fix order of SAEs (#456)

torchani/data/__init__.py

@@ -104,7 +104,7 @@ class Transformations:
     """Convert one reenterable iterable to another reenterable iterable"""
 
     @staticmethod
-    def species_to_indices(reenterable_iterable, species_order=('H', 'C', 'N', 'O', 'F', 'Cl', 'S')):
+    def species_to_indices(reenterable_iterable, species_order=('H', 'C', 'N', 'O', 'F', 'S', 'Cl')):
         if species_order == 'periodic_table':
             species_order = utils.PERIODIC_TABLE
         idx = {k: i for i, k in enumerate(species_order)}
@@ -141,7 +141,10 @@ class Transformations:
                     if len(counts[s]) != n + 1:
                         counts[s].append(0)
                 Y.append(d['energies'])
-            species = sorted(list(counts.keys()))
+
+            # sort based on the order in periodic table
+            species = sorted(list(counts.keys()), key=lambda x: utils.PERIODIC_TABLE.index(x))
+
             X = [counts[s] for s in species]
             if shifter.fit_intercept:
                 X.append([1] * n)