jax_dna.energy.rna2.nucleotide

Extends jax_md.rigid_body.RigidBody for RNA2 nucleotide.

Classes

Nucleotide

Nucleotide rigid body with additional sites for RNA2.

Module Contents

class jax_dna.energy.rna2.nucleotide.Nucleotide

Bases: jax_dna.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: jax_dna.utils.types.Arr_Nucleotide_3

orientation: jax_dna.utils.types.Arr_Nucleotide_3 | jax_md.rigid_body.Quaternion

stack_sites: jax_dna.utils.types.Arr_Nucleotide_3

back_sites: jax_dna.utils.types.Arr_Nucleotide_3

base_sites: jax_dna.utils.types.Arr_Nucleotide_3

back_base_vectors: jax_dna.utils.types.Arr_Nucleotide_3

base_normals: jax_dna.utils.types.Arr_Nucleotide_3

cross_prods: jax_dna.utils.types.Arr_Nucleotide_3

bb_p3_sites: jax_dna.utils.types.Arr_Nucleotide_3

bb_p5_sites: jax_dna.utils.types.Arr_Nucleotide_3

stack3_sites: jax_dna.utils.types.Arr_Nucleotide_3

stack5_sites: jax_dna.utils.types.Arr_Nucleotide_3

static from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, com_to_backbone_x: jax_dna.utils.types.Scalar, com_to_backbone_y: jax_dna.utils.types.Scalar, com_to_stacking: jax_dna.utils.types.Scalar, com_to_hb: jax_dna.utils.types.Scalar, p3_x: jax_dna.utils.types.Scalar, p3_y: jax_dna.utils.types.Scalar, p3_z: jax_dna.utils.types.Scalar, p5_x: jax_dna.utils.types.Scalar, p5_y: jax_dna.utils.types.Scalar, p5_z: jax_dna.utils.types.Scalar, pos_stack_3_a1: jax_dna.utils.types.Scalar, pos_stack_3_a2: jax_dna.utils.types.Scalar, pos_stack_5_a1: jax_dna.utils.types.Scalar, pos_stack_5_a2: jax_dna.utils.types.Scalar) → Nucleotide

Class method to precompute nucleotide sites from a rigid body.