Merge branch 'main' into 561-layered-dihedrals

gmso/formats/mol2.py

@@ -96,6 +96,7 @@ def _parse_lj(top, section):
                 warnings.warn(
                     f"No charge was detected for site {content[1]} with index {content[0]}"
                 )
+                charge = None
 
             atom = Atom(
                 name=content[1],

gmso/tests/files/methane_missing_charge.mol2

@@ -0,0 +1,12 @@
+@<TRIPOS>MOLECULE
+RES
+1 0 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    5.0000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH4         0.0000     0.0000     0.0000 CH4          1 RES
+@<TRIPOS>BOND
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 **** ROOT      0

gmso/tests/test_mol2.py

@@ -6,6 +6,7 @@
 from gmso import Topology
 from gmso.formats.mol2 import from_mol2
 from gmso.tests.base_test import BaseTest
+from gmso.tests.utils import get_path
 from gmso.utils.io import get_fn
 
 
@@ -102,6 +103,15 @@ def test_lj_system(self):
         top = Topology.load(get_fn("methane.mol2"), site_type="lj")
         assert np.all([site.element == None for site in top.sites])
 
+    def test_no_charge_lj(self):
+        with pytest.warns(
+            UserWarning,
+            match="No charge was detected for site .* with index \d+$",
+        ):
+            top = Topology.load(
+                get_path("methane_missing_charge.mol2"), site_type="lj"
+            )
+
     def test_wrong_path(self):
         with pytest.raises(
             OSError, match=r"Provided path to file that does not exist"