Merge pull request #440 from ReactionMechanismGenerator/AddTest_speci…

…es_xyz_to_2d_get_formula Add unit test for MolGraph.get_formula after fixing bug in same
ReactionMechanismGenerator · Dec 25, 2020 · 747756b · 747756b
2 parents 20e68d2 + d91f074
commit 747756b
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Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/arc/species/speciesTest.py b/arc/species/speciesTest.py
@@ -31,7 +31,7 @@
                                  check_xyz,
                                  determine_rotor_symmetry,
                                  determine_rotor_type)
-
+from arc.species.xyz_to_2d import MolGraph
 
 class TestARCSpecies(unittest.TestCase):
     """
@@ -1375,6 +1375,18 @@ def test_from_dict(self):
         self.assertEqual(tsg.method, 'autotst')
         self.assertTrue(isinstance(tsg.rmg_reaction, Reaction))
 
+    def test_xyz_to_2d_get_formula(self):
+        xyz_arb = {'symbols': ('H', 'C', 'H', 'H', 'O', 'N', 'O'),
+                 'isotopes': (1, 13, 1, 1, 16, 14, 16),
+                 'coords': ((-1.0, 0.0, 0.0),
+                            (0.0, 0.0, 0.0),
+                            (0.0, -1.0, 0.0),
+                            (0.0, 1.0, 0.0),
+                            (1.0, 0.0, 0.0),
+                            (2.0, 0.0, 0.0),
+                            (3.0, 0.0, 0.0),)}
+        mol_graph_1 = MolGraph(symbols=xyz_arb['symbols'], coords=xyz_arb['coords'])
+        self.assertEqual(mol_graph_1.get_formula(), 'CH3NO2')
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
diff --git a/arc/species/xyz_to_2d.py b/arc/species/xyz_to_2d.py
@@ -17,7 +17,7 @@
 
 class Atom(object):
     """
-    Represents an atopm in a molecular graph.
+    Represents an atom in a molecular graph.
     """
 
     def __init__(self, symbol=None, idx=None, coords=np.array([]), frozen=False):
@@ -150,7 +150,7 @@ def get_formula(self):
                 count = elements['H']
                 formula += 'H{:d}'.format(count) if count > 1 else 'H'
                 del elements['H']
-        keys = elements.keys()
+        keys = list(elements.keys())
         keys.sort()
         for key in keys:
             count = elements[key]