mdtraj.compute_neighbors¶
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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
- trajmd.Trajectory
An MDTraj trajectory
- cutofffloat
Distance cutoff to define ‘neighboring’
- query_indicesnp.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_indicesnp.ndarray, shape=(n_query_indices,), dtype=int, optional
If supplied, restrict the search to only those atoms in haystack_indices.
- periodicbool
If periodic is True and the trajectory contains unitcell information, we will compute distances under the minimum image convention.
- Returns
- matcheslist 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.