Source code for sknano.core.atoms._structure_atoms
# -*- coding: utf-8 -*-
"""
===============================================================================
Atom classes for structure analysis (:mod:`sknano.core.atoms._structure_atoms`)
===============================================================================
.. currentmodule:: sknano.core.atoms._structure_atoms
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from operator import attrgetter
from ._cn_atoms import CNAtom, CNAtoms
from ._id_atoms import IDAtom, IDAtoms
from ._charged_atoms import ChargedAtom, ChargedAtoms
from ._image_atoms import ImageAtom, ImageAtoms
from ._type_atoms import TypeAtom, TypeAtoms
from ._kdtree_atoms import KDTreeAtomMixin, KDTreeAtomsMixin
from ._poav_atoms import POAVAtomMixin, POAVAtomsMixin
from ._neighbor_atoms import NeighborAtomMixin, NeighborAtomsMixin
from ._periodic_atoms import PBCAtom, PBCAtoms
from ._lattice_atoms import LatticeAtom, LatticeAtoms
from ._xyz_atoms import XYZAtom, XYZAtoms
from ._velocity_atoms import VelocityAtom, VelocityAtoms
from ._bonds import Bonds
__all__ = ['StructureAtom', 'StructureAtoms']
[docs]class StructureAtom(NeighborAtomMixin, POAVAtomMixin, KDTreeAtomMixin,
CNAtom, VelocityAtom, ImageAtom, PBCAtom, LatticeAtom,
XYZAtom, ChargedAtom, TypeAtom, IDAtom):
"""An `Atom` class for structure analysis.
Parameters
----------
element : {str, int}, optional
A string representation of the element symbol or an integer specifying
an element atomic number.
id : int, optional
atom ID
mol : int, optional
molecule ID
type : int, optional
atom type
x, y, z : float, optional
:math:`x, y, z` components of `StructureAtom` position vector relative
to origin.
vx, vy, vz : float, optional
:math:`v_x, v_y, v_z` components of `StructureAtom` velocity.
"""
def __init__(self, *args, NN=None, **kwargs):
super().__init__(*args, **kwargs)
self._neighbors = None
if NN is not None:
self.NN = NN
self._POAV1 = None
self._POAV2 = None
self._POAVR = None
# self.fmtstr = super().fmtstr + ", NN={NN!r}"
def __dir__(self):
attrs = super().__dir__()
attrs.append('NN')
# attrs.extend(['NN', 'bonds'])
return attrs
@CNAtom.CN.getter
def CN(self):
"""`StructureAtom` coordination number."""
try:
return self.NN.Natoms
except AttributeError:
return super().CN
[docs]class StructureAtoms(NeighborAtomsMixin, POAVAtomsMixin, KDTreeAtomsMixin,
CNAtoms, VelocityAtoms, ImageAtoms, PBCAtoms,
LatticeAtoms, XYZAtoms, ChargedAtoms, TypeAtoms, IDAtoms):
"""An `Atoms` sub-class for structure analysis.
Sub-class of `Atoms` class, and a container class for lists of
:class:`~sknano.core.atoms.StructureAtom` instances.
Parameters
----------
atoms : {None, sequence, `StructureAtoms`}, optional
if not `None`, then a list of `StructureAtom` instance objects or an
existing `StructureAtoms` instance object.
kNN : :class:`~python:int`
Number of nearest neighbors to return when querying the kd-tree.
NNrc : :class:`~python:float`
Nearest neighbor radius cutoff.
"""
def __init__(self, atoms=None, kNN=16, NNrc=2.0, **kwargs):
super().__init__(atoms, **kwargs)
self.kNN = kNN
self.NNrc = NNrc
self.bonds = atoms.bonds if hasattr(atoms, 'bonds') else Bonds()
@property
def __atom_class__(self):
return StructureAtom
[docs] def sort(self, key=attrgetter('CN', 'v', 'i', 'r', 'q', 'type', 'mol',
'id', 'mass', 'Z', 'element'),
reverse=False):
super().sort(key=key, reverse=reverse)
@property
def volume(self):
"""Volume of region containing atoms."""
try:
return self._volume
except AttributeError:
return self.bounds.volume
@volume.setter
def volume(self, value):
self._volume = float(value)