Source code for prody.atomic.improper

# -*- 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)]