# -*- coding: utf-8 -*-
"""
===============================================================================
Mixin classes for ring statistics (:mod:`sknano.core.atoms.mixins.ring_atoms`)
===============================================================================
.. currentmodule:: sknano.core.atoms.mixins.ring_atoms
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from collections import Counter, OrderedDict
import numpy as np
import pandas as pd
from sknano.core import timethis
from sknano.core.analysis import find_rings
# from sknano.core.math import Vector
__all__ = ['RingAtomMixin', 'RingAtomsMixin']
[docs]class RingAtomMixin:
"""Mixin `Atom` class for ring statistics/network connectivity analysis."""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.Rn = 0
[docs]class RingAtomsMixin:
"""Mixin `Atoms` class for ring statistics analysis."""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.ring_counter = Counter()
self.rings = OrderedDict()
@property
def rings_per_atom(self):
"""Rings per atom list."""
return [atom.Rn for atom in self]
@property
def Rn_counter(self):
"""Return rings per atom counter.
Returns
-------
:class:`~python:collections.Counter`
"""
return Counter([atom.Rn for atom in self])
@property
def ring_stats(self):
""":class:`~python:dict` of ring statistics."""
try:
return self._ring_stats
except AttributeError:
self.update_ring_stats()
return self._ring_stats
[docs] def update_ring_stats(self, angle_reference=None, bond_reference=None,
dihedral_reference=None, improper_reference=None):
# stats = {}
# stats['rings_per_atom'] = self.rings_per_atom
data = []
index = []
rings = OrderedDict(sorted(self.rings.items()))
for n, lor in rings.items():
index.append(n)
datadict = {}
datadict['count'] = len(lor)
datadict['centroids'] = centroids = []
datadict['mean_angles'] = mean_angles = []
datadict['mean_bonds'] = mean_bonds = []
datadict['mean_angle_strains'] = mean_angle_strains = []
datadict['mean_bond_strains'] = mean_bond_strains = []
for ring in lor:
centroids.append(ring.centroid)
angles = ring.angles
mean_angles.append(angles.mean)
if angle_reference is not None:
angles.compute_strains(angle_reference)
mean_angle_strains.append(np.mean(angles.strains))
bonds = ring.bonds
mean_bonds.append(bonds.mean)
if bond_reference is not None:
bonds.compute_strains(bond_reference)
mean_bond_strains.append(np.mean(bonds.strains))
# dihedrals = ring.dihedrals
# impropers = ring.impropers
data.append(datadict)
self._ring_stats = pd.DataFrame(data, index=index)
[docs] def add_ring(self, nodes):
"""Append ring atoms to :attr:`~RingAtomsMixin.rings`."""
for nidx in nodes:
self[abs(nidx)].Rn += 1
n = len(nodes)
rings = self.rings
if n not in rings:
rings[n] = []
rings[n].append(self.__class__([self[abs(nidx)] for nidx in nodes],
update_item_class=False, **self.kwargs))
@timethis
[docs] def analyze_network(self, cutoff=np.inf, max_ring_size=None, eps=0.0001,
retcodes=None, pyversion=False):
"""Analyze the network connectivity.
Parameters
----------
cutoff : :class:`~python:float`, optional
max_ring_size : :class:`~python:int`, optional
eps : :class:`~python:float`, optional
retcodes : :class:`~python:tuple`, optional
"""
if max_ring_size is None:
max_ring_size = -1
self.reset_attrs(rings=True)
if self.verbose:
print('Analyzing the network connectivity...')
if not self.neighbors_analyzed:
self.update_neighbors(cutoffs=[cutoff])
self.update_neighbor_lists()
Natoms = self.Natoms
NNN = self.NNN
nn_idx = self.nn_idx
nn_seed = self.nn_seed
nn_amat = self.nn_adjacency_matrix
nn_vecs = self.nn_vectors
ring_counts, nodes_list = \
find_rings(Natoms, NNN, nn_idx, nn_seed, nn_amat, nn_vecs,
max_ring_size, eps, pyversion)
self._update_ring_counter(ring_counts)
self._update_rings(nodes_list)
if retcodes is not None and isinstance(retcodes, (tuple, list)):
return tuple([getattr(self, attr, None) for attr in retcodes])
def _update_ring_counter(self, ring_counts):
"""Private method for updating ring counter."""
cntr = self.ring_counter
for i, counts in enumerate(ring_counts):
if counts > 0:
cntr[i] = counts
def _update_rings(self, nodes_list):
for nodes in nodes_list:
self.add_ring(nodes)
[docs] def reset_attrs(self, rings=False, **kwargs):
"""Reset the :class:`RingAtomsMixin` class attributes, then call \
parent class `reset_attrs` method."""
if rings:
self.reset_ring_atoms_attrs()
super().reset_attrs(**kwargs)
[docs] def reset_ring_atoms_attrs(self):
"""Reset the :class:`RingAtomsMixin` class attributes."""
self.ring_counter = Counter()
self.rings = OrderedDict()
[setattr(atom, 'Rn', 0) for atom in self]
[docs] def update_attrs(self, rings=False, **kwargs):
"""Update the :class:`RingAtomsMixin` class attributes."""
super().update_attrs(**kwargs)
if rings:
self.analyze_network(**kwargs)
