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: AtomGroup, box: Optional[Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]] = None)

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.

Parameters

• atom_list (AtomGroup) – list of atoms

• box (array-like or None, optional, default None) – Simulation cell dimensions in the form of MDAnalysis.trajectory.timestep.Timestep.dimensions when periodic boundary conditions should be taken into account for the calculation of contacts.

search(atoms: AtomGroup, radius: float, level: str = 'A') → Optional[Union[AtomGroup, ResidueGroup, SegmentGroup]]

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

Parameters

• atoms (AtomGroup, MDAnalysis.core.groups.AtomGroup) – AtomGroup object

• radius (float) – Radius for search in Angstrom.

• level (str) – char (A, R, S). Return atoms(A), residues(R) or segments(S) within radius of atoms.

Returns

• 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