Amended hbond test for full coverage, added _get_dh_pairs ability to …

…find hydrogen atoms.
MDAnalysis · Sep 27, 2022 · 299b898 · 299b898
1 parent f7f8bf5
commit 299b898
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Showing 2 changed files with 40 additions and 1 deletion.
diff --git a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py
@@ -592,7 +592,12 @@ def _get_dh_pairs(self):
         # Otherwise, use d_h_cutoff as a cutoff distance
         else:
 
-            hydrogens = self.u.select_atoms(self.hydrogens_sel)
+            if self.hydrogens_sel is None:
+                hydrogens_sel = self.guess_hydrogens()
+            else:
+                hydrogens_sel = self.hydrogens_sel
+
+            hydrogens = self.u.select_atoms(hydrogens_sel)
             donors = self.u.select_atoms(self.donors_sel)
             donors_indices, hydrogen_indices = capped_distance(
                 donors.positions,

diff --git a/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py b/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py
@@ -335,6 +335,40 @@ def test_no_bond_info_exception(self, universe):
             h = HydrogenBondAnalysis(universe, **kwargs)
             h._get_dh_pairs()
 
+    def test_no_bond_no_mass_donor_sel(self, universe):
+
+        kwargs = {
+            'donors_sel': "type O",
+            'hydrogens_sel': None,
+            'acceptors_sel': None,
+            'd_h_cutoff': 1.2,
+            'd_a_cutoff': 3.0,
+            'd_h_a_angle_cutoff': 120.0
+        }
+
+        with pytest.raises(NoDataError, match="not contain mass information"):
+            h = HydrogenBondAnalysis(universe, **kwargs)
+            h._get_dh_pairs()
+
+    def test_no_bond_donor_sel(self, universe):
+
+        kwargs = {
+            'donors_sel': "type O",
+            'hydrogens_sel': None,
+            'acceptors_sel': None,
+            'd_h_cutoff': 1.2,
+            'd_a_cutoff': 3.0,
+            'd_h_a_angle_cutoff': 120.0
+        }
+        u = universe.copy()
+        n_residues = 2
+        u.add_TopologyAttr('mass', [15.999, 1.008, 1.008] * n_residues)
+        u.add_TopologyAttr('charge', [-1.04, 0.52, 0.52] * n_residues)
+        h = HydrogenBondAnalysis(u, **kwargs)
+        pairs = h._get_dh_pairs()
+
+        assert len(pairs) == 2
+
     def test_first_hbond(self, hydrogen_bonds):
         assert len(hydrogen_bonds.results.hbonds) == 2
         frame_no, donor_index, hydrogen_index, acceptor_index, da_dst, angle =\