jax_dna.energy.dna2.nucleotide

Extends jax_md.rigid_body.RigidBody for DNA2 nucleotide.

Classes

Nucleotide rigid body with additional sites for DNA2.

Module Contents

class jax_dna.energy.dna2.nucleotide.Nucleotide[source]

Bases: jax_dna.energy.base.BaseNucleotide

Nucleotide rigid body with additional sites for DNA2.

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

back_sites_dna1: 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

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_backbone_dna1: jax_dna.utils.types.Scalar, com_to_hb: jax_dna.utils.types.Scalar, com_to_stacking: jax_dna.utils.types.Scalar) → Nucleotide[source]: Class method to precompute nucleotide sites from a rigid body.