Review changes

package/MDAnalysis/core/groups.py

@@ -679,11 +679,8 @@ def center(self, weights, pbc=None, compound='group', unwrap=False):
             will be returned as an array of position vectors, i.e. a 2d array.
             Note that, in any case, *only* the positions of :class:`Atoms<Atom>`
             *belonging to the group* will be taken into account.
-        unwrap : bool or None, optional
-            If ``True`` and `compound` is ``'group'``, the atoms will be unwrapped
-            before calculations. If ``True`` and `compound` is
-            ``'segments'`` or ``'residues'``, all molecules will be unwrapped before
-             calculation to keep the compounds intact.
+        unwrap : bool, optional
+            If ``True``, compounds will be unwrapped before computing their centers.
 
         Returns
         -------
@@ -739,6 +736,9 @@ def center(self, weights, pbc=None, compound='group', unwrap=False):
 
         comp = compound.lower()
         if comp == 'group':
+            if unwrap and pbc:
+                raise ValueError("'unwrap' and 'pbc' cannot be true at the same time "
+                                 "for compound='group")
             if unwrap:
                 coords = atoms.unwrap(compound=comp, reference=None, inplace=False)
             if pbc:
@@ -776,8 +776,6 @@ def center(self, weights, pbc=None, compound='group', unwrap=False):
                              " one of 'group', 'residues', 'segments', "
                              "'molecules', or 'fragments'.".format(compound))
 
-
-
         # Sort positions and weights by compound index and promote to dtype if
         # required:
         sort_indices = np.argsort(compound_indices)

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -543,6 +543,13 @@ def test_center_unwrap(self, level, compound, is_triclinic):
         ref_center = u.center(compound=compound)
         assert_almost_equal(ref_center, center, decimal=4)
 
+    def test_center_unwrap_pbc_true(self):
+        u = UnWrapUniverse(is_triclinic=False)
+        # select group appropriate for compound:
+        group = u.atoms[39:47]  # molecule 12
+        with pytest.raises(ValueError):
+            group.center(weights=None, compound="group", unwrap=True, pbc=True)
+
 
 class TestSplit(object):
 

testsuite/MDAnalysisTests/core/util.py

@@ -579,28 +579,28 @@ def center(self, compound):
             center_pos = np.zeros((12, 3), dtype=np.float32)
 
         for base in range(3):
-            loc_centre = relpos[base, :]
-            center_pos[pos,:] = loc_centre
+            loc_center = relpos[base, :]
+            center_pos[pos,:] = loc_center
             pos+=1
 
         for base in range(3, 15, 3):
-            loc_centre = np.mean(relpos[base:base + 3, :], axis=0)
-            center_pos[pos,:] = loc_centre
+            loc_center = np.mean(relpos[base:base + 3, :], axis=0)
+            center_pos[pos,:] = loc_center
             pos+=1
 
         if compound=="residues":
             for base in range(15, 47, 4):
-                loc_centre = np.mean(relpos[base:base + 4, :], axis=0)
-                center_pos[pos,:] = loc_centre
+                loc_center = np.mean(relpos[base:base + 4, :], axis=0)
+                center_pos[pos,:] = loc_center
                 pos+=1
         else:
             for base in range(15, 23, 4):
-                loc_centre = np.mean(relpos[base:base + 4, :], axis=0)
-                center_pos[pos,:] = loc_centre
+                loc_center = np.mean(relpos[base:base + 4, :], axis=0)
+                center_pos[pos,:] = loc_center
                 pos+=1
             for base in range(23, 47, 8):
-                loc_centre = np.mean(relpos[base:base + 8, :], axis=0)
-                center_pos[pos,:] = loc_centre
+                loc_center = np.mean(relpos[base:base + 8, :], axis=0)
+                center_pos[pos,:] = loc_center
                 pos+=1
 
         if compound == "group":