document IC_Residue.ak_set, implement __contains__(AtomKey) for IC_Re…

…sidue and Edron

Bio/PDB/internal_coords.py

@@ -2271,6 +2271,8 @@ class IC_Residue:
     atom_coords: AtomKey indexed dict of numpy [4] arrays
         **removed**
         Use AtomKeys and atomArrayIndex to build if needed
+    ak_set: set of AtomKeys in dihedra
+        AtomKeys in all dihedra overlapping this residue (see __contains__())
     alt_ids: list of char
         AltLoc IDs from PDB file
     bfactors: dict
@@ -2587,6 +2589,18 @@ def __deepcopy__(self, memo):
         # still need to update: rnext, rprev, akc, ak_set, di/hedra
         return dup
 
+    def __contains__(self, ak: "AtomKey") -> bool:
+        """Return True if atomkey is in this residue."""
+        if ak in self.ak_set:
+            akl = ak.akl
+            if (
+                int(akl[0]) == self.rbase[0]
+                and akl[1] == self.rbase[1]
+                and akl[2] == self.rbase[2]
+            ):
+                return True
+        return False
+
     def rak(self, atm: Union[str, Atom]) -> "AtomKey":
         """Cache calls to AtomKey for this residue."""
         try:
@@ -3929,6 +3943,10 @@ def __deepcopy__(self, memo):
         dup.atomkeys = copy.deepcopy(self.atomkeys, memo)
         return dup
 
+    def __contains__(self, ak: "AtomKey") -> bool:
+        """Return True if atomkey is in this edron."""
+        return ak in self.atomkeys
+
     def is_backbone(self) -> bool:
         """Report True for contains only N, C, CA, O, H atoms."""
         return all(ak.is_backbone() for ak in self.atomkeys)

Tests/test_PDB_internal_coords.py

@@ -554,6 +554,8 @@ def test_seq_as_PIC(self):
             msg="covalent radii assignment error for chi1",
         )
 
+        self.assertTrue(all(ak in rt for ak in chi1.atomkeys))
+        self.assertFalse(all(ak in rt for ak in psi.atomkeys))
         tau = rt.pick_angle("tau")
         self.assertEqual(
             tau.__repr__(),