Bugfix: torsions in 3-membered rings

* The code allowed the torsion around a 3-membered ring which had the same atom at
  each end of the torsion. This is not a valid torsion, and the code now checks for
  it and removes it.

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2025.1.21 -- Bugfix: torsions in 3-membered rings
+   * The code allowed the torsion around a 3-membered ring which had the same atom at
+     each end of the torsion. This is not a valid torsion, and the code now checks for
+     it and removes it.
+
 2024.6.27 -- Support for local forcefield files
    * Added support for local forcefields files which can either be used directly
      or included by existing files.

seamm_ff_util/forcefield.py

@@ -2508,6 +2508,9 @@ def setup_topology(self, configuration, style=""):
                 for l in bonds_from_atom[k]:  # noqa: E741
                     if l == j:  # noqa: E741
                         continue
+                    if i == l:
+                        # 3 membered rings.
+                        continue
                     torsions.append((i, j, k, l))
 
         # Out-of-planes