Merge branch 'main' of https://github.com/mosdef-hub/gmso into 748-re…

…move-gmso-xml-conversions
mosdef-hub · Aug 10, 2023 · 60025c0 · 60025c0
2 parents d6bc933 + 8b639c6
commit 60025c0
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Showing 2 changed files with 30 additions and 3 deletions.
diff --git a/gmso/external/convert_parmed.py b/gmso/external/convert_parmed.py
@@ -568,15 +568,16 @@ def _atom_types_from_gmso(top, structure, atom_map):
         atype_charge = float(atom_type.charge.to("Coulomb").value) / (
             1.6 * 10 ** (-19)
         )
-        atype_mass = float(atom_type.mass.to("amu"))
         atype_sigma = float(atom_type.parameters["sigma"].to("angstrom").value)
         atype_epsilon = float(
             atom_type.parameters["epsilon"].to("kcal/mol").value
         )
         if atom_type.mass:
-            atype_mass = atom_type.mass.to("amu").value
+            atype_mass = float(atom_type.mass.to("amu").value)
         else:
-            atype_mass = element_by_symbol(atom_type.name).mass.to("amu").value
+            atype_mass = float(
+                element_by_symbol(atom_type.name).mass.to("amu").value
+            )
         atype_atomic_number = getattr(
             element_by_symbol(atom_type.name), "atomic_number", None
         )

diff --git a/gmso/tests/test_convert_parmed.py b/gmso/tests/test_convert_parmed.py
@@ -716,3 +716,29 @@ def test_pmd_complex_ureybradleys(self, parmed_methylnitroaniline):
                 for t in dihedrals_list
             )
         )
+
+    def test_to_and_from_parmed_with_topology(self, typed_ethane):
+        top = typed_ethane
+        struc = to_parmed(top)
+        top_from_struc = from_parmed(struc)
+        assert top.n_sites == top_from_struc.n_sites
+        assert top.n_bonds == top_from_struc.n_bonds
+        assert top.n_angles == top_from_struc.n_angles
+        assert top.n_dihedrals == top_from_struc.n_dihedrals
+        assert len(top.atom_types) == len(top_from_struc.atom_types)
+
+    def test_to_and_from_parmed_with_impropers_dihedrals(
+        self, typed_methylnitroaniline
+    ):
+        top = typed_methylnitroaniline
+        struc = to_parmed(top)
+        top_from_struc = from_parmed(struc)
+        assert top.n_sites == top_from_struc.n_sites
+        assert top.n_bonds == top_from_struc.n_bonds
+        assert top.n_angles == top_from_struc.n_angles
+        assert top.n_dihedrals == top_from_struc.n_dihedrals
+        assert top.n_impropers == top_from_struc.n_impropers
+        assert len(top.atom_types) == len(top_from_struc.atom_types)
+        assert len(top.dihedral_types(filter_by=pfilter)) == len(
+            top_from_struc.dihedral_types(filter_by=pfilter)
+        )