parse rigid sites from site.molecule, update test

gmso/external/convert_hoomd.py

@@ -293,18 +293,16 @@ def _parse_particle_information(
             else 1 * base_units["mass"]
         )
         charges[idx] = site.charge if site.charge else 0 * u.elementary_charge
-    # Check for rigid IDs
-    rigid_ids = [site.rigid_id for site in top.sites]
-    rigid_ids_set = set(rigid_ids)
-    if None not in rigid_ids:
-        n_rigid = len(rigid_ids_set)
-        write_rigid = True
-    else:
-        write_rigid = False
-        n_rigid = 0
+
     unique_types = sorted(list(set(types)))
     typeids = np.array([unique_types.index(t) for t in types])
-    if write_rigid:
+    # Check for rigid molecules
+    rigid_mols = any([site.molecule.isrigid for site in top.sites])
+    if rigid_mols:
+        rigid_ids = [site.molecule.number for site in top.sites]
+        rigid_ids_set = set(rigid_ids)
+        n_rigid = len(rigid_ids_set)
+        write_rigid = True
         rigid_masses = np.zeros(n_rigid)
         rigid_xyz = np.zeros((n_rigid, 3))
         # Rigid particle type defaults to "R"; add to front of list
@@ -326,6 +324,9 @@ def _parse_particle_information(
         masses = np.concatenate((rigid_masses, masses))
         xyz = np.concatenate((rigid_xyz, xyz))
         rigid_id_tags = np.concatenate((np.arange(n_rigid), np.array(rigid_ids)))
+    else:
+        write_rigid = False
+        n_rigid = 0
 
     """
     Permittivity of free space = 2.39725e-4 e^2/((kcal/mol)(angstrom)),

gmso/tests/test_hoomd.py

@@ -60,21 +60,19 @@ class TestGsd(BaseTest):
     def test_rigid_bodies(self):
         ethane = mb.lib.molecules.Ethane()
         box = mb.fill_box(ethane, n_compounds=2, box=[2, 2, 2])
-        box_no_rigid = mb.clone(box)
-        for i, child in enumerate(box.children):
-            for p in child.particles():
-                p.rigid_id = i
-
         top = from_mbuild(box)
-        top_no_rigid = from_mbuild(box_no_rigid)
+        for site in top.sites:
+            site.molecule.isrigid = True
+
+        top_no_rigid = from_mbuild(box)
 
-        rigid_ids = [site.rigid_id for site in top.sites]
-        assert len(rigid_ids) == box.n_particles
-        assert len(set(rigid_ids)) == 2
+        rigid_ids = [site.molecule.number for site in top.sites]
+        assert set(rigid_ids) == {0, 1}
 
         snapshot, refs = to_gsd_snapshot(top)
         snapshot_no_rigid, refs = to_gsd_snapshot(top_no_rigid)
         assert "R" in snapshot.particles.types
+        assert "R" not in snapshot_no_rigid.particles.types
         assert snapshot.particles.N - 2 == snapshot_no_rigid.particles.N
 
     @pytest.mark.skipif(