# -*- coding: utf-8 -*-
"""
======================================================================================
Class representations of dihedral angles (:mod:`sknano.core.atoms.mixins.dihedrals`)
======================================================================================
.. currentmodule:: sknano.core.atoms.mixins.dihedrals
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from collections import namedtuple
import numpy as np
from sknano.core.math import vector as vec
from .bonds import Bond
from .topology_base import AngularTopology, AngularTopologyCollection, \
TopologyStats, check_operands as check_operands_
__all__ = ['compute_dihedral', 'Dihedral', 'Dihedrals', 'DihedralStats']
DihedralStats = namedtuple('DihedralStats', TopologyStats._fields)
[docs]def compute_dihedral(*atoms, check_operands=True, degrees=False):
"""Compute dihedral angle.
Parameters
----------
*atoms : {:class:`~python:list`, :class:`~sknano.core.atoms.Atoms`}
:class:`~python:list` of :class:`~sknano.core.atoms.Atom`\ s
or an :class:`~sknano.core.atoms.Atoms` object.
check_operands : :class:`~python:bool`, optional
degrees : :class:`~python:bool`, optional
Returns
-------
:class:`~python:float`
Raises
------
:class:`~python:TypeError`
if `atoms` is not a list of :class:`~sknano.core.atoms.Atom` objects
or an :class:`~sknano.core.atoms.Atoms` object.
:class:`~python:ValueError`
if len(atoms) != 4.
"""
if check_operands:
atoms = check_operands_(*atoms, size=4)
atom1, atom2, atom3, atom4 = atoms
b12 = Bond(atom1, atom2).vector
b23 = Bond(atom2, atom3).vector
b34 = Bond(atom3, atom4).vector
m = b12.cross(b23)
n = b23.cross(b34)
sina = vec.dot(m, b34) * b23.norm
cosa = vec.dot(m, n)
angle = np.arctan2(sina, cosa)
if degrees:
angle = np.degrees(angle)
return angle
[docs]class Dihedral(AngularTopology):
"""Class representation of dihedral angle between 4 `Atom` objects.
Parameters
----------
*atoms : {:class:`~python:list`, :class:`~sknano.core.atoms.Atoms`}
:class:`~python:list` of :class:`~sknano.core.atoms.Atom`\ s
or an :class:`~sknano.core.atoms.Atoms` object.
size : :class:`~python:int`
parent : Parent :class:`~sknano.core.atoms.Molecule`, if any.
id : :class:`~python:int`
check_operands : :class:`~python:bool`, optional
degrees : :class:`~python:bool`, optional
Raises
------
:class:`~python:TypeError`
if `atoms` is not a list of :class:`~sknano.core.atoms.Atom` objects
or an :class:`~sknano.core.atoms.Atoms` object.
:class:`~python:ValueError`
if len(atoms) != 4.
"""
def __init__(self, *args, **kwargs):
super().__init__(*args, size=4, **kwargs)
self.fmtstr = "{atom1!r}, {atom2!r}, {atom3!r}, {atom4!r} " + \
super().fmtstr
def __str__(self):
"""Return nice string representation of `Dihedral`."""
return "Dihedral({!r}->{!r}->{!r}->{!r})".format(self.atom1.id,
self.atom2.id,
self.atom3.id,
self.atom4.id)
@property
def atom1(self):
""":class:`~sknano.core.atoms.Atom` 1 in `Dihedral`."""
return self.atoms[0]
@property
def atom2(self):
""":class:`~sknano.core.atoms.Atom` 2 in `Dihedral`."""
return self.atoms[1]
@property
def atom3(self):
""":class:`~sknano.core.atoms.Atom` 3 in `Dihedral`."""
return self.atoms[2]
@property
def atom4(self):
""":class:`~sknano.core.atoms.Atom` 4 in `Dihedral`."""
return self.atoms[3]
@property
def dihedral(self):
"""An alias for :attr:`Topology.measure`."""
return self.dihedral
[docs] def compute_measure(self):
"""Compute the bond angle, which is the measure of an :class:`Angle`.
Returns
-------
:class:`~python:float`
"""
return compute_dihedral(*self.atoms, degrees=self.degrees)
[docs] def todict(self):
"""Return :class:`~python:dict` of constructor parameters."""
super_dict = super().todict()
super_dict.update(dict(atom1=self.atom1, atom2=self.atom2,
atom3=self.atom3, atom4=self.atom4))
return super_dict
[docs]class Dihedrals(AngularTopologyCollection):
"""Base class for collection of atom `Dihedral`\ s.
Parameters
----------
topolist : {None, sequence, `Dihedrals`}, optional
if not `None`, then a list of `Dihedral` objects
parent : Parent :class:`~sknano.core.atoms.Molecule`, if any.
degrees : :class:`~python:bool`, optional
"""
@property
def __item_class__(self):
return Dihedral
@property
def Ndihedrals(self):
"""Number of `Dihedral`\ s in `Dihedrals`."""
return len(self)
@property
def dihedrals(self):
""":class:`~numpy:numpy.ndarray` of :attr:`~Dihedral.dihedral`\ s."""
return self.measures
@property
def mean_dihedral(self):
"""Mean dihedral angle."""
return self.mean_measure
@property
def statistics(self):
"""Dihedral stats."""
return DihedralStats(**super().statistics._asdict())
