update unit test for surface site to work with Pt

Author: sevyharris

rmgpy/molecule/adjlist.py

@@ -92,7 +92,9 @@ def check_partial_charge(atom):
         the theoretical one:
 
         """
-        if atom.symbol in {'X','L','R'} or 'X' in [z.label for z in get_atomtype(atom, atom.bonds).generic]:
+        # if atom.symbol in {'X','L','R'} or 'X' in [z.label for z in get_atomtype(atom, atom.bonds).generic]:
+        # TODO handle this in a more generic way so we don't have to add more metals here
+        if atom.symbol in {'X','L','R','Pt'}:
             return  # because we can't check it.
 
         valence = PeriodicSystem.valence_electrons[atom.symbol]

rmgpy/molecule/atomtype.py

@@ -294,8 +294,8 @@ def get_features(self):
                             single=[0], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0],
                             benzene=[0], lone_pairs=[0])
 ATOMTYPES['Pto'] = AtomType(label='Pto', generic=['Rx', 'Rx!H', 'X', 'Pt', 'Xo'], specific=[],
-                            single=[0], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0],
-                            benzene=[0], lone_pairs=[0])
+                            single=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], all_double=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], r_double=[], o_double=[], s_double=[], triple=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18],
+                            quadruple=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], benzene=[0], lone_pairs=[0])
 
 # Non-surface atomTypes, R being the most generic:
 ATOMTYPES['R'] = AtomType(label='R', generic=['Rx'], specific=[

rmgpy/molecule/translator.py

@@ -370,6 +370,11 @@ def _rdkit_translator(input_object, identifier_type, mol=None):
         output = from_rdkit_mol(mol, rdkitmol)
     elif isinstance(input_object, mm.Molecule):
         # We are converting from a molecule to a string identifier
+        generic_X = False # keep track of whether this is generic 'X' or specific 'Pt'
+        for atom in input_object.vertices:
+            if atom.element.symbol == 'X':
+                generic_X = True
+                break
         if identifier_type == 'smi':
             rdkitmol = to_rdkit_mol(input_object, sanitize=False)
         else:
@@ -391,6 +396,8 @@ def _rdkit_translator(input_object, identifier_type, mol=None):
     else:
         raise ValueError('Unexpected input format. Should be a Molecule or a string.')
 
+    if generic_X:
+        output = output.replace('Pt', 'X')
     return output
 
 

test/rmgpy/molecule/moleculeTest.py

@@ -262,7 +262,7 @@ def test_is_surface_site(self):
         """
         for element in element_list:
             atom = Atom(element=element, radical_electrons=0, charge=0, label="*1", lone_pairs=0)
-            if element.symbol == "X":
+            if element.symbol in ["X", "Pt"]:
                 assert atom.is_surface_site()
             else:
                 assert not atom.is_surface_site()