Merge pull request #2231 from MDAnalysis/issue-2218-2-OH

fixed 2'-hydroxyl dihedral calculation

.travis.yml

@@ -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"

package/CHANGELOG

@@ -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()

package/MDAnalysis/analysis/nuclinfo.py

@@ -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:

testsuite/MDAnalysisTests/analysis/test_nuclinfo.py

@@ -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,
@@ -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)

testsuite/MDAnalysisTests/core/test_atomselections.py

@@ -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,
@@ -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):