fixes #1795 (#2074)

* fixes #1795

SphericalZone and SphericalLayer no longer shift atoms to inside
primary unit cell when calculating center of reference group

* additional tests for sphzone

package/CHANGELOG

@@ -106,6 +106,9 @@ Fixes
   * Modifying coordinates by assignation is consistently persistent when using
     the memory reader (Issue #2018)
   * Allow import of WaterBridgeAnalysis from analysis.hbonds (#2064)
+  * Fixed SphericalLayer and SphericalZone selections with pbc=True.  Previously
+    these shifted all atoms to inside the primary unit cell when calculating the
+    center of the reference group (Issue #1795)
 
 Changes
   * TopologyAttrs are now statically typed (Issue #1876)

package/MDAnalysis/core/selection.py

@@ -288,8 +288,7 @@ def apply(self, group):
         sel = self.sel.apply(group)
         box = self.validate_dimensions(group.dimensions)
         periodic = box is not None
-        ref = sel.center_of_geometry(pbc=periodic).reshape(1, 3).astype(
-            np.float32)
+        ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
         pairs = distances.capped_distance(ref, group.positions, self.exRadius,
                                           min_cutoff=self.inRadius,
                                           box=box,
@@ -314,8 +313,7 @@ def apply(self, group):
         sel = self.sel.apply(group)
         box = self.validate_dimensions(group.dimensions)
         periodic = box is not None
-        ref = sel.center_of_geometry(pbc=periodic).reshape(1, 3).astype(
-            np.float32)
+        ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
         pairs = distances.capped_distance(ref, group.positions, self.cutoff,
                                           box=box,
                                           return_distances=False)

testsuite/MDAnalysisTests/core/test_atomselections.py

@@ -530,7 +530,7 @@ def test_spherical_layer(self, u, periodic):
 
         r1 = u.select_atoms('resid 1')
         box = u.dimensions if periodic else None
-        cog = r1.center_of_geometry(pbc=periodic).reshape(1, 3)
+        cog = r1.center_of_geometry().reshape(1, 3)
         d = distance_array(u.atoms.positions, cog, box=box)
         ref = set(np.where((d > 2.4) & (d < 6.0))[0])
 
@@ -548,7 +548,7 @@ def test_spherical_zone(self, u, periodic):
 
         r1 = u.select_atoms('resid 1')
         box = u.dimensions if periodic else None
-        cog = r1.center_of_geometry(pbc=periodic).reshape(1, 3)
+        cog = r1.center_of_geometry().reshape(1, 3)
         d = distance_array(u.atoms.positions, cog, box=box)
         ref = set(np.where(d < 5.0)[0])
 
@@ -603,6 +603,12 @@ def test_cyzone(self, u, meth, periodic):
 
         assert ref == set(result.indices)
 
+    @pytest.mark.parametrize('periodic,expected', ([True, 33], [False, 25]))
+    def test_sphzone(self, u, periodic, expected):
+        sel = u.select_atoms('sphzone 5.0 resid 1', periodic=periodic)
+
+        assert len(sel) == expected
+
 
 class TestTriclinicDistanceSelections(BaseDistanceSelection):
     @pytest.fixture()