_coax_6 :type: float | None :value: None .. py:attribute:: dna_a_coax_6 :type: float | None :value: None .. py:attribute:: dna_a_coax_1_f6 :type: float | None :value: None .. py:attribute:: dna_b_coax_1_f6 :type: float | None :value: None .. py:attribute:: rna_dr_low_coax :type: float | None :value: None .. py:attribute:: rna_dr_high_coax :type: float | None :value: None .. py:attribute:: rna_k_coax :type: float | None :value: None .. py:attribute:: rna_dr0_coax :type: float | None :value: None .. py:attribute:: rna_dr_c_coax :type: float | None :value: None .. py:attribute:: rna_theta0_coax_4 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_coax_4 :type: float | None :value: None .. py:attribute:: rna_a_coax_4 :type: float | None :value: None .. py:attribute:: rna_theta0_coax_1 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_coax_1 :type: float | None :value: None .. py:attribute:: rna_a_coax_1 :type: float | None :value: None .. py:attribute:: rna_theta0_coax_5 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_coax_5 :type: float | None :value: None .. py:attribute:: rna_a_coax_5 :type: float | None :value: None .. py:attribute:: rna_theta0_coax_6 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_coax_6 :type: float | None :value: None .. py:attribute:: rna_a_coax_6 :type: float | None :value: None .. py:attribute:: rna_cos_phi3_star_coax :type: float | None :value: None .. py:attribute:: rna_a_coax_3p :type: float | None :value: None .. py:attribute:: rna_cos_phi4_star_coax :type: float | None :value: None .. py:attribute:: rna_a_coax_4p :type: float | None :value: None .. py:attribute:: drh_dr_low_coax :type: float | None :value: None .. py:attribute:: drh_dr_high_coax :type: float | None :value: None .. py:attribute:: drh_k_coax :type: float | None :value: None .. py:attribute:: drh_dr0_coax :type: float | None :value: None .. py:attribute:: drh_dr_c_coax :type: float | None :value: None .. py:attribute:: drh_theta0_coax_4 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_coax_4 :type: float | None :value: None .. py:attribute:: drh_a_coax_4 :type: float | None :value: None .. py:attribute:: drh_theta0_coax_1 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_coax_1 :type: float | None :value: None .. py:attribute:: drh_a_coax_1 :type: float | None :value: None .. py:attribute:: drh_theta0_coax_5 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_coax_5 :type: float | None :value: None .. py:attribute:: drh_a_coax_5 :type: float | None :value: None .. py:attribute:: drh_theta0_coax_6 :type: float | None :value: None .. py:attribute:: drh_delta_theta_star_coax_6 :type: float | None :value: None .. py:attribute:: drh_a_coax_6 :type: float | None :value: None .. py:attribute:: drh_cos_phi3_star_coax :type: float | None :value: None .. py:attribute:: drh_a_coax_3p :type: float | None :value: None .. py:attribute:: drh_cos_phi4_star_coax :type: float | None :value: None .. py:attribute:: drh_a_coax_4p :type: float | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna2.CoaxialStackingConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna1.CoaxialStackingConfiguration | None :value: None .. py:attribute:: drh_config :type: mythos.energy.dna1.CoaxialStackingConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_dr_low_coax', 'dna_dr_high_coax', 'dna_k_coax', 'dna_dr0_coax',... .. py:method:: init_params() -> CoaxialStackingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: CoaxialStacking Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Coaxial stacking energy function for NA1 model. .. py:attribute:: params :type: CoaxialStackingConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide.