mythos.energy.na1.nucleotide

Extends jax_md.rigid_body.RigidBody for NA1 nucleotide.

Classes

Nucleotide rigid body with additional sites for NA1.

class mythos.energy.na1.nucleotide.HybridNucleotide[source]

Nucleotide rigid body with additional sites for NA1.

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.

static from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, dna_com_to_backbone_x: mythos.utils.types.Scalar, dna_com_to_backbone_y: mythos.utils.types.Scalar, dna_com_to_backbone_dna1: mythos.utils.types.Scalar, dna_com_to_hb: mythos.utils.types.Scalar, dna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_backbone_x: mythos.utils.types.Scalar, rna_com_to_backbone_y: mythos.utils.types.Scalar, rna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_hb: mythos.utils.types.Scalar, rna_p3_x: mythos.utils.types.Scalar, rna_p3_y: mythos.utils.types.Scalar, rna_p3_z: mythos.utils.types.Scalar, rna_p5_x: mythos.utils.types.Scalar, rna_p5_y: mythos.utils.types.Scalar, rna_p5_z: mythos.utils.types.Scalar, rna_pos_stack_3_a1: mythos.utils.types.Scalar, rna_pos_stack_3_a2: mythos.utils.types.Scalar, rna_pos_stack_5_a1: mythos.utils.types.Scalar, rna_pos_stack_5_a2: mythos.utils.types.Scalar) → HybridNucleotide[source]: Class method to precompute nucleotide sites from a rigid body.