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Pytest Style analysis/test_nuclinfo.py (#1549)
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@utkbansal @richardjgowers
utkbansal authored and richardjgowers committed Jul 26, 2017
1 parent 1b8c667 commit 53410cd
Showing 1 changed file with 144 additions and 139 deletions.
283 changes: 144 additions & 139 deletions testsuite/MDAnalysisTests/analysis/test_nuclinfo.py
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Expand Up @@ -21,148 +21,153 @@
#
from __future__ import absolute_import

from unittest import TestCase

import MDAnalysis as mda
import pytest
from MDAnalysis.analysis import nuclinfo
from MDAnalysisTests.datafiles import NUCL
from numpy.testing import (
assert_,
assert_almost_equal,
assert_allclose,
)

import MDAnalysis as mda
from MDAnalysis.analysis import nuclinfo

from MDAnalysisTests.datafiles import NUCL


class TestNuclinfo(TestCase):
def setUp(self):
self.u = mda.Universe(NUCL)

def tearDown(self):
del self.u

def test_wc_pair_1(self):
val = nuclinfo.wc_pair(self.u, 1, 2, seg1='RNAA', seg2='RNAA')

assert_almost_equal(val, 4.449, decimal=3)

def test_wc_pair_2(self):
val = nuclinfo.wc_pair(self.u, 22, 23, seg1='RNAA', seg2='RNAA')
assert_almost_equal(val, 4.601, decimal=3)

def test_minor_pair_1(self):
val = nuclinfo.minor_pair(self.u, 3, 17, seg1='RNAA', seg2='RNAA')
assert_almost_equal(val, 16.649, decimal=3)

def test_minor_pair_2(self):
val = nuclinfo.minor_pair(self.u, 20, 5, seg1='RNAA', seg2='RNAA')
assert_almost_equal(val, 4.356, decimal=3)

def test_major_pair_1(self):
val = nuclinfo.major_pair(self.u, 2, 12, seg1='RNAA', seg2='RNAA')
assert_almost_equal(val, 30.001, decimal=3)

def test_major_pair_2(self):
val = nuclinfo.major_pair(self.u, 5, 9, seg1='RNAA', seg2='RNAA')
assert_almost_equal(val, 12.581, decimal=3)

def test_phase_cp_1(self):
val = nuclinfo.phase_cp(self.u, seg='RNAA', i=9)
assert_almost_equal(val, 14.846, decimal=3)

def test_phase_cp_2(self):
val = nuclinfo.phase_cp(self.u, seg='RNAA', i=21)
assert_almost_equal(val, 16.199, decimal=3)

def test_phase_as_1(self):
val = nuclinfo.phase_as(self.u, seg='RNAA', i=1)
assert_almost_equal(val, 8.565, decimal=3)

def test_phase_as_2(self):
val = nuclinfo.phase_as(self.u, seg='RNAA', i=11)
assert_almost_equal(val, 151.397, decimal=3)

def test_tors_1(self):
val = nuclinfo.tors(self.u, seg='RNAA', i=5)
assert_allclose(val, [ 296.103016, 179.084427,
47.712818, 81.49588 , 205.350479,
284.046562, 198.58165 ], rtol=1e-03)

def test_tors_2(self):
val = nuclinfo.tors(self.u, seg='RNAA', i=21)
assert_allclose(val, [ 300.047634, 172.476593,
50.744877, 82.144211, 206.106445,
286.208565, 195.652176], rtol=1e-03)

def test_tors_alpha_1(self):
val = nuclinfo.tors_alpha(self.u, seg='RNAA', i=6)
assert_almost_equal(val, 299.278, decimal=3)

def test_tors_alpha_2(self):
val = nuclinfo.tors_alpha(self.u, seg='RNAA', i=18)
assert_almost_equal(val, 304.093, decimal=3)

def test_tors_beta_1(self):
val = nuclinfo.tors_beta(self.u, seg='RNAA', i=7)
assert_almost_equal(val, 177.041, decimal=3)

def test_tors_beta_2(self):
val = nuclinfo.tors_beta(self.u, seg='RNAA', i=15)
assert_almost_equal(val, 162.441, decimal=3)

def test_tors_gamma_1(self):
val = nuclinfo.tors_gamma(self.u, seg='RNAA', i=7)
assert_almost_equal(val, 47.201, decimal=3)

def test_tors_gamma_2(self):
val = nuclinfo.tors_gamma(self.u, seg='RNAA', i=15)
assert_almost_equal(val, 64.276, decimal=3)

def test_tors_delta_1(self):
val = nuclinfo.tors_delta(self.u, seg='RNAA', i=7)
assert_almost_equal(val, 80.223, decimal=3)

def test_tors_delta_2(self):
val = nuclinfo.tors_delta(self.u, seg='RNAA', i=15)
assert_almost_equal(val, 81.553, decimal=3)

def test_tors_eps_1(self):
val = nuclinfo.tors_eps(self.u, seg='RNAA', i=7)
assert_almost_equal(val, 207.476, decimal=3)

def test_tors_eps_2(self):
val = nuclinfo.tors_eps(self.u, seg='RNAA', i=15)
assert_almost_equal(val, 202.352, decimal=3)

def test_tors_zeta_1(self):
val = nuclinfo.tors_zeta(self.u, seg='RNAA', i=7)
assert_almost_equal(val, 289.429, decimal=3)

def test_tors_zeta_2(self):
val = nuclinfo.tors_zeta(self.u, seg='RNAA', i=15)
assert_almost_equal(val, 289.318, decimal=3)

def test_tors_chi_1(self):
val = nuclinfo.tors_chi(self.u, seg='RNAA', i=1)
assert_almost_equal(val, 198.601, decimal=3)

def test_tors_chi_2(self):
val = nuclinfo.tors_chi(self.u, seg='RNAA', i=2)
assert_almost_equal(val, 198.932, decimal=3)

def test_hydroxyl_1(self):
val = nuclinfo.hydroxyl(self.u, seg='RNAA', i=20)
assert_almost_equal(val, 122.689, decimal=3)

def test_hydroxyl_2(self):
val = nuclinfo.hydroxyl(self.u, seg='RNAA', i=5)
assert_almost_equal(val, 122.965, decimal=3)

def test_pseudo_dihe_baseflip_1(self):
val = nuclinfo.pseudo_dihe_baseflip(self.u, 16, 2, 3, seg1='RNAA',seg2='RNAA', seg3='RNAA' )
assert_almost_equal(val, 308.244, decimal=3)

def test_pseudo_dihe_baseflip_2(self):
val = nuclinfo.pseudo_dihe_baseflip(self.u, 8, 9, 10, seg1='RNAA',seg2='RNAA', seg3='RNAA')
assert_almost_equal(val, 25.224, decimal=3)
@pytest.fixture(scope='module')
def u():
return mda.Universe(NUCL)


@pytest.mark.parametrize('i, bp, seg1, seg2, expected_value', (
(1, 2, 'RNAA', 'RNAA', 4.449),
(22, 23, 'RNAA', 'RNAA', 4.601)
))
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', 16.649),
(20, 5, 'RNAA', 'RNAA', 4.356)
))
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', 30.001),
(5, 9, 'RNAA', 'RNAA', 12.581)
))
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, 14.846),
('RNAA', 21, 16.199)
))
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, 8.565),
('RNAA', 11, 151.397)
))
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, [296.103016, 179.084427, 47.712818, 81.49588, 205.350479,
284.046562, 198.58165]),
('RNAA', 21, [300.047634, 172.476593, 50.744877, 82.144211, 206.106445,
286.208565, 195.652176])
))
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, 299.278),
('RNAA', 18, 304.093)
))
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, 177.041),
('RNAA', 15, 162.441)
))
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, 47.201),
('RNAA', 15, 64.276)
))
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, 80.223),
('RNAA', 15, 81.553)
))
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, 207.476),
('RNAA', 15, 202.352)
))
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, 289.429),
('RNAA', 15, 289.318)
))
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, 198.601),
('RNAA', 2, 198.932)
))
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, 122.689),
('RNAA', 5, 122.965)
))
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', 308.244),
(8, 9, 10, 'RNAA', 'RNAA', 'RNAA', 25.224),
))
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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