Add match_stereo to compare.

api.py

@@ -18,6 +18,12 @@
 }
 
 
+bond_dir = {
+    'single_up': Chem.BondDir.BEGINWEDGE,
+    'single_down': Chem.BondDir.BEGINDASH
+}
+
+
 def check_authorization(provided_key: str) -> bool:
     allowed_key = environ.get('API_KEY')
     if not allowed_key:
@@ -59,18 +65,26 @@ def graph_to_mol(g: nx.Graph) -> Chem.rdchem.RWMol:
         index[v] = mol.AddAtom(a)
 
     for u, v in g.edges:
-        mol.AddBond(index[u], index[v], bond_type[g.edges[(u,v)]['type']])
+        type = g.edges[(u,v)]['type']
+        bond = mol.AddBond(index[u], index[v], bond_type[type])
+        if type in bond_dir:
+            mol.GetBondWithIdx(bond - 1).SetBondDir(bond_dir[type])
 
     # Build 2D conformer.
     conf = Chem.Conformer(mol.GetNumAtoms())
+    conf.Set3D(False)
     for v in g.nodes:
         # Note that we add a Z-coordinate with value 0.
         conf.SetAtomPosition(index[v], g.nodes[v]['position'] + (0,))
 
     # Assign conformer and compute stereochemistry.
     mol = mol.GetMol()
     mol.AddConformer(conf)
-    Chem.AssignStereochemistryFrom3D(mol)
+
+    Chem.SanitizeMol(mol)
+    Chem.DetectBondStereochemistry(mol)
+    Chem.AssignChiralTypesFromBondDirs(mol)
+    Chem.AssignStereochemistry(mol)
 
     return mol
 
@@ -93,21 +107,27 @@ def _graph_to_smiles(g: nx.Graph) -> str:
     return Chem.rdmolfiles.MolToSmiles(mol, isomericSmiles=True)
 
 
-def compare_components(g1: nx.Graph, g2: nx.Graph) -> bool:
-    return (
-        nx.is_isomorphic(g1, g2, _node_match, _edge_match) and
-        _graph_to_smiles(g1) == _graph_to_smiles(g2))
+def compare_components(g1: nx.Graph, g2: nx.Graph, match_stereo: bool) -> bool:
+    if nx.is_isomorphic(g1, g2, _node_match, _edge_match):
+        if match_stereo:
+            try:
+                return _graph_to_smiles(g1) == _graph_to_smiles(g2)
+            except ValueError:
+                return False
+        else:
+            return True
 
 
-def compare(diagram1, diagram2) -> bool:
+def compare(diagram1, diagram2, match_stereo = True) -> bool:
     g1 = json_to_graph(diagram1)
     g2 = json_to_graph(diagram2)
     cs1 = list(map(lambda c: g1.subgraph(c), nx.connected_components(g1)))
     cs2 = list(map(lambda c: g2.subgraph(c), nx.connected_components(g2)))
 
     # Check if every component in g1 matches a unique component in g2.
     for c1 in cs1:
-        match = (i for i, c2 in enumerate(cs2) if compare_components(c1, c2))
+        match = (i for i, c2 in enumerate(cs2) if
+                 compare_components(c1, c2, match_stereo))
         index = next(match, None)
         if index is None:
             return False
@@ -119,9 +139,8 @@ def compare(diagram1, diagram2) -> bool:
 
 
 def validate(diagram) -> bool:
-    mol = json_to_mol(diagram)
     try:
-        Chem.SanitizeMol(mol)
+        json_to_mol(diagram)
         return True
     except ValueError:
         return False
@@ -137,7 +156,8 @@ def handle_compare(body):
     return {
         'equal': compare(
             body['reference_diagram'],
-            body['student_diagram'])
+            body['student_diagram'],
+            body['match_stereo'])
     }