sknano.core.atoms.POAVAtoms

class sknano.core.atoms.POAVAtoms(atoms=None, copylist=True, deepcopy=False)

An Atoms sub-class for POAV analysis.

Sub-class of KDTAtoms class, and a container class for lists of POAVAtom instances.

Parameters:

atoms : {None, sequence, POAVAtoms}, optional

if not None, then a list of POAVAtom instance objects or an existing POAVAtoms instance object.

copylist : bool, optional

perform shallow copy of atoms list

deepcopy : bool, optional

perform deepcopy of atoms list

Attributes

CM	Center-of-Mass coordinates of Atoms.
M	Total mass of Atoms.
NNrc	Only return neighbors within this distance when querying the kd-tree.
Natoms	Number of atoms in Atoms.
Ntypes	Number of atomtypes.
POAV1	List of POAVAtom POAV1 POAV1 attribute.
POAV2	List of POAVAtom POAV2 POAV2 attribute.
POAVR	List of POAVAtom POAVR POAVR attribute.
atom_ids	Return array of XAtom IDs.
atom_tree	scipy.spatial.KDTree of
atomtypes	atomtypes dict.
bonds	Return list of bonds.
bounds	Bounds of Atoms.
centroid	Centroid of Atoms.
charges	Return array of XAtom charges.
coordination_numbers	Return array of KDTAtom coordination numbers.
coords	numpy.ndarray of Atoms \(x, y, z\) coordinates.
inertia_tensor	Return the inertia tensor.
kNN	Number of nearest neighbors to return when querying the kd-tree.
masses	Return list of Atom masses.
nearest_neighbors	Return array of nearest-neighbor atoms for each KDTAtom.
q	Return the total net charge of XAtoms.
symbols	Return list of Atom symbols.
velocities	Return array of XAtom velocities.
x	numpy.ndarray of Atoms \(x\) coordinates.
y	numpy.ndarray of Atoms \(y\) coordinates.
z	numpy.ndarray of Atoms \(z\) coordinates.

Methods

add_atomtype(atom)	Add atom type to atomtypes.
add_atomtypes([atoms])	Add atomtype for each atom in atoms to atomtypes dictionary.
append(item)
assign_unique_ids([starting_id])	Assign unique ID to each XAtom in XAtoms.
center_CM([axes])	Center atoms on CM coordinates.
clear()
clip_bounds(region[, center_before_clipping])	Remove atoms outside the given limits along given dimension.
compute_POAVs()	Compute POAV1, POAV2, POAVR.
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Return Atoms by XAtoms.atom_ids in atom_ids.
get_POAV_attr(POAV_class, attr)	Return list of POAVAtom POAV1 POAV2 or POAVR attribute.
get_atom(atomID)	Get XAtom with Xatom.atomID == atomID.
get_atoms([asarray])	Return list of Atoms.
get_coords([asdict])	Return atom coords.
getatomattr(attr)	Get numpy.ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr(attr, from_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.
remove(item)
reverse()
rezero([epsilon])	Set really really small coordinates to zero.
rezero_coords([epsilon])	Alias for Atoms.rezero.
rezero_xyz([epsilon])	Alias for Atoms.rezero.
rotate([angle, rot_axis, anchor_point, ...])	Rotate Atom position vectors.
select(cmd)
select_within(volume)
sort([key, reverse])
translate(t[, fix_anchor_points])	Translate Atom position vectors by Vector t.
update_attrs()	Alisas for POAVAtoms.compute_POAVs
update_bonds()	Update KDTAtom.bonds list.
update_coordination_numbers()	Update KDTAtom.CN.
update_nearest_neighbors()	Update KDTAtom.NN.