# -*- coding: utf-8 -*-
"""
==============================================================================
Base composition classes (:mod:`sknano.core.structures.compositions`)
==============================================================================
.. currentmodule:: sknano.core.structures.compositions
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from functools import total_ordering
from operator import attrgetter
import numpy as np
from sknano.core import BaseClass, UserList
from sknano.core.math import convert_condition_str, rotation_matrix
__all__ = ['Composition', 'Compositions']
@total_ordering
[docs]class Composition(BaseClass):
"""Base class for abstract representation of a composition.
Parameters
----------
components : {None, sequence, `Atoms`}, optional
if not `None`, then a list of `Atom` instances or an
`Atoms` instance.
"""
def __init__(self, components=None, **kwargs):
super().__init__(**kwargs)
self.components = components
self.fmtstr = "components={components!r}"
def __eq__(self, other):
"""Test equality of two `Composition` object instances."""
return self is other or self.components == other.components
def __lt__(self, other):
"""Test if `self` is *less than* `other`."""
return self.components < other.components
[docs] def rezero(self, *args, **kwargs):
assert not hasattr(super(), 'rezero')
[docs] def rotate(self, **kwargs):
assert not hasattr(super(), 'rotate')
[docs] def translate(self, *args, **kwargs):
assert not hasattr(super(), 'translate')
[docs] def todict(self):
"""Return :class:`~python:dict` of `Composition` constructor \
parameters."""
return dict(components=self.components)
[docs]class Compositions(UserList):
"""Base class for collection of `Composition` objects.
Parameters
----------
compositions : {None, sequence, `Compositions`}, optional
if not `None`, then a list of `Composition` instance objects or an
existing `Compositions` instance object.
"""
def __init__(self, compositions=None, update_item_class=True, **kwargs):
super().__init__(initlist=compositions)
self.fmtstr = "{compositions!r}"
@property
def __item_class__(self):
return Composition
def sort(self, key=attrgetter('id'), reverse=False):
super().sort(key=key, reverse=reverse)
@property
def Ncompositions(self):
"""Number of compositions in `Compositions`."""
return len(self)
@property
def masses(self):
"""Return list of `Composition` masses."""
return np.asarray([composition.mass for composition in self])
def filter(self, condition, invert=False):
"""Filter `Compositions` by `condition`.
Parameters
----------
condition : array_like, bool
invert : bool, optional
Returns
-------
filtered_compositions : `Compositions`
"""
if isinstance(condition, str):
condition = convert_condition_str(self, condition)
if invert:
condition = ~condition
try:
self.data = np.asarray(self)[condition].tolist()
except AttributeError:
self.data = np.asarray(self)[condition]
def filtered(self, condition, invert=False):
if isinstance(condition, str):
condition = convert_condition_str(self, condition)
if invert:
condition = ~condition
try:
return self.__class__(components=np.asarray(self)[condition].tolist(),
**self.kwargs)
except AttributeError:
return self.__class__(components=np.asarray(self)[condition],
**self.kwargs)
def get_compositions(self, asarray=False):
"""Return list of `Compositions`.
Parameters
----------
asarray : bool, optional
Returns
-------
sequence or ndarray
"""
if asarray:
return np.asarray(self.data)
else:
return self.data
def rezero(self, epsilon=1.0e-10):
"""Set really really small coordinates to zero.
Set all coordinates with absolute value less than
epsilon to zero.
Parameters
----------
epsilon : float
smallest allowed absolute value of any :math:`x,y,z` component.
"""
[composition.rezero(epsilon=epsilon) for composition in self]
def rotate(self, **kwargs):
"""Rotate `Composition` position vectors.
Parameters
----------
angle : float
axis : :class:`~sknano.core.math.Vector`, optional
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
degrees : bool, optional
transform_matrix : :class:`~numpy:numpy.ndarray`
"""
if kwargs.get('transform_matrix', None) is None:
kwargs['transform_matrix'] = rotation_matrix(**kwargs)
[composition.rotate(**kwargs) for composition in self]
def translate(self, t, fix_anchor_points=True):
"""Translate `Composition` position vectors by :class:`Vector` `t`.
Parameters
----------
t : :class:`Vector`
fix_anchor_points : bool, optional
"""
[composition.translate(t, fix_anchor_point=fix_anchor_points)
for composition in self]
def todict(self):
return dict(compositions=self.data)
