Updated atom ID representation order to match AtomGroup (#4191)

* Updated atom ID representation order to match AtomGroup

package/AUTHORS

@@ -219,6 +219,7 @@ Chronological list of authors
   - Daniel J. Evans
   - Mohit Kumar
   - Shubham Kumar
+  - Zaheer Timol
 
 External code
 -------------

package/CHANGELOG

@@ -13,7 +13,8 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen
+
+??/??/?? IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen, ztimol
 
  * 2.6.0
 
@@ -29,6 +30,9 @@ Enhancements
     (Issue #3546)
 
 Changes
+  * Atom ID representation order updated to match that of associated
+    AtomGroup indices.
+    (PR #4191, Issue #4181)
   * Package license has been updated to GPLv3+ to better reflect the
     compatibility of GPLv2+ with Apache and GPLv3 licenced codes (PR #4219).
   * All new contributions are now made under LGPLv2.1+ (PR #4219).

package/MDAnalysis/core/topologyobjects.py

@@ -52,6 +52,8 @@ class TopologyObject(object):
        via the ``is_guessed`` managed property.
     .. versionadded:: 0.11.0
        Added the `value` method to return the size of the object
+    .. versionchanged:: 2.6.0
+       Updated Atom ID representation order to match that of AtomGroup indices
     """
     __slots__ = ("_ix", "_u", "btype", "_bondtype", "_guessed", "order")
 
@@ -116,13 +118,12 @@ def __hash__(self):
         return hash((self._u, tuple(self.indices)))
 
     def __repr__(self):
-        indices = (self.indices if self.indices[0] < self.indices[-1]
-                   else self.indices[::-1])
+        """Return representation in same order of AtomGroup indices"""
         return "<{cname} between: {conts}>".format(
             cname=self.__class__.__name__,
             conts=", ".join([
                 "Atom {0}".format(i)
-                for i in indices]))
+                for i in self.indices]))
 
     def __contains__(self, other):
         """Check whether an atom is in this :class:`TopologyObject`"""

testsuite/MDAnalysisTests/core/test_topologyobjects.py

@@ -157,7 +157,7 @@ def test_angle(self, PSFDCD):
     def test_angle_repr(self, PSFDCD):
         angle = PSFDCD.atoms[[30, 10, 20]].angle
 
-        assert_equal(repr(angle), '<Angle between: Atom 20, Atom 10, Atom 30>')
+        assert_equal(repr(angle), '<Angle between: Atom 30, Atom 10, Atom 20>')
 
     def test_angle_180(self):
         # we edit the coordinates, so make our own universe
@@ -183,7 +183,7 @@ def test_dihedral_repr(self, PSFDCD):
         dihedral = PSFDCD.atoms[[4, 7, 8, 1]].dihedral
 
         assert_equal(repr(dihedral),
-                     '<Dihedral between: Atom 1, Atom 8, Atom 7, Atom 4>')
+                     '<Dihedral between: Atom 4, Atom 7, Atom 8, Atom 1>')
 
     # Improper_Dihedral class check
     def test_improper(self, PSFDCD):
@@ -197,12 +197,12 @@ def test_improper_repr(self, PSFDCD):
 
         assert_equal(
             repr(imp),
-            '<ImproperDihedral between: Atom 1, Atom 8, Atom 7, Atom 4>')
+            '<ImproperDihedral between: Atom 4, Atom 7, Atom 8, Atom 1>')
 
     def test_ureybradley_repr(self, PSFDCD):
         ub = PSFDCD.atoms[[30, 10]].ureybradley
 
-        assert_equal(repr(ub), '<UreyBradley between: Atom 10, Atom 30>')
+        assert_equal(repr(ub), '<UreyBradley between: Atom 30, Atom 10>')
 
     def test_ureybradley_repr_VE(self, PSFDCD):
         with pytest.raises(ValueError):
@@ -221,7 +221,7 @@ def test_cmap_repr(self, PSFDCD):
 
         assert_equal(
             repr(cmap),
-            '<CMap between: Atom 2, Atom 1, Atom 8, Atom 7, Atom 4>')
+            '<CMap between: Atom 4, Atom 7, Atom 8, Atom 1, Atom 2>')
 
     def test_cmap_repr_VE(self, PSFDCD):
         with pytest.raises(ValueError):