Merge pull request #851 from chrisjonesBSU/fix/molecule

Fix `__repr__` method in `abstract_site.Molecule` and `abstract_site.Residue`

gmso/abc/abstract_site.py

@@ -24,7 +24,7 @@
 class Molecule(GMSOBase):
     def __repr__(self):
         return (
-            f"Molecule(name={self.name}, residue={self.residue}, isrigid={self.isrigid}"
+            f"Molecule(name={self.name}, number={self.number}, isrigid={self.isrigid})"
         )
 
     __iterable_attributes__: ClassVar[set] = {
@@ -88,7 +88,7 @@ def __eq__(self, other):
 
 class Residue(GMSOBase):
     def __repr__(self):
-        return f"Residue(name={self.name}, residue={self.residue}"
+        return f"Residue(name={self.name}, number={self.number}"
 
     __iterable_attributes__: ClassVar[set] = {
         "name",
@@ -149,6 +149,17 @@ def default_position():
 
 
 class Site(GMSOBase):
+    def __repr__(self):
+        """Return the formatted representation of the site."""
+        return (
+            f"<{self.__class__.__name__} {self.name},\n "
+            f"position: {self.position},\n "
+            f"label: {self.label if self.label else None},\n "
+            f"Molecule: {self.molecule},\n"
+            f"Residue: {self.residue},\n"
+            f"id: {id(self)}>"
+        )
+
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "label",
@@ -254,15 +265,6 @@ def residue(self):
     def serialize_position(self, position_: PositionType):
         return unyt_to_dict(position_)
 
-    def __repr__(self):
-        """Return the formatted representation of the site."""
-        return (
-            f"<{self.__class__.__name__} {self.name},\n "
-            f"position: {self.position},\n "
-            f"label: {self.label if self.label else None},\n "
-            f"id: {id(self)}>"
-        )
-
     def __str__(self):
         """Return the string representation of the site."""
         return (

gmso/tests/abc/test_abc.py

@@ -0,0 +1,21 @@
+import pytest
+
+from gmso.abc.abstract_site import Molecule, Residue, Site
+from gmso.tests.base_test import BaseTest
+
+
+class TestSite(BaseTest):
+    def test_molecule(self):
+        molecule = Molecule()
+        molecule.__repr__()
+        assert molecule.number == 0
+        assert molecule.isrigid is False
+
+    def test_residue(self):
+        residue = Residue()
+        residue.__repr__()
+        assert residue.number == 0
+
+    def test_site(self):
+        with pytest.raises(TypeError):
+            Site()