mythos.energy.utils
===================

.. py:module:: mythos.energy.utils

.. autoapi-nested-parse::

   Utility functions for energy calculations.



Functions
---------

.. autoapisummary::

   mythos.energy.utils.q_to_back_base
   mythos.energy.utils.q_to_base_normal
   mythos.energy.utils.q_to_cross_prod
   mythos.energy.utils.get_pair_probs
   mythos.energy.utils.compute_seq_dep_weight
   mythos.energy.utils.default_configs_for


Module Contents
---------------

.. py:function:: q_to_back_base(q: jax_md.rigid_body.Quaternion) -> jax.numpy.ndarray

   Get the vector from the center to the base of the nucleotide.


.. py:function:: q_to_base_normal(q: jax_md.rigid_body.Quaternion) -> jax.numpy.ndarray

   Get the normal vector to the base of the nucleotide.


.. py:function:: q_to_cross_prod(q: jax_md.rigid_body.Quaternion) -> jax.numpy.ndarray

   Get the cross product vector of the nucleotide.


.. py:function:: get_pair_probs(seq: mythos.utils.types.Arr_Nucleotide_4, i: int, j: int) -> jax.numpy.ndarray

   Get the pair probabilities for a sequence.


.. py:function:: 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

   Computes the sequence-dependent weight for an interaction given a probabilistic sequence.


.. py:function:: default_configs_for(base: str) -> tuple[jaxtyping.PyTree, jaxtyping.PyTree]

   Return the default simulation and energy configuration files for a given type.