Fix hbond cannot deal with atoms too far (PR #1325)

* add check that s2 selection is empty
* add test
* add change log entry

package/CHANGELOG

@@ -14,6 +14,7 @@ The rules for this file:
 
 ------------------------------------------------------------------------------
 
+
 mm/dd/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma
 
 
@@ -33,6 +34,8 @@ Fixes
     (issue #1324)
   * Fixed bug "no molecules in water selection" in waterdynamics analysis
     module.
+  * Fix hbond_analysis cannot deal with Universe where no two atoms are with 3A.
+    (PR #1325)
 
 Changes
   * Enable various pylint warnings to increase python 3 compatibility

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -823,6 +823,8 @@ def _update_selection_2(self):
         self._s2_donors = {}
         self._s2_donors_h = {}
         self._s2_acceptors = {}
+        if not self._s2:
+            return None
         if self.selection1_type in ('donor', 'both'):
             self._s2_acceptors = self._s2.select_atoms(
                 'name {0}'.format(' '.join(self.acceptors)))

testsuite/MDAnalysisTests/analysis/test_hbonds.py

@@ -31,6 +31,7 @@
 
 import itertools
 import warnings
+from six import StringIO
 
 from MDAnalysisTests.datafiles import PDB_helix, GRO, XTC
 # For type guessing:
@@ -87,6 +88,17 @@ def test_generate_table(self):
         assert_array_equal(h.table.donor_resid, self.values['donor_resid'])
         assert_array_equal(h.table.acceptor_resnm, self.values['acceptor_resnm'])
 
+    @staticmethod
+    def test_atoms_too_far():
+        pdb = '''
+ATOM      1  N   LEU     1      32.310  13.778  14.372  1.00  0.00      SYST N 0
+ATOM      2  OW  SOL     2       3.024   4.456   4.147  1.00  0.00      SYST H 0'''
+
+        u = MDAnalysis.Universe(StringIO(pdb), format="pdb")
+        h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u, 'resname SOL', 'protein')
+        h.run(verbose=False)
+        assert_equal(h.timeseries, [[]])
+
     @staticmethod
     def test_true_traj():
         u = MDAnalysis.Universe(GRO, XTC)