mythos.energy.na1 ================= .. py:module:: mythos.energy.na1 .. autoapi-nested-parse:: Implementation of the oxNA energy model in mythos. Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/mythos/energy/na1/bonded_excluded_volume/index /autoapi/mythos/energy/na1/coaxial_stacking/index /autoapi/mythos/energy/na1/cross_stacking/index /autoapi/mythos/energy/na1/debye/index /autoapi/mythos/energy/na1/fene/index /autoapi/mythos/energy/na1/hydrogen_bonding/index /autoapi/mythos/energy/na1/nucleotide/index /autoapi/mythos/energy/na1/stacking/index /autoapi/mythos/energy/na1/unbonded_excluded_volume/index /autoapi/mythos/energy/na1/utils/index Classes ------- .. autoapisummary:: mythos.energy.na1.BondedExcludedVolume mythos.energy.na1.BondedExcludedVolumeConfiguration mythos.energy.na1.CoaxialStacking mythos.energy.na1.CoaxialStackingConfiguration mythos.energy.na1.CrossStacking mythos.energy.na1.CrossStackingConfiguration mythos.energy.na1.Debye mythos.energy.na1.DebyeConfiguration mythos.energy.na1.Fene mythos.energy.na1.FeneConfiguration mythos.energy.na1.HydrogenBonding mythos.energy.na1.HydrogenBondingConfiguration mythos.energy.na1.HybridNucleotide mythos.energy.na1.Stacking mythos.energy.na1.StackingConfiguration mythos.energy.na1.UnbondedExcludedVolume mythos.energy.na1.UnbondedExcludedVolumeConfiguration Package Contents ---------------- .. py:class:: BondedExcludedVolume Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Bonded excluded volume energy function for NA1 model. .. py:attribute:: params :type: BondedExcludedVolumeConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: BondedExcludedVolumeConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the bonded excluded volume energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: dna_eps_exc :type: float | None :value: None .. py:attribute:: dna_dr_star_base :type: float | None :value: None .. py:attribute:: dna_sigma_base :type: float | None :value: None .. py:attribute:: dna_sigma_back_base :type: float | None :value: None .. py:attribute:: dna_sigma_base_back :type: float | None :value: None .. py:attribute:: dna_dr_star_back_base :type: float | None :value: None .. py:attribute:: dna_dr_star_base_back :type: float | None :value: None .. py:attribute:: rna_eps_exc :type: float | None :value: None .. py:attribute:: rna_dr_star_base :type: float | None :value: None .. py:attribute:: rna_sigma_base :type: float | None :value: None .. py:attribute:: rna_sigma_back_base :type: float | None :value: None .. py:attribute:: rna_sigma_base_back :type: float | None :value: None .. py:attribute:: rna_dr_star_back_base :type: float | None :value: None .. py:attribute:: rna_dr_star_base_back :type: float | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_sigma_back_base',... .. py:method:: init_params() -> BondedExcludedVolumeConfiguration 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. .. 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:: CrossStacking Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Cross-stacking energy function for NA1 model. .. py:attribute:: params :type: CrossStackingConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: CrossStackingConfiguration 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_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: mythos.energy.dna1.CrossStackingConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.rna2.CrossStackingConfiguration | None :value: None .. py:attribute:: drh_config :type: mythos.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:: Debye Bases: :py:obj:`mythos.energy.dna2.Debye` Debye-huckel energy function for NA1 model. .. py:attribute:: params :type: DebyeConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: DebyeConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the debye-huckel energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: half_charged_ends :type: bool | None :value: None .. py:attribute:: kt :type: float | None :value: None .. py:attribute:: salt_conc :type: float | None :value: None .. py:attribute:: dna_q_eff :type: float | None :value: None .. py:attribute:: dna_lambda_factor :type: float | None :value: None .. py:attribute:: dna_prefactor_coeff :type: float | None :value: None .. py:attribute:: rna_q_eff :type: float | None :value: None .. py:attribute:: rna_lambda_factor :type: float | None :value: None .. py:attribute:: rna_prefactor_coeff :type: float | None :value: None .. py:attribute:: drh_q_eff :type: float | None :value: None .. py:attribute:: drh_lambda_factor :type: float | None :value: None .. py:attribute:: drh_prefactor_coeff :type: float | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna2.DebyeConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna2.DebyeConfiguration | None :value: None .. py:attribute:: drh_config :type: mythos.energy.dna2.DebyeConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'half_charged_ends', 'kt', 'salt_conc', 'dna_q_eff', 'dna_lambda_factor',... .. py:method:: init_params() -> DebyeConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: Fene Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` FENE energy function for NA1 model. .. py:attribute:: params :type: FeneConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: FeneConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the FENE energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: dna_eps_backbone :type: float | None :value: None .. py:attribute:: dna_r0_backbone :type: float | None :value: None .. py:attribute:: dna_delta_backbone :type: float | None :value: None .. py:attribute:: dna_fmax :type: float | None :value: None .. py:attribute:: dna_finf :type: float | None :value: None .. py:attribute:: rna_eps_backbone :type: float | None :value: None .. py:attribute:: rna_r0_backbone :type: float | None :value: None .. py:attribute:: rna_delta_backbone :type: float | None :value: None .. py:attribute:: rna_fmax :type: float | None :value: None .. py:attribute:: rna_finf :type: float | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna1.FeneConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna1.FeneConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_eps_backbone', 'dna_r0_backbone', 'dna_delta_backbone', 'dna_fmax', 'dna_finf',... .. py:method:: init_params() -> FeneConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: HydrogenBonding Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Hydrogen bonding energy function for NA1 model. .. py:attribute:: params :type: HydrogenBondingConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: HydrogenBondingConfiguration 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_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 :value: 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 :value: 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 :value: None .. py:attribute:: pseq :type: mythos.utils.types.Probabilistic_Sequence | None :value: None .. py:attribute:: pseq_constraints :type: mythos.input.sequence_constraints.SequenceConstraints | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna1.HydrogenBondingConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna1.HydrogenBondingConfiguration | None :value: None .. py:attribute:: drh_config :type: mythos.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:: HybridNucleotide Nucleotide rigid body with additional sites for NA1. This class is inteneded to be used as a dataclass for a nucleotide rigid body as a `rigid_body_transform_fn` in `jax_md.energy.ComposedEnergyFunction`. .. py:attribute:: dna :type: mythos.energy.dna2.nucleotide.Nucleotide .. py:attribute:: rna :type: mythos.energy.rna2.nucleotide.Nucleotide .. py:method:: from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, dna_com_to_backbone_x: mythos.utils.types.Scalar, dna_com_to_backbone_y: mythos.utils.types.Scalar, dna_com_to_backbone_dna1: mythos.utils.types.Scalar, dna_com_to_hb: mythos.utils.types.Scalar, dna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_backbone_x: mythos.utils.types.Scalar, rna_com_to_backbone_y: mythos.utils.types.Scalar, rna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_hb: mythos.utils.types.Scalar, rna_p3_x: mythos.utils.types.Scalar, rna_p3_y: mythos.utils.types.Scalar, rna_p3_z: mythos.utils.types.Scalar, rna_p5_x: mythos.utils.types.Scalar, rna_p5_y: mythos.utils.types.Scalar, rna_p5_z: mythos.utils.types.Scalar, rna_pos_stack_3_a1: mythos.utils.types.Scalar, rna_pos_stack_3_a2: mythos.utils.types.Scalar, rna_pos_stack_5_a1: mythos.utils.types.Scalar, rna_pos_stack_5_a2: mythos.utils.types.Scalar) -> HybridNucleotide :staticmethod: Class method to precompute nucleotide sites from a rigid body. .. py:class:: Stacking Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Stacking energy function for DNA1 model. .. py:attribute:: params :type: StackingConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: StackingConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the stacking energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: kt :type: float | None :value: None .. py:attribute:: dna_eps_stack_base :type: float | None :value: None .. py:attribute:: dna_eps_stack_kt_coeff :type: float | None :value: None .. py:attribute:: dna_dr_low_stack :type: float | None :value: None .. py:attribute:: dna_dr_high_stack :type: float | None :value: None .. py:attribute:: dna_a_stack :type: float | None :value: None .. py:attribute:: dna_dr0_stack :type: float | None :value: None .. py:attribute:: dna_dr_c_stack :type: float | None :value: None .. py:attribute:: dna_theta0_stack_4 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_stack_4 :type: float | None :value: None .. py:attribute:: dna_a_stack_4 :type: float | None :value: None .. py:attribute:: dna_theta0_stack_5 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_stack_5 :type: float | None :value: None .. py:attribute:: dna_a_stack_5 :type: float | None :value: None .. py:attribute:: dna_theta0_stack_6 :type: float | None :value: None .. py:attribute:: dna_delta_theta_star_stack_6 :type: float | None :value: None .. py:attribute:: dna_a_stack_6 :type: float | None :value: None .. py:attribute:: dna_neg_cos_phi1_star_stack :type: float | None :value: None .. py:attribute:: dna_a_stack_1 :type: float | None :value: None .. py:attribute:: dna_neg_cos_phi2_star_stack :type: float | None :value: None .. py:attribute:: dna_a_stack_2 :type: float | None :value: None .. py:attribute:: dna_ss_stack_weights :type: numpy.ndarray | None :value: None .. py:attribute:: rna_eps_stack_base :type: float | None :value: None .. py:attribute:: rna_eps_stack_kt_coeff :type: float | None :value: None .. py:attribute:: rna_dr_low_stack :type: float | None :value: None .. py:attribute:: rna_dr_high_stack :type: float | None :value: None .. py:attribute:: rna_a_stack :type: float | None :value: None .. py:attribute:: rna_dr0_stack :type: float | None :value: None .. py:attribute:: rna_dr_c_stack :type: float | None :value: None .. py:attribute:: rna_theta0_stack_5 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_stack_5 :type: float | None :value: None .. py:attribute:: rna_a_stack_5 :type: float | None :value: None .. py:attribute:: rna_theta0_stack_6 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_stack_6 :type: float | None :value: None .. py:attribute:: rna_a_stack_6 :type: float | None :value: None .. py:attribute:: rna_theta0_stack_9 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_stack_9 :type: float | None :value: None .. py:attribute:: rna_a_stack_9 :type: float | None :value: None .. py:attribute:: rna_theta0_stack_10 :type: float | None :value: None .. py:attribute:: rna_delta_theta_star_stack_10 :type: float | None :value: None .. py:attribute:: rna_a_stack_10 :type: float | None :value: None .. py:attribute:: rna_neg_cos_phi1_star_stack :type: float | None :value: None .. py:attribute:: rna_a_stack_1 :type: float | None :value: None .. py:attribute:: rna_neg_cos_phi2_star_stack :type: float | None :value: None .. py:attribute:: rna_a_stack_2 :type: float | None :value: None .. py:attribute:: rna_ss_stack_weights :type: numpy.ndarray | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna1.StackingConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.rna2.StackingConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'kt', 'dna_eps_stack_base', 'dna_eps_stack_kt_coeff', 'dna_dr_low_stack',... .. py:method:: init_params() -> StackingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: UnbondedExcludedVolume Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Unbonded excluded volume energy function for NA1 model. .. py:attribute:: params :type: UnbondedExcludedVolumeConfiguration .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar Compute the energy of the system given the nucleotide. .. py:class:: UnbondedExcludedVolumeConfiguration Bases: :py:obj:`mythos.energy.configuration.BaseConfiguration` Configuration for the unbonded excluded volume energy function. .. py:attribute:: nt_type :type: mythos.utils.types.Arr_Nucleotide | None :value: None .. py:attribute:: dna_eps_exc :type: float | None :value: None .. py:attribute:: dna_dr_star_base :type: float | None :value: None .. py:attribute:: dna_sigma_base :type: float | None :value: None .. py:attribute:: dna_dr_star_back_base :type: float | None :value: None .. py:attribute:: dna_sigma_back_base :type: float | None :value: None .. py:attribute:: dna_dr_star_base_back :type: float | None :value: None .. py:attribute:: dna_sigma_base_back :type: float | None :value: None .. py:attribute:: dna_dr_star_backbone :type: float | None :value: None .. py:attribute:: dna_sigma_backbone :type: float | None :value: None .. py:attribute:: rna_eps_exc :type: float | None :value: None .. py:attribute:: rna_dr_star_base :type: float | None :value: None .. py:attribute:: rna_sigma_base :type: float | None :value: None .. py:attribute:: rna_dr_star_back_base :type: float | None :value: None .. py:attribute:: rna_sigma_back_base :type: float | None :value: None .. py:attribute:: rna_dr_star_base_back :type: float | None :value: None .. py:attribute:: rna_sigma_base_back :type: float | None :value: None .. py:attribute:: rna_dr_star_backbone :type: float | None :value: None .. py:attribute:: rna_sigma_backbone :type: float | None :value: None .. py:attribute:: drh_eps_exc :type: float | None :value: None .. py:attribute:: drh_dr_star_base :type: float | None :value: None .. py:attribute:: drh_sigma_base :type: float | None :value: None .. py:attribute:: drh_dr_star_back_base :type: float | None :value: None .. py:attribute:: drh_sigma_back_base :type: float | None :value: None .. py:attribute:: drh_dr_star_base_back :type: float | None :value: None .. py:attribute:: drh_sigma_base_back :type: float | None :value: None .. py:attribute:: drh_dr_star_backbone :type: float | None :value: None .. py:attribute:: drh_sigma_backbone :type: float | None :value: None .. py:attribute:: dna_config :type: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None :value: None .. py:attribute:: rna_config :type: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None :value: None .. py:attribute:: drh_config :type: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_dr_star_back_base',... .. py:method:: init_params() -> UnbondedExcludedVolumeConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present.