mythos.energy.rna2

Implementation of the oxRNA2 energy model in mythos.

Submodules

Classes

`CrossStacking`	Cross-stacking energy function for RNA2 model.
`CrossStackingConfiguration`	Configuration for the cross-stacking energy function.
`Nucleotide`	Nucleotide rigid body with additional sites for RNA2.
`Stacking`	Stacking energy function for DNA1 model.
`StackingConfiguration`	Configuration for the stacking energy function.

Package Contents

class mythos.energy.rna2.CrossStacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Cross-stacking energy function for RNA2 model.

params: CrossStackingConfiguration

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[source]: Computes the cross stacking energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.rna2.nucleotide.Nucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.rna2.CrossStackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

dr_low_cross: float | None = None

dr_high_cross: float | None = None

k_cross: float | None = None

r0_cross: float | None = None

dr_c_cross: float | None = None

theta0_cross_1: float | None = None

delta_theta_star_cross_1: float | None = None

a_cross_1: float | None = None

theta0_cross_2: float | None = None

delta_theta_star_cross_2: float | None = None

a_cross_2: float | None = None

theta0_cross_3: float | None = None

delta_theta_star_cross_3: float | None = None

a_cross_3: float | None = None

theta0_cross_7: float | None = None

delta_theta_star_cross_7: float | None = None

a_cross_7: float | None = None

theta0_cross_8: float | None = None

delta_theta_star_cross_8: float | None = None

a_cross_8: float | None = None

b_low_cross: float | None = None

dr_c_low_cross: float | None = None

b_high_cross: float | None = None

dr_c_high_cross: float | None = None

b_cross_1: float | None = None

delta_theta_cross_1_c: float | None = None

b_cross_2: float | None = None

delta_theta_cross_2_c: float | None = None

b_cross_3: float | None = None

delta_theta_cross_3_c: float | None = None

b_cross_7: float | None = None

delta_theta_cross_7_c: float | None = None

b_cross_8: float | None = None

delta_theta_cross_8_c: float | None = None

required_params: tuple[str] = ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',...

init_params() → CrossStackingConfiguration[source]

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.rna2.Nucleotide[source]

Bases: 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.

center: mythos.utils.types.Arr_Nucleotide_3

orientation: mythos.utils.types.Arr_Nucleotide_3 | jax_md.rigid_body.Quaternion

stack_sites: mythos.utils.types.Arr_Nucleotide_3

back_sites: mythos.utils.types.Arr_Nucleotide_3

base_sites: mythos.utils.types.Arr_Nucleotide_3

back_base_vectors: mythos.utils.types.Arr_Nucleotide_3

base_normals: mythos.utils.types.Arr_Nucleotide_3

cross_prods: mythos.utils.types.Arr_Nucleotide_3

bb_p3_sites: mythos.utils.types.Arr_Nucleotide_3

bb_p5_sites: mythos.utils.types.Arr_Nucleotide_3

stack3_sites: mythos.utils.types.Arr_Nucleotide_3

stack5_sites: mythos.utils.types.Arr_Nucleotide_3

static 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[source]: Class method to precompute nucleotide sites from a rigid body.

class mythos.energy.rna2.Stacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Stacking energy function for DNA1 model.

params: StackingConfiguration

compute_v_stack(body: mythos.energy.rna2.nucleotide.Nucleotide, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the sequence-independent energy for each bonded pair.

pseq_weights(i: int, j: int, seq: mythos.utils.types.Probabilistic_Sequence) → float[source]: Computes the probabilistic sequence-dependent weight for a bonded pair.

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[source]: Computes the stacking energy for each bonded pair.

compute_energy(nucleotide: mythos.energy.rna2.nucleotide.Nucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.rna2.StackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

eps_stack_base: float | None = None

eps_stack_kt_coeff: float | None = None

dr_low_stack: float | None = None

dr_high_stack: float | None = None

a_stack: float | None = None

dr0_stack: float | None = None

dr_c_stack: float | None = None

theta0_stack_5: float | None = None

delta_theta_star_stack_5: float | None = None

a_stack_5: float | None = None

theta0_stack_6: float | None = None

delta_theta_star_stack_6: float | None = None

a_stack_6: float | None = None

theta0_stack_9: float | None = None

delta_theta_star_stack_9: float | None = None

a_stack_9: float | None = None

theta0_stack_10: float | None = None

delta_theta_star_stack_10: float | None = None

a_stack_10: float | None = None

neg_cos_phi1_star_stack: float | None = None

a_stack_1: float | None = None

neg_cos_phi2_star_stack: float | None = None

a_stack_2: float | None = None

pseq: mythos.utils.types.Probabilistic_Sequence | None = None

pseq_constraints: mythos.input.sequence_constraints.SequenceConstraints | None = None

kt: float | None = None

ss_stack_weights: numpy.ndarray | None = None

b_low_stack: float | None = None

dr_c_low_stack: float | None = None

b_high_stack: float | None = None

dr_c_high_stack: float | None = None

b_stack_5: float | None = None

delta_theta_stack_5_c: float | None = None

b_stack_6: float | None = None

delta_theta_stack_6_c: float | None = None

b_stack_9: float | None = None

delta_theta_stack_9_c: float | None = None

b_stack_10: float | None = None

delta_theta_stack_10_c: float | None = None

b_neg_cos_phi1_stack: float | None = None

neg_cos_phi1_c_stack: float | None = None

b_neg_cos_phi2_stack: float | None = None

neg_cos_phi2_c_stack: float | None = None

eps_stack: float | None = None

required_params: tuple[str] = ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...

init_params() → StackingConfiguration[source]

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.