Add LayeredDihedral and LayeredImproper support

gmso/core/dihedral.py

@@ -108,7 +108,7 @@ class Config:
 
 
 class Dihedral(BaseDihedral):
-    __base_doc__ = """A 4-Partner connection between 2 sites with a single dihedral type association
+    __base_doc__ = """A 4-Partner connection between 4 sites with a **single** dihedral type association
 
     Notes
     -----
@@ -143,7 +143,7 @@ class Config:
 
 
 class LayeredDihedral(BaseDihedral):
-    __base_doc__ = """A 4-Partner connection between 2 sites with a multiple dihedral type associations
+    __base_doc__ = """A 4-Partner connection between 4 sites with a **multiple** dihedral type associations
 
     Notes
     -----

gmso/core/improper.py

@@ -11,7 +11,7 @@
 
 
 class BaseImproper(Connection):
-    __base_doc__ = """sA 4-partner connection between sites.
+    __base_doc__ = """A 4-partner connection between sites.
 
     This is a subclass of the gmso.Connection superclass.
     This class has strictly 4 members in its connection_members.
@@ -159,7 +159,7 @@ def __setattr__(self, key, value):
             super().__setattr__(key, value)
 
     @validator("improper_types_", pre=True, always=True)
-    def validate_dihedral_types(cls, improper_types):
+    def validate_improper_types(cls, improper_types):
         if not isinstance(improper_types, Iterable):
             raise ValidationError("ImproperTypes should be iterable", cls)
 

gmso/core/topology.py

@@ -600,28 +600,18 @@ def update_connection_types(self):
                         c.connection_type = self._angle_types[connection_type]
                     if isinstance(connection_type, DihedralType):
                         if c.is_layered():
-                            if c.connection_types is None:
-                                c.connection_types = IndexedSet(
-                                    [self._dihedrals_types[connection_type]]
-                                )
-                            else:
-                                c.connection_types.add(
-                                    self._dihedral_types[connection_type]
-                                )
+                            c.connection_types.add(
+                                self._dihedral_types[connection_type]
+                            )
                         else:
                             c.connection_type = self._dihedral_types[
                                 connection_type
                             ]
                     if isinstance(connection_type, ImproperType):
                         if c.is_layered():
-                            if c.connection_types is None:
-                                c.connection_types = IndexedSet(
-                                    [self._improper_types[connection_type]]
-                                )
-                            else:
-                                c.connection_types.add(
-                                    self._improper_types[connection_type]
-                                )
+                            c.connection_types.add(
+                                self._improper_types[connection_type]
+                            )
                         else:
                             c.connection_type = self._improper_types[
                                 connection_type

gmso/tests/base_test.py

@@ -487,6 +487,20 @@ def pairpotentialtype_top(self):
         top.add_pairpotentialtype(pptype12)
         return top
 
+    @pytest.fixture(scope="session")
+    def residue_top(self):
+        top = Topology()
+        for i in range(1, 26):
+            atom = Atom(
+                name=f"atom_{i + 1}",
+                residue_number=i % 5,
+                residue_name="MY_RES_EVEN" if i % 2 == 0 else f"MY_RES_ODD",
+            )
+            top.add_site(atom, update_types=False)
+        top.update_topology()
+
+        return top
+
     @pytest.fixture
     def ld_top(self):
         lib = PotentialTemplateLibrary()
@@ -512,7 +526,7 @@ def ld_top(self):
         )
 
         top = Topology(name="Topology")
-        atoms = [Atom(name=f"Atom{i+1}") for i in range(0, 100)]
+        atoms = [Atom(name=f"Atom{i + 1}") for i in range(0, 100)]
         dihedrals_group = [
             (atoms[i], atoms[i + 1], atoms[i + 2], atoms[i + 3])
             for i in range(0, 100, 4)
@@ -530,4 +544,5 @@ def ld_top(self):
                 dh.connection_types = [rb_type, periodic_type]
             top.add_connection(connection=dh)
         top.update_topology()
+
         return top

gmso/tests/test_topology.py

@@ -753,3 +753,33 @@ def test_top_with_layered_dihedrals(self, ld_top):
                 assert isinstance(ld_top._dihedrals[j], Dihedral)
             else:
                 assert isinstance(ld_top._dihedrals[j], LayeredDihedral)
+
+    def test_iter_sites(self, residue_top):
+        for site in residue_top.iter_sites("residue_name", "MY_RES_EVEN"):
+            assert site.residue_name == "MY_RES_EVEN"
+
+        for site in residue_top.iter_sites("residue_name", "MY_RES_ODD"):
+            assert site.residue_name == "MY_RES_ODD"
+
+        sites = list(residue_top.iter_sites("residue_number", 4))
+        assert len(sites) == 5
+
+    def test_iter_sites_non_iterable_attribute(self, residue_top):
+        with pytest.raises(ValueError):
+            for site in residue_top.iter_sites("atom_type", "abc"):
+                pass
+
+    def test_iter_sites_none(self, residue_top):
+        with pytest.raises(ValueError):
+            for site in residue_top.iter_sites("residue_name", None):
+                pass
+
+    def test_iter_sites_by_residue_name(self, pairpotentialtype_top):
+        assert (
+            len(list(pairpotentialtype_top.iter_sites_by_residue_name("AAA")))
+            == 0
+        )
+
+    def test_iter_sites_by_residue_number(self, residue_top):
+        sites = list(residue_top.iter_sites_by_residue_number(4))
+        assert len(sites) == 5