avoid replacing chiral C with R groups #33

RanDepict/randepict.py

@@ -3244,6 +3244,7 @@ def get_valid_replacement_positions(self, smiles: str) -> List[int]:
                         "f",
                         "d",
                         "n",
+                        "@"  # replacing chiral C leads to invalid SMILES
                     ]:
                         replacement_positions.append(index - 1)
         return replacement_positions

Tests/test_functions.py

@@ -539,3 +539,11 @@ def test_get_valid_replacement_positions_caffeine(self):
         observed = self.markush_creator.get_valid_replacement_positions("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
         expected = [0, 3, 11, 18, 25, 27]
         assert observed == expected
+
+    def test_get_valid_replacement_positions_alanine(self):
+        # Example with stereo
+        smiles = "C([H])([H])([H])[C@@]([H])(C(=O)O[H])N([H])[H]"
+        observed = self.markush_creator.get_valid_replacement_positions(smiles)
+        expected = [0, 3, 8, 13, 23, 27, 34, 40, 44]
+        assert observed == expected
+