Add splicing module and related tests

- Add src/splicing/ module with scaffold_prep, fragment_prep, and engine
- Add tylosin_splicer.py entry script
- Add unit tests for splicing components

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/test_splicing_engine.py

@@ -0,0 +1,77 @@
+import pytest
+from rdkit import Chem
+from src.splicing.engine import splice_molecule
+
+def test_splice_benzene_methyl():
+    """
+    Test splicing a benzene scaffold (isotope 1) with a methyl fragment.
+    Scaffold: c1ccccc1[1*] (Phenyl radical-ish dummy)
+    Fragment: C* (Methyl radical-ish dummy)
+    Result: Cc1ccccc1 (Toluene)
+    """
+    scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
+    fragment = Chem.MolFromSmiles("C*")
+    
+    assert scaffold is not None
+    assert fragment is not None
+    
+    product = splice_molecule(scaffold, fragment, position=1)
+    
+    # Expected result: Toluene
+    expected_smiles = "Cc1ccccc1"
+    expected_mol = Chem.MolFromSmiles(expected_smiles)
+    expected_canonical = Chem.MolToSmiles(expected_mol, isomericSmiles=True)
+    
+    product_canonical = Chem.MolToSmiles(product, isomericSmiles=True)
+    
+    assert product_canonical == expected_canonical
+
+def test_splice_missing_isotope():
+    """Test that error is raised if the requested position is not found on scaffold."""
+    scaffold = Chem.MolFromSmiles("c1ccccc1[2*]") # Isotope 2
+    fragment = Chem.MolFromSmiles("C*")
+    
+    with pytest.raises(ValueError, match="Scaffold dummy atom with isotope 1 not found"):
+        splice_molecule(scaffold, fragment, position=1)
+
+def test_splice_no_fragment_dummy():
+    """Test that error is raised if fragment has no dummy atom."""
+    scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
+    fragment = Chem.MolFromSmiles("C") # Methane, no dummy
+    
+    with pytest.raises(ValueError, match="Fragment does not contain a dummy atom"):
+        splice_molecule(scaffold, fragment, position=1)
+
+def test_complex_splicing():
+    """
+    Test splicing with more complex structures.
+    Scaffold: Pyridine derivative n1cccc1CC[1*]
+    Fragment: Cyclopropane C1CC1*
+    Result: n1cccc1CCC1CC1
+    """
+    scaffold = Chem.MolFromSmiles("n1cccc1CC[1*]")
+    fragment = Chem.MolFromSmiles("*C1CC1")
+    
+    product = splice_molecule(scaffold, fragment, position=1)
+    
+    expected = Chem.MolFromSmiles("n1cccc1CCC1CC1")
+    
+    assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)
+
+def test_scaffold_with_multiple_different_dummies():
+    """
+    Test splicing when scaffold has multiple dummies with different isotopes.
+    Scaffold: [1*]c1ccccc1[2*]
+    Fragment: C*
+    Target: Splicing at 1 should leave [2*] intact.
+    """
+    scaffold = Chem.MolFromSmiles("[1*]c1ccccc1[2*]")
+    fragment = Chem.MolFromSmiles("C*")
+    
+    # Splice at 1
+    product = splice_molecule(scaffold, fragment, position=1)
+    
+    # Expected: Cc1ccccc1[2*]
+    expected = Chem.MolFromSmiles("Cc1ccccc1[2*]")
+    
+    assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)