mythos.energy.utils

Utility functions for energy calculations.

Functions

`q_to_back_base`(→ jax.numpy.ndarray)	Get the vector from the center to the base of the nucleotide.
`q_to_base_normal`(→ jax.numpy.ndarray)	Get the normal vector to the base of the nucleotide.
`q_to_cross_prod`(→ jax.numpy.ndarray)	Get the cross product vector of the nucleotide.
`get_pair_probs`(→ jax.numpy.ndarray)	Get the pair probabilities for a sequence.
`compute_seq_dep_weight`(→ float)	Computes the sequence-dependent weight for an interaction given a probabilistic sequence.
`default_configs_for`(→ tuple[jaxtyping.PyTree, ...)	Return the default simulation and energy configuration files for a given type.

mythos.energy.utils.q_to_back_base(q: jax_md.rigid_body.Quaternion) → jax.numpy.ndarray[source]: Get the vector from the center to the base of the nucleotide.

mythos.energy.utils.q_to_base_normal(q: jax_md.rigid_body.Quaternion) → jax.numpy.ndarray[source]: Get the normal vector to the base of the nucleotide.

mythos.energy.utils.q_to_cross_prod(q: jax_md.rigid_body.Quaternion) → jax.numpy.ndarray[source]: Get the cross product vector of the nucleotide.

mythos.energy.utils.get_pair_probs(seq: mythos.utils.types.Arr_Nucleotide_4, i: int, j: int) → jax.numpy.ndarray[source]: Get the pair probabilities for a sequence.

mythos.energy.utils.compute_seq_dep_weight(pseq: mythos.utils.types.Probabilistic_Sequence, nt1: int, nt2: int, weights_table: numpy.ndarray, is_unpaired: mythos.utils.types.Arr_Nucleotide_Int, idx_to_unpaired_idx: mythos.utils.types.Arr_Nucleotide_Int, idx_to_bp_idx: mythos.utils.types.Arr_Nucleotide_2_Int) → float[source]: Computes the sequence-dependent weight for an interaction given a probabilistic sequence.

mythos.energy.utils.default_configs_for(base: str) → tuple[jaxtyping.PyTree, jaxtyping.PyTree][source]: Return the default simulation and energy configuration files for a given type.