make Atom target class of ResidueAttr by default (MDAnalysis#2805)

* make Atom target class by default

* make molnums apply to segmentgroup

package/CHANGELOG

@@ -19,6 +19,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * ResidueAttrs now have Atom as a target class by default; ICodes and 
+    Molnums now have default target_classes (#2803, PR #2805)
   * Selections on emtpy AtomGroups now return an empty AtomGroup instead of an
     error (Issue #2765)
   * TOPParser no longer guesses elements when missing atomic number records

package/MDAnalysis/core/topologyattrs.py

@@ -764,7 +764,6 @@ def phi_selections(residues, c_name='C', n_name='N', ca_name='CA'):
 
     transplants[ResidueGroup].append(('phi_selections', phi_selections))
 
-
     def psi_selection(residue, c_name='C', n_name='N', ca_name='CA'):
         """Select AtomGroup corresponding to the psi protein backbone dihedral
         N-CA-C-N'.
@@ -891,7 +890,6 @@ def _get_prev_residues_by_resid(residues):
                     pvres[i] = None
         return pvres
 
-
     transplants[ResidueGroup].append(('_get_prev_residues_by_resid',
                                       _get_prev_residues_by_resid))
 
@@ -1081,7 +1079,7 @@ def chi1_selection(residue, n_name='N', ca_name='CA', cb_name='CB',
         """
         names = [n_name, ca_name, cb_name, cg_name]
         ags = [residue.atoms[residue.atoms.names == n] for n in names]
-        if any(len(ag)!= 1 for ag in ags):
+        if any(len(ag) != 1 for ag in ags):
             return None
         return sum(ags)
 
@@ -1827,7 +1825,7 @@ def _gen_initial_values(na, nr, ns):
 class ResidueAttr(TopologyAttr):
     attrname = 'residueattrs'
     singular = 'residueattr'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Residue]
+    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
     per_object = 'residue'
 
     def get_atoms(self, ag):
@@ -1862,7 +1860,6 @@ class Resids(ResidueAttr):
     """Residue ID"""
     attrname = 'resids'
     singular = 'resid'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
     dtype = int
 
     @staticmethod
@@ -1931,7 +1928,6 @@ def set_residues(self, rg, values):
 class Resnames(_ResidueStringAttr):
     attrname = 'resnames'
     singular = 'resname'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
     transplants = defaultdict(list)
     dtype = object
 
@@ -2041,7 +2037,6 @@ def sequence(self, **kwargs):
 class Resnums(ResidueAttr):
     attrname = 'resnums'
     singular = 'resnum'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
     dtype = int
 
     @staticmethod
@@ -2063,18 +2058,14 @@ class Moltypes(_ResidueStringAttr):
     """
     attrname = 'moltypes'
     singular = 'moltype'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
     dtype = object
 
 
 class Molnums(ResidueAttr):
-    """Name of the molecule type
-
-    Two molecules that share a molecule type share a common template topology.
+    """Index of molecule from 0
     """
     attrname = 'molnums'
     singular = 'molnum'
-    target_classes = [AtomGroup, ResidueGroup, Atom, Residue]
     dtype = np.intp
 
 # segment attributes
@@ -2086,7 +2077,8 @@ class SegmentAttr(TopologyAttr):
     """
     attrname = 'segmentattrs'
     singular = 'segmentattr'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Segment]
+    target_classes = [AtomGroup, ResidueGroup,
+                      SegmentGroup, Atom, Residue, Segment]
     per_object = 'segment'
 
     def get_atoms(self, ag):
@@ -2172,8 +2164,6 @@ def set_segments(self, sg, values):
 class Segids(_SegmentStringAttr):
     attrname = 'segids'
     singular = 'segid'
-    target_classes = [AtomGroup, ResidueGroup, SegmentGroup,
-                      Atom, Residue, Segment]
     transplants = defaultdict(list)
     dtype = object
 

testsuite/MDAnalysisTests/core/test_topologyattrs.py

@@ -223,6 +223,10 @@ def test_get_atoms(self, attr):
         assert_equal(attr.get_atoms(DummyGroup([7, 3, 9])),
                      self.values[[3, 2, 2]])
 
+    def test_get_atom(self, universe):
+        attr = getattr(universe.atoms[0], self.attrclass.singular)
+        assert_equal(attr, self.values[0])
+
     def test_get_residues(self, attr):
         assert_equal(attr.get_residues(DummyGroup([1, 2, 1, 3])),
                      self.values[[1, 2, 1, 3]])
@@ -254,6 +258,9 @@ def test_get_segments(self, attr):
         assert_equal(attr.get_segments(DummyGroup([0, 1, 1])),
                            [self.values[[0, 3]], self.values[[1, 2]], self.values[[1, 2]]])
 
+class TestICodes(TestResidueAttr):
+    values = np.array(['a', 'b', '', 'd'])
+    attrclass = tpattrs.ICodes
 
 class TestResnames(TestResidueAttr):
     attrclass = tpattrs.Resnames