# -*- coding: utf-8 -*-
"""This module defines :class:`Improper` for dealing with improper information provided
by using :meth:`.AtomGroup.setImpropers` method."""
from numbers import Integral
import numpy as np
RAD2DEG = 180 / np.pi
__all__ = ['Improper']
[docs]class Improper(object):
"""A pointer class for improperd atoms. Following built-in functions are
customized for this class:
* :func:`len` returns improper 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, four = self._indices
names = self._ag._getNames()
return '<Improper: {0}({1})--{2}({3})--{4}({5}--{6}({7})) from {8}>'.format(
names[one], one, names[two], two,
names[three], three, names[four], four,
str(self._ag))
def __str__(self):
one, two, three, four = self._indices
names = self._ag._getNames()
return '{0}({1})--{2}({3})--{4}({5})--{6}({7})'.format(
names[one], one, names[two], two,
names[three], three, names[four], four)
def __eq__(self, other):
return (isinstance(other, Improper) 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 improperd atoms."""
return (self._ag[self._indices[0]], self._ag[self._indices[1]], self._ag[self._indices[2]])
[docs] def getIndices(self):
"""Returns indices of improperd atoms."""
return self._indices.copy()
[docs] def getSize(self):
"""Returns improper size."""
one, two, three, four = self._indices
acsi = self.getACSIndex()
atoms1 = self._ag._coords[acsi, one]
atoms2 = self._ag._coords[acsi, two]
atoms3 = self._ag._coords[acsi, three]
atoms4 = self._ag._coords[acsi, four]
return calcImproper(atoms1, atoms2, atoms3, atoms4)
[docs] def getVectors(self):
"""Returns bond vectors that originate from the central atom."""
one, two, three, four = self._indices
acsi = self.getACSIndex()
vector1 = self._ag._coords[acsi, one] - self._ag._coords[acsi, two]
vector2 = self._ag._coords[acsi, two] - self._ag._coords[acsi, three]
vector3 = self._ag._coords[acsi, three] - self._ag._coords[acsi, four]
return vector1, vector2, vector3
[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 evalImpropers(impropers, n_atoms):
"""Returns an array mapping atoms to their improperd neighbors and an array
that stores number of impropers made by each atom."""
numimpropers = np.bincount(impropers.reshape((impropers.shape[0] * 4)))
imap = np.zeros((n_atoms, numimpropers.max(), 3), int)
imap.fill(-1)
index = np.zeros(n_atoms, int)
for improper in impropers:
a, b, c, d = improper
imap[a, index[a]] = [b, c, d]
imap[b, index[b]] = [a, c, d]
imap[c, index[c]] = [a, b, d]
imap[d, index[d]] = [a, b, c]
index[improper] += 1
return imap, numimpropers
def trimImpropers(impropers, indices):
"""Returns impropers between atoms at given indices."""
iset = set(indices)
impropers = [improper for improper in impropers if improper[0]
in iset and improper[1] in iset and improper[2] in iset and improper[3] in iset]
if impropers:
newindices = np.zeros(indices.max()+1, int)
newindices[indices] = np.arange(len(indices))
return newindices[np.array(impropers)]
