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Merge pull request #2231 from MDAnalysis/issue-2218-2-OH
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fixed 2'-hydroxyl dihedral calculation
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@orbeckst
orbeckst authored Apr 3, 2019
2 parents 9428866 + 4f8dc17 commit 6a60c8a
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Showing 10 changed files with 58 additions and 888 deletions.
1 change: 1 addition & 0 deletions .travis.yml
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Expand Up @@ -50,6 +50,7 @@ matrix:
- env: NAME="Doc"
MAIN_CMD="cd package && python setup.py"
SETUP_CMD="build_sphinx"
PYTHON_VERSION=3.7
BUILD_DOCS=true
BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
INSTALL_HOLE="false"
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Expand Up @@ -91,6 +91,8 @@ Fixes
* Fixed documentation of MDAnalysis.analysis.contacts
* Enforced consistent dtype (numpy.float32) of Universe.dimensions and
Timestep.dimensions for all Universes and Readers (Issue #2190, PR #2213)
* Fixed analysis.nucleic.hydroxyl() function: correctly recognize the
2'-hydroxyl hydrogen H2'; gave wrong results (Issue #2218)

Deprecations
* analysis.polymer.PersistenceLength no longer requires the perform_fit()
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8 changes: 4 additions & 4 deletions package/MDAnalysis/analysis/nuclinfo.py
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Expand Up @@ -704,10 +704,10 @@ def hydroxyl(universe, seg, i):
.. versionadded:: 0.7.6
"""
h = universe.select_atoms(" atom {0!s} {1!s} C1\' ".format(seg, i),
" atom {0!s} {1!s} C2\' ".format(seg, i),
" atom {0!s} {1!s} O2\' ".format(seg, i),
" atom {0!s} {1!s} H2\'\' ".format(seg, i))
h = universe.select_atoms("atom {0!s} {1!s} C1'".format(seg, i),
"atom {0!s} {1!s} C2'".format(seg, i),
"atom {0!s} {1!s} O2'".format(seg, i),
"atom {0!s} {1!s} H2'".format(seg, i))
try:
hydr = h.dihedral.value() % 360
except ValueError:
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72 changes: 38 additions & 34 deletions testsuite/MDAnalysisTests/analysis/test_nuclinfo.py
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Expand Up @@ -25,7 +25,7 @@
import MDAnalysis as mda
import pytest
from MDAnalysis.analysis import nuclinfo
from MDAnalysisTests.datafiles import NUCL
from MDAnalysisTests.datafiles import RNA_PSF, RNA_PDB
from numpy.testing import (
assert_almost_equal,
assert_allclose,
Expand All @@ -34,140 +34,144 @@

@pytest.fixture(scope='module')
def u():
return mda.Universe(NUCL)
return mda.Universe(RNA_PSF, RNA_PDB)


@pytest.mark.parametrize('i, bp, seg1, seg2, expected_value', (
(1, 2, 'RNAA', 'RNAA', 4.449),
(22, 23, 'RNAA', 'RNAA', 4.601)
( 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', 16.649),
(20, 5, 'RNAA', 'RNAA', 4.356)
( 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', 30.001),
(5, 9, 'RNAA', 'RNAA', 12.581)
(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, 14.846),
('RNAA', 21, 16.199)
('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, 8.565),
('RNAA', 11, 151.397)
('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, [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])
('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, 299.278),
('RNAA', 18, 304.093)
('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, 177.041),
('RNAA', 15, 162.441)
('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, 47.201),
('RNAA', 15, 64.276)
('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, 80.223),
('RNAA', 15, 81.553)
('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, 207.476),
('RNAA', 15, 202.352)
('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, 289.429),
('RNAA', 15, 289.318)
('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, 198.601),
('RNAA', 2, 198.932)
('RNAA', 1, 177.12643),
('RNAA', 2, 212.08998),
('RNAA', 7, 209.56533),
('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, 122.689),
('RNAA', 5, 122.965)
('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', 308.244),
(8, 9, 10, 'RNAA', 'RNAA', 'RNAA', 25.224),
(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)
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18 changes: 10 additions & 8 deletions testsuite/MDAnalysisTests/core/test_atomselections.py
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Expand Up @@ -42,7 +42,7 @@
PSF, DCD,
PRMpbc, TRJpbc_bz2,
PSF_NAMD, PDB_NAMD,
GRO, NUCL, NUCLsel, TPR, XTC,
GRO, RNA_PSF, NUCLsel, TPR, XTC,
TRZ_psf, TRZ,
PDB_icodes,
PDB_HOLE,
Expand Down Expand Up @@ -449,20 +449,22 @@ def test_molnum(self, universe, selection_string, reference):


class TestSelectionsNucleicAcids(object):
@pytest.fixture()
@pytest.fixture(scope='class')
def universe(self):
return MDAnalysis.Universe(NUCL)
return MDAnalysis.Universe(RNA_PSF)

@pytest.fixture(scope='class')
def universe2(self):
return MDAnalysis.Universe(NUCLsel)


def test_nucleic(self, universe):
rna = universe.select_atoms("nucleic")
assert_equal(rna.n_atoms, 739)
assert_equal(rna.n_residues, 23)

def test_nucleic_all(self, universe):
u = mda.Universe(NUCLsel)

sel = u.select_atoms('nucleic')

def test_nucleic_all(self, universe2):
sel = universe2.select_atoms('nucleic')
assert len(sel) == 34

def test_nucleicbackbone(self, universe):
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