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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import numpy as np
from numpy.testing import assert_allclose
import pytest
import MDAnalysis as mda
from MDAnalysis.lib import qcprot
from MDAnalysisTests.datafiles import PSF, DCD
@pytest.mark.parametrize("dtype", [np.float64, np.float32])
class TestQCProt:
def test_dummy(self, dtype):
a = np.array([[1.0, 1.0, 2.0]], dtype=dtype)
b = np.array([[1.0, 1.0, 1.0]], dtype=dtype)
rot = np.zeros(9, dtype=dtype)
r = qcprot.CalcRMSDRotationalMatrix(a, b, 1, rot, None)
err = 0.0001 if dtype is np.float32 else 0.000001
assert r == pytest.approx(0.7174389197644676, abs=err)
assert rot.dtype == dtype
assert_allclose(rot.reshape(3, 3), np.eye(3))
def test_regression(self, dtype):
u = mda.Universe(PSF, DCD)
prot = u.select_atoms("protein")
weights = prot.masses.astype(dtype)
weights /= np.mean(weights)
p1 = prot.positions.astype(dtype)
u.trajectory[1]
p2 = prot.positions.astype(dtype)
rot = np.zeros(9, dtype=dtype)
r = qcprot.CalcRMSDRotationalMatrix(p1, p2, len(prot), rot, weights)
rot_ref = np.array(
[
0.999998,
0.001696,
0.001004,
-0.001698,
0.999998,
0.001373,
-0.001002,
-0.001375,
0.999999,
],
dtype=dtype,
)
err = 0.001 if dtype is np.float32 else 0.000001
assert r == pytest.approx(0.6057544485785074, abs=err)
assert_allclose(rot, rot_ref, atol=err)
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