mythos.utils.neighbors

Utilities for using neighbor lists.

Attributes

ERR_NEIGHBORS_INVALID_BONDED_NEIGHBORS

Functions

get_neighbor_list_fn(→ collections.abc.Callable)

Construct a neighbor list function for unbonded pairs.

Module Contents

mythos.utils.neighbors.ERR_NEIGHBORS_INVALID_BONDED_NEIGHBORS = 'Indices of bonded neighbors must be bewteen 0 and n_nucleotides-1'

mythos.utils.neighbors.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.