mythos.utils.neighbors
======================

.. py:module:: mythos.utils.neighbors

.. autoapi-nested-parse::

   Utilities for using neighbor lists.



Attributes
----------

.. autoapisummary::

   mythos.utils.neighbors.ERR_NEIGHBORS_INVALID_BONDED_NEIGHBORS


Functions
---------

.. autoapisummary::

   mythos.utils.neighbors.get_neighbor_list_fn


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

.. py:data:: ERR_NEIGHBORS_INVALID_BONDED_NEIGHBORS
   :value: 'Indices of bonded neighbors must be bewteen 0 and n_nucleotides-1'


.. py:function:: get_neighbor_list_fn(bonded_neighbors: numpy.ndarray, n_nucleotides: int, displacement_fn: collections.abc.Callable, box_size: float, r_cutoff: float = 10.0, dr_threshold: float = 0.2) -> collections.abc.Callable

   Construct a neighbor list function for unbonded pairs.

   This function constructs a neighbor list function for identifying neighboring
   particles that are not bonded. To achieve this, it uses the provided list of
   bonded neighbors to explicitly exclude bonded pairs from the neighbor list
   by creating a mask.