mdtraj.compute_neighbors¶

mdtraj.compute_neighbors(traj, cutoff, query_indices, haystack_indices=None, periodic=True)¶

Find (spatially) neighboring atoms in a trajectory.

Given a set of query_indices representing and a distance cutoff, compute the indices of all atoms whose distance to 1 or more of the query points is less than cutoff.

Parameters:

traj : md.Trajectory An MDTraj trajectory cutoff : float Distance cutoff to define ‘neighboring’ query_indices : np.ndarray, shape=(n_query_indices,), dtype=int The matching atoms are those that are within cutoff of one or more of the atoms with indices in query_indices. haystack_indices : np.ndarray, shape=(n_query_indices,), dtype=int, optional If supplied, restrict the search to only those atoms in haystack_indices. periodic : bool If periodic is True and the trajectory contains unitcell information, we will compute distances under the minimum image convention.

Returns:

matches : list of np.ndarray, shape=(n_matches,), dtype=int List of arrays, of length n_frames. Each item in the list is a 1D array of the indices of the matching atoms.