13.2.3. Neighbor Search wrapper for MDAnalysis —
This module contains classes that allow neighbor searches directly with AtomGroup objects from MDAnalysis.
AtomNeighborSearch(atom_group, box=None, bucket_size=10)¶
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 uses the BioPython KDTree and its wrapper PeriodicKDTree for non-periodic and periodic systems, respectively.
- 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.
- bucket_size (int) – Number of entries in leafs of the KDTree. If you suffer poor performance you can play around with this number. Increasing the bucket_size will speed up the construction of the KDTree but slow down the search.
search(atoms, radius, level='A')¶
Return all atoms/residues/segments that are within radius of the atoms in atoms.