Improve error message when calling AtmGroup.unwrap() without bonds

package/MDAnalysis/core/groups.py

@@ -1874,9 +1874,13 @@ def unwrap(self, compound='fragments', reference='com', inplace=True):
         """
         atoms = self.atoms
         # bail out early if no bonds in topology:
-        if not hasattr(atoms, 'bonds'):
-            raise NoDataError("{}.unwrap() not available; this requires Bonds"
-                              "".format(self.__class__.__name__))
+        if not hasattr(atoms, 'bonds'): 
+            raise NoDataError(
+                f"{self.__class__.__name__}.unwrap() not available; this AtomGroup lacks defined bonds. "
+                "To resolve this, you can either:\n"
+                "1. Guess the bonds at universe creation using `guess_bonds = True`, or\n"
+                "2. Create a universe using a topology format where bonds are pre-defined."
+            )
         unique_atoms = atoms.unsorted_unique
 
         # Parameter sanity checking

testsuite/MDAnalysisTests/core/test_groups.py

@@ -1434,46 +1434,52 @@ def test_component_set_plural(self, attr, groupname):
             setattr(comp, attr, 24)
 
 class TestAttributeGetting(object):
-    
+
     @staticmethod
     @pytest.fixture()
     def universe():
         return make_Universe(extras=('masses', 'altLocs'))
 
+    @staticmethod
+    @pytest.fixture()
+    def atoms():
+        u = make_Universe(extras=("masses",), size=(3, 1, 1))
+        return u.atoms
+
     @pytest.mark.parametrize('attr', ['masses', 'altLocs'])
     def test_get_present_topattr_group(self, universe, attr):
         values = getattr(universe.atoms, attr)
         assert values is not None
-    
+
     @pytest.mark.parametrize('attr', ['mass', 'altLoc'])
     def test_get_present_topattr_component(self, universe, attr):
         value = getattr(universe.atoms[0], attr)
         assert value is not None
 
     @pytest.mark.parametrize('attr,singular', [
-        ('masses', 'mass'), 
+        ('masses', 'mass'),
         ('altLocs', 'altLoc')])
     def test_get_plural_topattr_from_component(self, universe, attr, singular):
         with pytest.raises(AttributeError) as exc:
             getattr(universe.atoms[0], attr)
         assert ('Do you mean ' + singular) in str(exc.value)
-    
+
     @pytest.mark.parametrize('attr,singular', [
-        ('masses', 'mass'), 
+        ('masses', 'mass'),
         ('altLocs', 'altLoc')])
     def test_get_sing_topattr_from_group(self, universe, attr, singular):
         with pytest.raises(AttributeError) as exc:
             getattr(universe.atoms, singular)
-        assert ('Do you mean '+attr) in str(exc.value)
-    
+        assert ('Do you mean ' + attr) in str(exc.value)
+
     @pytest.mark.parametrize('attr,singular', [
-        ('elements', 'element'), 
+        ('elements', 'element'),
         ('tempfactors', 'tempfactor'),
         ('bonds', 'bonds')])
     def test_get_absent_topattr_group(self, universe, attr, singular):
         with pytest.raises(NoDataError) as exc:
             getattr(universe.atoms, attr)
-        assert 'does not contain '+singular in str(exc.value)
+        assert 'does not contain ' + singular in str(exc.value)
 
     def test_get_non_topattr(self, universe):
         with pytest.raises(AttributeError) as exc:
@@ -1483,9 +1489,13 @@ def test_get_non_topattr(self, universe):
     def test_unwrap_without_bonds(self, universe):
         with pytest.raises(NoDataError) as exc:
             universe.atoms.unwrap()
-        err = ('AtomGroup.unwrap() not available; '
-               'this requires Bonds')
-        assert str(exc.value) == err
+        expected_message = (
+            "AtomGroup.unwrap() not available; this AtomGroup lacks defined bonds. "
+            "To resolve this, you can either:\n"
+            "1. Guess the bonds at universe creation using `guess_bonds = True`, or\n"
+            "2. Create a universe using a topology format where bonds are pre-defined."
+        )
+        assert str(exc.value) == expected_message
 
     def test_get_absent_attr_method(self, universe):
         with pytest.raises(NoDataError) as exc:
@@ -1512,7 +1522,7 @@ def test_attrmethod_wrong_group(self, universe):
             universe.atoms[0].center_of_mass()
         err = ('center_of_mass() is a method of AtomGroup, not Atom')
         assert str(exc.value) == err
-    
+
     @pytest.mark.parametrize('attr', ['altlocs', 'alt_Locs'])
     def test_wrong_name(self, universe, attr):
         with pytest.raises(AttributeError) as exc:
@@ -1521,7 +1531,6 @@ def test_wrong_name(self, universe, attr):
                'Did you mean altLocs?').format(attr)
         assert str(exc.value) == err
 
-
 class TestInitGroup(object):
     @staticmethod
     @pytest.fixture(

testsuite/MDAnalysisTests/core/test_unwrap.py

@@ -21,6 +21,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import numpy as np
+import re
 from numpy.testing import (assert_raises, assert_almost_equal,
                            assert_array_equal)
 import pytest
@@ -336,7 +337,13 @@ def test_unwrap_no_bonds_exception_safety(self, level, compound, reference):
             group = group.segments
         # store original positions:
         orig_pos = group.atoms.positions
-        with pytest.raises(NoDataError):
+        error_message = (
+            f"{group.__class__.__name__}.unwrap() not available; this AtomGroup lacks defined bonds. "
+            "To resolve this, you can either:\n"
+            "1. Guess the bonds at universe creation using `guess_bonds = True`, or\n"
+            "2. Create a universe using a topology format where bonds are pre-defined."
+        )
+        with pytest.raises(NoDataError, match=re.escape(error_message)):
             group.unwrap(compound=compound, reference=reference, inplace=True)
         # make sure atom positions are unchanged:
         assert_array_equal(group.atoms.positions, orig_pos)