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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 MDAnalysis as mda
import pytest
from MDAnalysis.analysis import nuclinfo
from MDAnalysisTests.datafiles import RNA_PSF, RNA_PDB
from numpy.testing import (
assert_almost_equal,
assert_allclose,
)
@pytest.fixture(scope="module")
def u():
return mda.Universe(RNA_PSF, RNA_PDB)
@pytest.mark.parametrize(
"i, bp, seg1, seg2, expected_value",
(
(1, 2, "RNAA", "RNAA", 4.3874702),
(22, 23, "RNAA", "RNAA", 4.1716404),
),
)
def test_wc_pair(u, i, bp, seg1, seg2, expected_value):
val = nuclinfo.wc_pair(u, i, bp, seg1=seg1, seg2=seg2)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"i, bp, seg1, seg2, expected_value",
(
(3, 17, "RNAA", "RNAA", 15.06506),
(20, 5, "RNAA", "RNAA", 3.219116),
),
)
def test_minor_pair(u, i, bp, seg1, seg2, expected_value):
val = nuclinfo.minor_pair(u, i, bp, seg1=seg1, seg2=seg2)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"i, bp, seg1, seg2, expected_value",
(
(2, 12, "RNAA", "RNAA", 26.884272),
(5, 9, "RNAA", "RNAA", 13.578535),
),
)
def test_major_pair(u, i, bp, seg1, seg2, expected_value):
val = nuclinfo.major_pair(u, i, bp, seg1=seg1, seg2=seg2)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 9, 3.16497),
("RNAA", 21, 22.07721),
),
)
def test_phase_cp(u, seg, i, expected_value):
val = nuclinfo.phase_cp(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 1, 359.57580),
("RNAA", 11, 171.71645),
),
)
def test_phase_as(u, seg, i, expected_value):
val = nuclinfo.phase_as(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
(
"RNAA",
5,
[
302.203802,
179.043077,
35.271411,
79.499729,
201.000393,
282.14321,
210.709327,
],
),
(
"RNAA",
21,
[
280.388619,
185.12919,
56.616215,
64.87354,
187.153367,
279.340915,
215.332144,
],
),
),
)
def test_tors(u, seg, i, expected_value):
val = nuclinfo.tors(u, seg=seg, i=i)
assert_allclose(val, expected_value, rtol=1e-03)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 6, 279.15103),
("RNAA", 18, 298.09936),
),
)
def test_tors_alpha(u, seg, i, expected_value):
val = nuclinfo.tors_alpha(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 7, 184.20501),
("RNAA", 15, 169.70042),
),
)
def test_tors_beta(u, seg, i, expected_value):
val = nuclinfo.tors_beta(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 7, 52.72022),
("RNAA", 15, 54.59684),
),
)
def test_tors_gamma(u, seg, i, expected_value):
val = nuclinfo.tors_gamma(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 7, 84.80554),
("RNAA", 15, 82.00043),
),
)
def test_tors_delta(u, seg, i, expected_value):
val = nuclinfo.tors_delta(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 7, 200.40990),
("RNAA", 15, 210.96953),
),
)
def test_tors_eps(u, seg, i, expected_value):
val = nuclinfo.tors_eps(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value", (("RNAA", 7, 297.84736), ("RNAA", 15, 330.24898))
)
def test_tors_zeta(u, seg, i, expected_value):
val = nuclinfo.tors_zeta(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 1, 178.37435),
("RNAA", 2, 202.03418),
("RNAA", 7, 200.91674),
("RNAA", 15, 209.32109),
),
)
def test_tors_chi(u, seg, i, expected_value):
val = nuclinfo.tors_chi(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"seg, i, expected_value",
(
("RNAA", 20, 103.07024),
("RNAA", 5, 156.62223),
("RNAA", 7, 77.94538),
("RNAA", 15, 130.18539),
),
)
def test_hydroxyl(u, seg, i, expected_value):
val = nuclinfo.hydroxyl(u, seg=seg, i=i)
assert_almost_equal(val, expected_value, decimal=3)
@pytest.mark.parametrize(
"bp1, bp2, i, seg1, seg2, seg3, expected_value",
(
(16, 2, 3, "RNAA", "RNAA", "RNAA", 314.69804),
(8, 9, 10, "RNAA", "RNAA", "RNAA", 34.50106),
),
)
def test_pseudo_dihe_baseflip(
u, bp1, bp2, i, seg1, seg2, seg3, expected_value
):
val = nuclinfo.pseudo_dihe_baseflip(u, bp1, bp2, i, seg1, seg2, seg3)
assert_almost_equal(val, expected_value, decimal=3)
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