Minimum mass for hydrogen guess in HydrogenBondAnalysis (#2516)

* added minimum hydrogen mass

package/CHANGELOG

@@ -84,6 +84,8 @@ Enhancements
   * Improve the distance search in water bridge analysis with capped_distance (PR #2480)
 
 Changes
+  * Added `min_mass` parameter to `guess_hydrogens` function in `HydrogenBondAnalysis`
+    set to 0.9 by default (Issue #2472)
   * Removes `save()` function from contacts, diffusionmap, hole, LinearDensity,
     and rms (Issue #1745).
   * Removes; `save_table()` from :class:`HydrogenBondAnalysis`,

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -169,7 +169,7 @@
 """
 from __future__ import absolute_import, division
 
-import numpy as  np
+import numpy as np
 
 from .. import base
 from MDAnalysis.lib.distances import capped_distance, calc_angles
@@ -234,7 +234,12 @@ def __init__(self, universe, donors_sel=None, hydrogens_sel=None, acceptors_sel=
         self.d_h_a_angle = d_h_a_angle_cutoff
         self.update_selections = update_selections
 
-    def guess_hydrogens(self, selection='all', max_mass=1.1, min_charge=0.3):
+    def guess_hydrogens(self,
+                        selection='all',
+                        max_mass=1.1,
+                        min_charge=0.3,
+                        min_mass=0.9
+                        ):
         """Guesses which hydrogen atoms should be used in the analysis.
 
         Parameters
@@ -263,14 +268,21 @@ def guess_hydrogens(self, selection='all', max_mass=1.1, min_charge=0.3):
         Alternatively, this function may be used to quickly generate a :class:`str` of potential hydrogen atoms involved
         in hydrogen bonding. This str may then be modified before being used to set the attribute
         :attr:`hydrogens_sel`.
+
+        .. versionchanged: 1.0.0
+            Added `min_mass` parameter to specify minimum mass (Issue #2472)
         """
 
+        if min_mass > max_mass:
+            raise ValueError("min_mass is higher than (or equal to) max_mass")
+
         ag = self.u.select_atoms(selection)
         hydrogens_ag = ag[
-            np.logical_and(
+            np.logical_and.reduce((
                 ag.masses < max_mass,
-                ag.charges > min_charge
-            )
+                ag.charges > min_charge,
+                ag.masses > min_mass,
+            ))
         ]
 
         hydrogens_list = np.unique(

testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py

@@ -57,7 +57,7 @@ def h(self, universe):
 
     def test_hbond_analysis(self, h):
 
-        assert len(np.unique(h.hbonds[:,0])) == 10
+        assert len(np.unique(h.hbonds[:, 0])) == 10
         assert len(h.hbonds) == 32
 
         reference = {
@@ -98,6 +98,7 @@ def test_count_by_ids(self, h):
 
         assert_array_equal(counts, ref_counts)
 
+
 class TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_(TestHydrogenBondAnalysisTIP3P):
     """Uses the same distance and cutoff hydrogen bond criteria as :class:`TestHydrogenBondAnalysisTIP3P`, so the
     results are identical, but the hydrogens and acceptors are guessed whilst the donor-hydrogen pairs are determined
@@ -111,6 +112,7 @@ class TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_(T
         'd_h_a_angle_cutoff': 120.0
     }
 
+
 class TestHydrogenBondAnalysisTIP3P_GuessDonors_NoTopology(object):
     """Guess the donor atoms involved in hydrogen bonds using the partial charges of the atoms.
     """
@@ -141,6 +143,58 @@ def test_guess_donors(self, h):
         assert donors == ref_donors
 
 
+class TestHydrogenBondAnalysisTIP3P_GuessHydrogens_NoTopology(object):
+    """
+    Guess the hydrogen atoms involved in hydrogen bonds using the mass and
+    partial charge of the atoms.
+    """
+
+    @staticmethod
+    @pytest.fixture(scope='class')
+    def universe():
+        return MDAnalysis.Universe(waterPSF, waterDCD)
+
+    kwargs = {
+        'donors_sel': None,
+        'hydrogens_sel': None,
+        'acceptors_sel': None,
+        'd_h_cutoff': 1.2,
+        'd_a_cutoff': 3.0,
+        'd_h_a_angle_cutoff': 120.0
+    }
+
+    @pytest.fixture(scope='class')
+    def h(self, universe):
+        h = HydrogenBondAnalysis(universe, **self.kwargs)
+        return h
+
+    def test_guess_hydrogens(self, h):
+
+        ref_hydrogens = "(resname TIP3 and name H1) or (resname TIP3 and name H2)"
+        hydrogens = h.guess_hydrogens(selection='all')
+        assert hydrogens == ref_hydrogens
+
+    pytest.mark.parametrize(
+        "min_mass, max_mass, min_charge",
+        [
+            (1.05, 1.10, 0.30),
+            (0.90, 0.95, 0.30),
+            (0.90, 1.10, 1.00)
+        ]
+    )
+    def test_guess_hydrogens_empty_selection(self, h):
+
+        hydrogens = h.guess_hydrogens(selection='all', min_charge=1.0)
+        assert hydrogens == ""
+
+    def test_guess_hydrogens_min_max_mass(self, h):
+
+        errmsg = "min_mass is higher than \(or equal to\) max_mass"
+
+        with pytest.raises(ValueError, match=errmsg):
+
+            h.guess_hydrogens(selection='all', min_mass=1.1, max_mass=0.9)
+
 class TestHydrogenBondAnalysisTIP3PStartStep(object):
     """Uses the same distance and cutoff hydrogen bond criteria as :class:`TestHydrogenBondAnalysisTIP3P` but starting
     with the second frame and using every other frame in the analysis.
@@ -168,7 +222,7 @@ def h(self, universe):
 
     def test_hbond_analysis(self, h):
 
-        assert len(np.unique(h.hbonds[:,0])) == 5
+        assert len(np.unique(h.hbonds[:, 0])) == 5
         assert len(h.hbonds) == 15
 
         reference = {