Source code for MDAnalysis.lib.NeighborSearch

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Neighbor Search wrapper for MDAnalysis --- :mod:`MDAnalysis.lib.NeighborSearch`

This module contains classes that allow neighbor searches directly with
`AtomGroup` objects from `MDAnalysis`.
import numpy as np
from MDAnalysis.lib.distances import capped_distance
from MDAnalysis.lib.util import unique_int_1d

[docs]class AtomNeighborSearch(object): """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 :class:`~MDAnalysis.lib.distances.capped_distance`. """ def __init__(self, atom_group, box=None): """ Parameters ---------- atom_list : AtomGroup list of atoms box : array-like or ``None``, optional, default ``None`` Simulation cell dimensions in the form of :attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when periodic boundary conditions should be taken into account for the calculation of contacts. """ self.atom_group = atom_group self._u = atom_group.universe self._box = box
[docs] def search(self, atoms, radius, level='A'): """ 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 : :class:`~MDAnalysis.core.groups.AtomGroup` When ``level='A'``, AtomGroup is being returned. ResidueGroup : :class:`~MDAnalysis.core.groups.ResidueGroup` When ``level='R'``, ResidueGroup is being returned. SegmentGroup : :class:`~MDAnalysis.core.groups.SegmentGroup` When ``level='S'``, SegmentGroup is being returned. .. versionchanged:: 2.0.0 Now returns :class:`AtomGroup` (when empty this is now an empty :class:`AtomGroup` instead of an empty list), :class:`ResidueGroup`, or a :class:`SegmentGroup` """ unique_idx = [] try: # For atom groups, take the positions attribute position = atoms.positions except AttributeError: # For atom, take the position attribute position = atoms.position pairs = capped_distance(position, self.atom_group.positions, radius, box=self._box, return_distances=False) if pairs.size > 0: unique_idx = unique_int_1d(np.asarray(pairs[:, 1], dtype=np.intp)) return self._index2level(unique_idx, level)
def _index2level(self, indices, level): """Convert list of atom_indices in a AtomGroup to either the Atoms or segments/residues containing these atoms. Parameters ---------- indices list of atom indices level : str char (A, R, S). Return atoms(A), residues(R) or segments(S) within *radius* of *atoms*. """ atomgroup = self.atom_group[indices] if level == 'A': return atomgroup elif level == 'R': return atomgroup.residues elif level == 'S': return atomgroup.segments else: raise NotImplementedError('{0}: level not implemented'.format(level))