13.2.3. Neighbor Search wrapper for MDAnalysis —
This module contains classes that allow neighbor searches directly with AtomGroup objects from MDAnalysis.
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
- 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.dimensionswhen periodic boundary conditions should be taken into account for the calculation of contacts.
search(atoms, radius, level='A')¶
Return all atoms/residues/segments that are within radius of the atoms in atoms.
Changed in version 2.0.0: Now returns
AtomGroup(when empty this is now an empty
AtomGroupinstead of an empty list),
ResidueGroup, or a