[Feature] Implemented SMARTS filtering for Rules (#246)

Reactant Filter SMARTS as well as Product Filter SMARTS are now reflected when applying rules.

Fixes #245

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#246

utilities/chem.py

@@ -279,6 +279,24 @@ class FormatConverter(object):
         except Exception:
             return False
 
+    @staticmethod
+    def smarts_matches(mol: str | Chem.Mol, smarts: str) -> bool:
+        """
+        Returns True if the SMARTS pattern matches the given SMILES / Molecule.
+        """
+        _mol = mol
+        if isinstance(mol, str):
+            _mol = Chem.MolFromSmiles(mol)
+
+        if _mol is None:
+            raise ValueError(f"Invalid Molecule: {mol}")
+
+        pattern = Chem.MolFromSmarts(smarts)
+        if pattern is None:
+            raise ValueError(f"Invalid SMARTS: {smarts}")
+
+        return _mol.HasSubstructMatch(pattern)
+
     @staticmethod
     def apply(
         smiles: str,
@@ -288,6 +306,8 @@ class FormatConverter(object):
         standardize: bool = True,
         kekulize: bool = True,
         remove_stereo: bool = True,
+        reactant_filter_smarts: str | None = None,
+        product_filter_smarts: str | None = None,
     ) -> List["ProductSet"]:
         logger.debug(f"Applying {smirks} on {smiles}")
 
@@ -306,6 +326,15 @@ class FormatConverter(object):
                 Chem.SanitizeMol(mol)
                 mol = Chem.AddHs(mol)
 
+            # Check if reactant_filter_smarts matches and we shouldn't apply the rule
+            if reactant_filter_smarts and FormatConverter.smarts_matches(
+                mol, reactant_filter_smarts
+            ):
+                logger.debug(
+                    f"Reactant {FormatConverter.to_smiles(mol)} matches {reactant_filter_smarts}, skipping"
+                )
+                return list(pss)
+
             # apply!
             sites = rxn.RunReactants((mol,))
             logger.debug(f"{len(sites)} products sets generated")
@@ -321,6 +350,17 @@ class FormatConverter(object):
                                 p = FormatConverter.standardize(
                                     Chem.MolToSmiles(p), remove_stereo=remove_stereo
                                 )
+
+                                if product_filter_smarts and FormatConverter.smarts_matches(
+                                    p, product_filter_smarts
+                                ):
+                                    logger.debug(
+                                        f"Product {FormatConverter.to_smiles(mol)} matches {product_filter_smarts}, skipping"
+                                    )
+                                    # clear products we might have already collected
+                                    prods.clear()
+                                    break
+
                                 prods.append(p)
 
                             # if kekulize:
@@ -357,7 +397,7 @@ class FormatConverter(object):
         except Exception as e:
             logger.error(f"Applying {smirks} on {smiles} failed:\n{e}")
 
-        return pss
+        return list(pss)
 
     @staticmethod
     def MACCS(smiles):