[Feature] Engineer Pathway (#256)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#256

utilities/chem.py

@@ -2,12 +2,13 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING
+from typing import List, Optional, Dict, TYPE_CHECKING, Union
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem, rdBase
 from rdkit.Chem import MACCSkeys, Descriptors, rdFingerprintGenerator
+from rdkit.Chem import rdchem
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
@@ -94,8 +95,15 @@ class FormatConverter(object):
         return Chem.MolToSmiles(mol, canonical=canonical)
 
     @staticmethod
-    def InChIKey(smiles):
-        return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
+    def InChIKey(mol_or_smiles: Union[rdchem.Mol | str]):
+        if isinstance(mol_or_smiles, str):
+            mol_or_smiles = mol_or_smiles.replace("~", "")
+            mol_or_smiles = FormatConverter.from_smiles(mol_or_smiles)
+
+        if mol_or_smiles is None:
+            return None
+
+        return Chem.MolToInchiKey(mol_or_smiles)
 
     @staticmethod
     def InChI(smiles):
@@ -352,7 +360,8 @@ class FormatConverter(object):
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
                                 p = FormatConverter.standardize(
-                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
+                                    Chem.MolToSmiles(p).replace("~", ""),
+                                    remove_stereo=remove_stereo,
                                 )
 
                                 if product_filter_smarts and FormatConverter.smarts_matches(