13.2.3. Neighbor Search wrapper for MDAnalysis — MDAnalysis.lib.NeighborSearch

This module contains classes that allow neighbor searches directly with AtomGroup objects from MDAnalysis.

class MDAnalysis.lib.NeighborSearch.AtomNeighborSearch(atom_group, box=None)[source]

This class can be used to find all atoms/residues/segments within the radius of a given query position.

For the neighbor search, this class is a wrapper around capped_distance.

  • atom_list (AtomGroup) – list of atoms
  • box (array-like or None, optional, default None) – Simulation cell dimensions in the form of MDAnalysis.trajectory.base.Timestep.dimensions when periodic boundary conditions should be taken into account for the calculation of contacts.
search(atoms, radius, level='A')[source]

Return all atoms/residues/segments that are within radius of the atoms in atoms.


  • AtomGroup (AtomGroup) – When level='A', AtomGroup is being returned.
  • ResidueGroup (ResidueGroup) – When level='R', ResidueGroup is being returned.
  • SegmentGroup (SegmentGroup) – When level='S', SegmentGroup is being returned.

Changed in version 2.0.0: Now returns AtomGroup (when empty this is now an empty AtomGroup instead of an empty list), ResidueGroup, or a SegmentGroup