Fix mismatched gmso residue name when molecule is loaded from mol2

hoomd_organics/base/molecule.py

@@ -261,6 +261,12 @@ def _validate_force_field(self):
     def assign_mol_name(self, name):
         for mol in self.molecules:
             mol.name = name
+            # TODO: This is a hack to make sure that the name of the children is
+            # also updated, so that when converting to gmso, all the sites have
+            # the correct name. This needs additional investigation into gmso's
+            # convert mbuilder to gmso functionality.
+            for child in mol.children:
+                child.name = name
 
 
 class Polymer(Molecule):

hoomd_organics/tests/base/test_system.py

@@ -26,6 +26,7 @@ def test_single_mol_type(self, benzene_molecule):
         )
         assert system.n_mol_types == 1
         assert len(system.all_molecules) == len(benzene_mols.molecules)
+        assert system.gmso_system.is_typed()
         assert len(system.hoomd_forcefield) > 0
         assert system.n_particles == system.hoomd_snapshot.particles.N
         assert system.hoomd_snapshot.particles.types == ["opls_145", "opls_146"]
@@ -47,6 +48,7 @@ def test_multiple_mol_types(self, benzene_molecule, ethane_molecule):
         )
         assert system.all_molecules[0].name == "0"
         assert system.all_molecules[-1].name == "1"
+        assert system.gmso_system.is_typed()
         assert len(system.hoomd_forcefield) > 0
         assert system.n_particles == system.hoomd_snapshot.particles.N
         assert system.hoomd_snapshot.particles.types == [
@@ -74,6 +76,7 @@ def test_multiple_mol_types_different_ff(
         ) + len(pps_mol.molecules)
         assert system.all_molecules[0].name == "0"
         assert system.all_molecules[-1].name == "1"
+        assert system.gmso_system.is_typed()
         assert len(system.hoomd_forcefield) > 0
         for hoomd_force in system.hoomd_forcefield:
             if isinstance(hoomd_force, hoomd.md.pair.LJ):
@@ -90,6 +93,19 @@ def test_multiple_mol_types_different_ff(
             "sh",
         ]
 
+    def test_system_from_mol2_mol_parameterization(self, benzene_molecule_mol2):
+        benzene_mol = benzene_molecule_mol2(n_mols=3)
+        system = Pack(
+            molecules=[benzene_mol],
+            density=0.8,
+            r_cut=2.5,
+            force_field=OPLS_AA(),
+            auto_scale=True,
+        )
+        assert system.gmso_system.is_typed()
+        assert len(system.hoomd_forcefield) > 0
+        assert system.n_particles == system.hoomd_snapshot.particles.N
+
     def test_remove_hydrogen(self, benzene_molecule):
         benzene_mol = benzene_molecule(n_mols=3)
         system = Pack(
@@ -100,6 +116,7 @@ def test_remove_hydrogen(self, benzene_molecule):
             auto_scale=True,
             remove_hydrogens=True,
         )
+        assert system.gmso_system.is_typed()
         assert len(system.hoomd_forcefield) > 0
         assert list(system.hoomd_forcefield[0].params.keys()) == [
             ("opls_145", "opls_145")

hoomd_organics/tests/base_test.py

@@ -113,6 +113,14 @@ def _benzene_molecule(n_mols):
 
         return _benzene_molecule
 
+    @pytest.fixture()
+    def benzene_molecule_mol2(self, benzene_mol2):
+        def _benzene_molecule(n_mols):
+            benzene = Molecule(num_mols=n_mols, file=benzene_mol2)
+            return benzene
+
+        return _benzene_molecule
+
     @pytest.fixture()
     def ethane_molecule(self, ethane_smiles):
         def _ethane_molecule(n_mols):