mythos.energy.rna2 ================== .. py:module:: mythos.energy.rna2 .. autoapi-nested-parse:: Implementation of the oxRNA2 energy model in mythos. Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/mythos/energy/rna2/cross_stacking/index /autoapi/mythos/energy/rna2/interactions/index /autoapi/mythos/energy/rna2/nucleotide/index /autoapi/mythos/energy/rna2/stacking/index Classes ------- .. autoapisummary:: mythos.energy.rna2.CrossStacking mythos.energy.rna2.CrossStackingConfiguration mythos.energy.rna2.Nucleotide mythos.energy.rna2.Stacking mythos.energy.rna2.StackingConfiguration Package Contents ---------------- .. py:class:: CrossStacking Bases: :py:obj:`mythos.energy.base.BaseEnergyFunction` Cross-stacking energy function for RNA2 model. .. py:attribute:: params :type: CrossStackingConfiguration .. py:method:: pairwise_energies(body_i: mythos.energy.rna2.nucleotide.Nucleotide, body_j: mythos.energy.rna2.nucleotide.Nucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) -> mythos.utils.types.Arr_Unbonded_Neighbors Computes the cross stacking energy for each unbonded pair. .. py:method:: compute_energy(nucleotide: mythos.energy.rna2.nucleotide.Nucleotide) -> 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:: dr_low_cross :type: float | None :value: None .. py:attribute:: dr_high_cross :type: float | None :value: None .. py:attribute:: k_cross :type: float | None :value: None .. py:attribute:: r0_cross :type: float | None :value: None .. py:attribute:: dr_c_cross :type: float | None :value: None .. py:attribute:: theta0_cross_1 :type: float | None :value: None .. py:attribute:: delta_theta_star_cross_1 :type: float | None :value: None .. py:attribute:: a_cross_1 :type: float | None :value: None .. py:attribute:: theta0_cross_2 :type: float | None :value: None .. py:attribute:: delta_theta_star_cross_2 :type: float | None :value: None .. py:attribute:: a_cross_2 :type: float | None :value: None .. py:attribute:: theta0_cross_3 :type: float | None :value: None .. py:attribute:: delta_theta_star_cross_3 :type: float | None :value: None .. py:attribute:: a_cross_3 :type: float | None :value: None .. py:attribute:: theta0_cross_7 :type: float | None :value: None .. py:attribute:: delta_theta_star_cross_7 :type: float | None :value: None .. py:attribute:: a_cross_7 :type: float | None :value: None .. py:attribute:: theta0_cross_8 :type: float | None :value: None .. py:attribute:: delta_theta_star_cross_8 :type: float | None :value: None .. py:attribute:: a_cross_8 :type: float | None :value: None .. py:attribute:: b_low_cross :type: float | None :value: None .. py:attribute:: dr_c_low_cross :type: float | None :value: None .. py:attribute:: b_high_cross :type: float | None :value: None .. py:attribute:: dr_c_high_cross :type: float | None :value: None .. py:attribute:: b_cross_1 :type: float | None :value: None .. py:attribute:: delta_theta_cross_1_c :type: float | None :value: None .. py:attribute:: b_cross_2 :type: float | None :value: None .. py:attribute:: delta_theta_cross_2_c :type: float | None :value: None .. py:attribute:: b_cross_3 :type: float | None :value: None .. py:attribute:: delta_theta_cross_3_c :type: float | None :value: None .. py:attribute:: b_cross_7 :type: float | None :value: None .. py:attribute:: delta_theta_cross_7_c :type: float | None :value: None .. py:attribute:: b_cross_8 :type: float | None :value: None .. py:attribute:: delta_theta_cross_8_c :type: float | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',... .. py:method:: init_params() -> CrossStackingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present. .. py:class:: Nucleotide Bases: :py:obj:`mythos.energy.base.BaseNucleotide` Nucleotide rigid body with additional sites for RNA2. 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:: center :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: orientation :type: mythos.utils.types.Arr_Nucleotide_3 | jax_md.rigid_body.Quaternion .. py:attribute:: stack_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: back_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: base_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: back_base_vectors :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: base_normals :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: cross_prods :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: bb_p3_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: bb_p5_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: stack3_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:attribute:: stack5_sites :type: mythos.utils.types.Arr_Nucleotide_3 .. py:method:: from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, com_to_backbone_x: mythos.utils.types.Scalar, com_to_backbone_y: mythos.utils.types.Scalar, com_to_stacking: mythos.utils.types.Scalar, com_to_hb: mythos.utils.types.Scalar, p3_x: mythos.utils.types.Scalar, p3_y: mythos.utils.types.Scalar, p3_z: mythos.utils.types.Scalar, p5_x: mythos.utils.types.Scalar, p5_y: mythos.utils.types.Scalar, p5_z: mythos.utils.types.Scalar, pos_stack_3_a1: mythos.utils.types.Scalar, pos_stack_3_a2: mythos.utils.types.Scalar, pos_stack_5_a1: mythos.utils.types.Scalar, pos_stack_5_a2: mythos.utils.types.Scalar) -> Nucleotide :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_v_stack(body: mythos.energy.rna2.nucleotide.Nucleotide, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) -> mythos.utils.types.Arr_Bonded_Neighbors Computes the sequence-independent energy for each bonded pair. .. py:method:: pseq_weights(i: int, j: int, seq: mythos.utils.types.Probabilistic_Sequence) -> float Computes the probabilistic sequence-dependent weight for a bonded pair. .. py:method:: pairwise_energies(body: mythos.energy.rna2.nucleotide.Nucleotide, seq: mythos.utils.types.Discrete_Sequence, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) -> mythos.utils.types.Arr_Bonded_Neighbors Computes the stacking energy for each bonded pair. .. py:method:: compute_energy(nucleotide: mythos.energy.rna2.nucleotide.Nucleotide) -> 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:: eps_stack_base :type: float | None :value: None .. py:attribute:: eps_stack_kt_coeff :type: float | None :value: None .. py:attribute:: dr_low_stack :type: float | None :value: None .. py:attribute:: dr_high_stack :type: float | None :value: None .. py:attribute:: a_stack :type: float | None :value: None .. py:attribute:: dr0_stack :type: float | None :value: None .. py:attribute:: dr_c_stack :type: float | None :value: None .. py:attribute:: theta0_stack_5 :type: float | None :value: None .. py:attribute:: delta_theta_star_stack_5 :type: float | None :value: None .. py:attribute:: a_stack_5 :type: float | None :value: None .. py:attribute:: theta0_stack_6 :type: float | None :value: None .. py:attribute:: delta_theta_star_stack_6 :type: float | None :value: None .. py:attribute:: a_stack_6 :type: float | None :value: None .. py:attribute:: theta0_stack_9 :type: float | None :value: None .. py:attribute:: delta_theta_star_stack_9 :type: float | None :value: None .. py:attribute:: a_stack_9 :type: float | None :value: None .. py:attribute:: theta0_stack_10 :type: float | None :value: None .. py:attribute:: delta_theta_star_stack_10 :type: float | None :value: None .. py:attribute:: a_stack_10 :type: float | None :value: None .. py:attribute:: neg_cos_phi1_star_stack :type: float | None :value: None .. py:attribute:: a_stack_1 :type: float | None :value: None .. py:attribute:: neg_cos_phi2_star_stack :type: float | None :value: None .. py:attribute:: a_stack_2 :type: float | 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:: kt :type: float | None :value: None .. py:attribute:: ss_stack_weights :type: numpy.ndarray | None :value: None .. py:attribute:: b_low_stack :type: float | None :value: None .. py:attribute:: dr_c_low_stack :type: float | None :value: None .. py:attribute:: b_high_stack :type: float | None :value: None .. py:attribute:: dr_c_high_stack :type: float | None :value: None .. py:attribute:: b_stack_5 :type: float | None :value: None .. py:attribute:: delta_theta_stack_5_c :type: float | None :value: None .. py:attribute:: b_stack_6 :type: float | None :value: None .. py:attribute:: delta_theta_stack_6_c :type: float | None :value: None .. py:attribute:: b_stack_9 :type: float | None :value: None .. py:attribute:: delta_theta_stack_9_c :type: float | None :value: None .. py:attribute:: b_stack_10 :type: float | None :value: None .. py:attribute:: delta_theta_stack_10_c :type: float | None :value: None .. py:attribute:: b_neg_cos_phi1_stack :type: float | None :value: None .. py:attribute:: neg_cos_phi1_c_stack :type: float | None :value: None .. py:attribute:: b_neg_cos_phi2_stack :type: float | None :value: None .. py:attribute:: neg_cos_phi2_c_stack :type: float | None :value: None .. py:attribute:: eps_stack :type: float | None :value: None .. py:attribute:: required_params :type: tuple[str] :value: ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',... .. py:method:: init_params() -> StackingConfiguration Initializes the dependent parameters in configuration. Should be implemented in the subclass if dependent parameters are present.