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)[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
.- Parameters
atom_list (AtomGroup) – list of atoms
box (array-like or
None
, optional, defaultNone
) – Simulation cell dimensions in the form ofMDAnalysis.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]] [source]
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
) – Whenlevel='A'
, AtomGroup is being returned.ResidueGroup (
ResidueGroup
) – Whenlevel='R'
, ResidueGroup is being returned.SegmentGroup (
SegmentGroup
) – Whenlevel='S'
, SegmentGroup is being returned.
Changed in version 2.0.0: Now returns
AtomGroup
(when empty this is now an emptyAtomGroup
instead of an empty list),ResidueGroup
, or aSegmentGroup