Functional Group Calculation (#44)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#44

utilities/chem.py

@@ -12,6 +12,7 @@ from rdkit.Chem import MACCSkeys
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
+from rdkit.Contrib.IFG import ifg
 
 logger = logging.getLogger(__name__)
 RDLogger.DisableLog('rdApp.*')
@@ -87,6 +88,21 @@ class FormatConverter(object):
         bitvec = MACCSkeys.GenMACCSKeys(mol)
         return bitvec.ToList()
 
+    @staticmethod
+    def get_functional_groups(smiles: str) -> List[str]:
+        res = list()
+
+        try:
+            m = Chem.MolFromSmiles(smiles)
+            fgs = ifg.identify_functional_groups(m)
+            for fg in fgs:
+                # TODO atoms or type?
+                res.append(fg.atoms)
+        except AttributeError:
+            logger.debug(f"Could not get functional groups for {smiles}")
+
+        return res
+
     @staticmethod
     def to_svg(smiles, mol_size=(200, 150), kekulize=True):
         mol = FormatConverter.from_smiles(smiles)