Source code for

# -*- coding: utf-8 -*-
"""This module defines :class:`Bond` for dealing with bond information provided
by using the :meth:`.AtomGroup.setBonds`or :meth:`.AtomGroup.inferBonds` method."""

from numbers import Integral
import numpy as np

__all__ = ['Bond']

[docs]class Bond(object): """A pointer class for bonded atoms. Following built-in functions are customized for this class: * :func:`len` returns bond length, i.e. :meth:`getLength` * :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 = self._indices names = self._ag._getNames() return '<Bond: {0}({1})--{2}({3}) from {4}>'.format( names[one], one, names[two], two, str(self._ag)) def __str__(self): one, two = self._indices names = self._ag._getNames() return '{0}({1})--{2}({3})'.format( names[one], one, names[two], two) def __eq__(self, other): return (isinstance(other, Bond) 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 __len__(self): return self.getLength() 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 bonded atoms.""" return (self._ag[self._indices[0]], self._ag[self._indices[1]])
[docs] def getIndices(self): """Returns indices of bonded atoms.""" return self._indices.copy()
[docs] def getLength(self): """Returns bond length.""" vector = self.getVector() return np.multiply(vector, vector, vector).sum() ** 0.5
[docs] def getVector(self): """Returns bond vector that originates from the first atom.""" one, two = self._indices acsi = self.getACSIndex() return self._ag._coords[acsi, two] - self._ag._coords[acsi, one]
[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 evalBonds(bonds, n_atoms): """Returns an array mapping atoms to their bonded neighbors and an array that stores number of bonds made by each atom.""" numbonds = np.bincount(bonds.reshape((bonds.shape[0] * 2))) bmap = np.zeros((n_atoms, numbonds.max()), int) bmap.fill(-1) index = np.zeros(n_atoms, int) for bond in bonds: a, b = bond bmap[a, index[a]] = b bmap[b, index[b]] = a index[bond] += 1 return bmap, numbonds def trimBonds(bonds, indices): """Returns bonds between atoms at given indices.""" iset = set(indices) bonds = [bond for bond in bonds if bond[0] in iset and bond[1] in iset] if bonds: newindices = np.zeros(indices.max()+1, int) newindices[indices] = np.arange(len(indices)) return newindices[np.array(bonds)]