mythos.energy.dna1.nucleotide

Extends jax_md.rigid_body.RigidBody for DNA1 nucleotide.

Classes

Nucleotide rigid body with additional sites for DNA1.

Module Contents

class mythos.energy.dna1.nucleotide.Nucleotide[source]

Bases: mythos.energy.base.BaseNucleotide

Nucleotide rigid body with additional sites for DNA1.

This class is intended 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

static from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, com_to_backbone: mythos.utils.types.Scalar, com_to_hb: mythos.utils.types.Scalar, com_to_stacking: mythos.utils.types.Scalar) → Nucleotide[source]: Class method to precompute nucleotide sites from a rigid body.