fix failing tests in handling charges from atom_type and not site

mosdef-hub · Dec 11, 2023 · a47016a · a47016a
1 parent cc16d53
commit a47016a
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/gmso/external/convert_parmed.py b/gmso/external/convert_parmed.py
@@ -85,7 +85,8 @@ def from_parmed(structure, refer_type=True):
                 if refer_type and isinstance(atom.atom_type, pmd.AtomType)
                 else None
             )
-            site.atom_type.charge = atom.charge * u.elementary_charge
+            if site.atom_type:
+                site.atom_type.charge = atom.charge * u.elementary_charge
             site_map[atom] = site
             top.add_site(site)
 

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
@@ -167,7 +167,9 @@ def write_top(top, filename, top_vars=None):
                         tag,
                         site.atom_type.tags["element"],
                         "1",  # TODO: care about charge groups
-                        site.charge.in_units(u.elementary_charge).value,
+                        site.atom_type.charge.in_units(
+                            u.elementary_charge
+                        ).value,
                         site.atom_type.mass.in_units(u.amu).value,
                     )
                 )

diff --git a/gmso/tests/files/typed_ethane_ref.top b/gmso/tests/files/typed_ethane_ref.top
@@ -6,8 +6,8 @@
 
 [ atomtypes ]
 ; name	at.num		mass	charge		ptype	sigma	epsilon
-opls_135    6       12.01078     0.00000	A        0.35000     0.27614
-opls_140    1        1.00795     0.00000	A        0.25000     0.12552
+opls_135    6       12.01078    -0.18000	A        0.35000     0.27614
+opls_140    1        1.00795     0.06000	A        0.25000     0.12552
 
 [ moleculetype ]
 ; name	nrexcl