hbond_analysis complete codecov

.gitignore

@@ -21,7 +21,7 @@ examples/output.txt
 # ignore Vagrant virtual machines
 .vagrant
 # ignore coverage files
-.coverage
+.coverage*
 .noseids
 htmlcov
 # ignore trajectory offset caches

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -486,7 +486,10 @@ def guess_donors(self, select='all', max_charge=-0.5):
             hydrogens_sel = self.hydrogens_sel
         hydrogens_ag = self.u.select_atoms(hydrogens_sel)
 
-        if hasattr(hydrogens_ag[0],"bonded_atoms") and hydrogens_ag[0].bonded_atoms:
+        # We're using u._topology.bonds rather than u.bonds as it is a million times faster to access.
+        # This is because u.bonds also calculates properties of each bond (e.g bond length).
+        # See https://github.com/MDAnalysis/mdanalysis/issues/2396#issuecomment-596251787
+        if (hasattr(self.u._topology, 'bonds') and len(self.u._topology.bonds.values) != 0):
             donors_ag = find_hydrogen_donors(hydrogens_ag)
         else:
             ag = hydrogens_ag.residues.atoms.select_atoms(

testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py

@@ -204,6 +204,23 @@ def test_no_bond_info_exception(self, universe):
             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)
+        donors = u.select_atoms(h.guess_donors())
+
     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 =\
@@ -319,6 +336,16 @@ def hydrogen_bonds(universe):
         h.run()
         return h
 
+    def test_count_by_type(self, universe):
+
+        h = HydrogenBondAnalysis(
+            universe,
+            **TestHydrogenBondAnalysisNoRes.kwargs
+        )
+        h.run()
+        counts = h.count_by_type()
+        ref_count = 2
+        assert int(counts[0, 2]) == ref_count
 
     def test_no_bond_info_exception(self, universe):
 
@@ -365,9 +392,9 @@ def test_no_bond_donor_sel(self, universe):
         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()
+        donors = u.select_atoms(h.guess_donors())
 
-        assert len(pairs) == 2
+        assert len(donors) == 2
 
     def test_first_hbond(self, hydrogen_bonds):
         assert len(hydrogen_bonds.results.hbonds) == 2