Add unit test and documentation

Author: rmatsum836

mbuild/compound.py

@@ -2476,6 +2476,8 @@ def to_parmed(self, box=None, title='', residues=None, show_ports=False,
                 if not val:
                     box_vec_max[dim] += 0.25
                     box_vec_min[dim] -= 0.25
+            # In rare cases `AssertionError` will be raised if `mins` is set before `maxs`
+            # As a result, set `maxs` before `mins`
             box.maxs = np.asarray(box_vec_max)
             box.mins = np.asarray(box_vec_min)
 

mbuild/tests/test_box.py

@@ -113,3 +113,20 @@ def test_sanity_checks(self):
             box.maxs[1] = box.mins[1] - 1
         with pytest.raises(AssertionError):
             box.lengths = -1
+
+    def test_compound_without_box(self, ethane):
+        # Set coordinates to trigger the case where `box.mins`
+        # coordinates can be less than [0, 0, 0]
+        ethane.xyz = np.array([[0.31079999, 0.0653, -0.85259998],
+                   [0.459, 0.0674, -0.8132],
+                   [0.281, -0.0349, -0.8761],
+                   [0.251, 0.1015, -0.7710],
+                   [0.295, 0.1278, -0.9380],
+                   [0.474, 0.0049, -0.7277],
+                   [0.518, 0.0312, -0.8946],
+                   [0.488, 0.1676, -0.7896]])
+        # Set periodicity
+        ethane.periodicity = np.array([0.767, 0.703, 0.710])
+        # Convert compound to pmd.structure to set Box info
+        # Conversion should happen without error
+        ethane.to_parmed()