# -*- coding: utf-8 -*-
"""This module defines :class:`Angle` for dealing with angle information provided
by using :meth:`.AtomGroup.setAngles` method."""
from numbers import Integral
import numpy as np
RAD2DEG = 180 / np.pi
__all__ = ['Angle']
[docs]class Angle(object):
"""A pointer class for angled atoms. Following built-in functions are
customized for this class:
* :func:`len` returns angle length, i.e. :meth:`getSize`
* :func:`iter` yields :class:`~.Atom` instances"""
__slots__ = ['_ag', '_acsi', '_indices']
def __init__(self, ag, indices, acsi=None):
self._ag = ag
self._indices = np.array(indices)
if acsi is None:
self._acsi = ag.getACSIndex()
else:
self._acsi = acsi
def __repr__(self):
one, two, three = self._indices
names = self._ag._getNames()
return '<Angle: {0}({1})--{2}({3})--{4}({5}) from {6}>'.format(
names[one], one, names[two], two,
names[three], three, str(self._ag))
def __str__(self):
one, two, three = self._indices
names = self._ag._getNames()
return '{0}({1})--{2}({3})--{4}({5})'.format(
names[one], one, names[two], two,
names[three], three)
def __eq__(self, other):
return (isinstance(other, Angle) and other.getAtomGroup() is self._ag
and (np.all(other.getIndices() == self._indices) or
np.all(other.getIndices() == list(reversed(self._indices)))))
def __ne__(self, other):
return not self.__eq__(other)
def __size__(self):
return self.getSize()
def __iter__(self):
for index in self._indices:
yield self._ag[index]
[docs] def getAtomGroup(self):
"""Returns atom group."""
return self._ag
[docs] def getAtoms(self):
"""Returns angled atoms."""
return (self._ag[self._indices[0]], self._ag[self._indices[1]], self._ag[self._indices[2]])
[docs] def getIndices(self):
"""Returns indices of angled atoms."""
return self._indices.copy()
[docs] def getSize(self, radian=False):
"""Returns angle size."""
v1, v2 = self.getVectors()
rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
if radian:
return rad
else:
return rad * RAD2DEG
[docs] def getVectors(self):
"""Returns bond vectors that originate from the central atom."""
one, two, three = self._indices
acsi = self.getACSIndex()
vector1 = self._ag._coords[acsi, one] - self._ag._coords[acsi, two]
vector2 = self._ag._coords[acsi, three] - self._ag._coords[acsi, two]
return vector1, vector2
[docs] def getACSIndex(self):
"""Returns index of the coordinate set."""
acsi = self._acsi
if acsi >= self._ag._n_csets:
raise ValueError('{0} has fewer coordsets than assumed by {1}'
.format(str(self._ag), str(self)))
return acsi
[docs] def setACSIndex(self, index):
"""Set the coordinate set at *index* active."""
if self._ag._coords is None:
raise AttributeError('coordinates are not set')
if not isinstance(index, Integral):
raise TypeError('index must be an integer')
n_csets = self._ag._n_csets
if n_csets <= index or n_csets < abs(index):
raise IndexError('coordinate set index is out of range')
if index < 0:
index += n_csets
self._acsi = index
def evalAngles(angles, n_atoms):
"""Returns an array mapping atoms to their angled neighbors and an array
that stores number of angles made by each atom."""
numangles = np.bincount(angles.reshape((angles.shape[0] * 3)))
angmap = np.zeros((n_atoms, numangles.max(), 2), int)
angmap.fill(-1)
index = np.zeros(n_atoms, int)
for angle in angles:
a, b, c = angle
angmap[a, index[a]] = [b,c]
angmap[b, index[b]] = [a,c]
angmap[c, index[c]] = [a,b]
index[angle] += 1
return angmap, numangles
def trimAngles(angles, indices):
"""Returns angles between atoms at given indices."""
iset = set(indices)
angles = [angle for angle in angles if angle[0] in iset and angle[1] in iset and angle[2] in iset]
if angles:
newindices = np.zeros(indices.max()+1, int)
newindices[indices] = np.arange(len(indices))
return newindices[np.array(angles)]
