Fix periodic table (#23) (#544)

* Change 0th index of periodic table

* Change species converter to reflect new convention

* Change None for 'Dummy' and fix flake8
Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>

torchani/nn.py

@@ -125,7 +125,7 @@ class SpeciesConverter(torch.nn.Module):
 
     def __init__(self, species):
         super().__init__()
-        rev_idx = {s: k for k, s in enumerate(utils.PERIODIC_TABLE, 1)}
+        rev_idx = {s: k for k, s in enumerate(utils.PERIODIC_TABLE)}
         maxidx = max(rev_idx.values())
         self.register_buffer('conv_tensor', torch.full((maxidx + 2,), -1, dtype=torch.long))
         for i, s in enumerate(species):

torchani/utils.py

@@ -376,7 +376,10 @@ def get_atomic_masses(species):
     return masses
 
 
-PERIODIC_TABLE = """
+# This constant, when indexed with the corresponding atomic number, gives the
+# element associated with it. Note that there is no element with atomic number
+# 0, so 'Dummy' returned in this case.
+PERIODIC_TABLE = ['Dummy'] + """
     H                                                                                                                           He
     Li  Be                                                                                                  B   C   N   O   F   Ne
     Na  Mg                                                                                                  Al  Si  P   S   Cl  Ar