NeighborAtoms

class sknano.core.atoms.NeighborAtoms(*args, kNN=16, NNrc=2.0, neighbor_cutoffs=None, neighbors_analyzed=False, **kwargs)

Bases: sknano.core.atoms.mixins.KDTreeAtomsMixin, sknano.core.atoms.atoms.Atoms

An Atoms sub-class for neighbor analysis.

Parameters:

• atoms ({None, sequence, NeighborAtoms}, optional) – if not None, then a list of StructureAtom instance objects or an existing NeighborAtoms instance object.
• kNN (int) – Number of nearest neighbors to return when querying the kd-tree.
• NNrc (float) – Nearest neighbor radius cutoff.
• neighbor_cutoffs (list, optional) –

Attributes

CN_counts	Alias for coordination_number_counts.
M	Total mass of Atoms.
NNN	Number of first nearest-neighbors.
NNrc	Nearest neighbor radius cutoff.
Natoms	Number of atoms in Atoms.
atom_tree	Concrete implementation of atom_tree.
coordination_counts	Alias for coordination_number_counts.
coordination_number_counts	Coordination number counts.
coordination_numbers	ndarray of NeighborAtom.CNs.
distances	Neighbor atoms distances.
elements	ndarray of Atom.elements.
first_neighbors	First neighbors.
fmtstr	Format string.
kNN	Max number of nearest-neighbors to return from kd-tree search.
masses	ndarray of Atom.masss.
nearest_neighbors	Return array of nearest-neighbor atoms for each KDTAtom.
neighbor_cutoffs	Nearest neighbor radius cutoff.
neighbor_distances	Neighbor distances
neighbors	Return array of neighbor atoms.
neighbors_analyzed	Return True if neighbors have been analyzed.
nn_adjacency_list	Return nearest-neighbor adjacency list
nn_adjacency_map	Return nearest-neighbor adjacency map
nn_adjacency_matrix	Return nearest-neighbor adjacency matrix.
nn_seed	Return nearest-neighbor seed list
nn_vectors	Return nearest-neighbor vectors.
second_neighbors	Second neighbors.
symbols	ndarray of Atom.symbols.
third_neighbors	Third neighbors.

Methods

append(atom)
clear()
copy()
count(item)
count_neighbors(other, r[, p])	Count how many nearby neighbor pairs can be formed.
count_neighbors_in_self(r[, p])	Count number of neighbor pairs for each atom in self.
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
get_atoms([asarray, aslist])	Return Atoms either as list (default) or numpy array or self.
get_nth_nearest_neighbors(n[, exclusive])	Return `n`th nearest neighbors.
getattr(attr[, default, recursive])	Get ndarray of atom attributes attr.
index(item, *args)
insert(i, atom)
mapatomattr([from_attr, to_attr, attrmap])	Set/update atom attribute from another atom attribute with dict.
pop([i])
query_atom_tree([k, eps, p, rc])	Query atom tree for nearest neighbors distances and indices.
query_ball_point(pts, r[, p, eps])	Find all Atoms within distance r of point(s) pts.
query_ball_tree(other, r[, p, eps])	Find all pairs of Atoms whose distance is at more r.
query_pairs(r[, p, eps])	Find all pairs of points within a distance r.
remove(item)
reset_attrs(**kwargs)	Call corresponding reset_attrs method on each atom
reverse()
rezero([epsilon])	Set values with absolute value less than epsilon to zero.
select([selstr, selstrlist, verbose])	Return Atom or Atoms from selection command.
sort([key, reverse])
todict()	Return dict of constructor parameters.
update_attrs(**kwargs)	Update NeighborAtoms attributes.
update_neighbor_lists()	Update neighbor lists
update_neighbors(**kwargs)	Update NeighborAtom.neighbors.