hotwa
68f171ad1d
- 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>
78 lines
2.7 KiB
Python
78 lines
2.7 KiB
Python
import pytest
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from rdkit import Chem
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from src.splicing.engine import splice_molecule
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def test_splice_benzene_methyl():
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"""
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Test splicing a benzene scaffold (isotope 1) with a methyl fragment.
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Scaffold: c1ccccc1[1*] (Phenyl radical-ish dummy)
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Fragment: C* (Methyl radical-ish dummy)
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Result: Cc1ccccc1 (Toluene)
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"""
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scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
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fragment = Chem.MolFromSmiles("C*")
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assert scaffold is not None
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assert fragment is not None
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product = splice_molecule(scaffold, fragment, position=1)
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# Expected result: Toluene
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expected_smiles = "Cc1ccccc1"
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expected_mol = Chem.MolFromSmiles(expected_smiles)
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expected_canonical = Chem.MolToSmiles(expected_mol, isomericSmiles=True)
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product_canonical = Chem.MolToSmiles(product, isomericSmiles=True)
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assert product_canonical == expected_canonical
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def test_splice_missing_isotope():
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"""Test that error is raised if the requested position is not found on scaffold."""
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scaffold = Chem.MolFromSmiles("c1ccccc1[2*]") # Isotope 2
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fragment = Chem.MolFromSmiles("C*")
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with pytest.raises(ValueError, match="Scaffold dummy atom with isotope 1 not found"):
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splice_molecule(scaffold, fragment, position=1)
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def test_splice_no_fragment_dummy():
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"""Test that error is raised if fragment has no dummy atom."""
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scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
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fragment = Chem.MolFromSmiles("C") # Methane, no dummy
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with pytest.raises(ValueError, match="Fragment does not contain a dummy atom"):
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splice_molecule(scaffold, fragment, position=1)
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def test_complex_splicing():
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"""
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Test splicing with more complex structures.
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Scaffold: Pyridine derivative n1cccc1CC[1*]
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Fragment: Cyclopropane C1CC1*
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Result: n1cccc1CCC1CC1
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"""
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scaffold = Chem.MolFromSmiles("n1cccc1CC[1*]")
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fragment = Chem.MolFromSmiles("*C1CC1")
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product = splice_molecule(scaffold, fragment, position=1)
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expected = Chem.MolFromSmiles("n1cccc1CCC1CC1")
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assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)
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def test_scaffold_with_multiple_different_dummies():
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"""
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Test splicing when scaffold has multiple dummies with different isotopes.
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Scaffold: [1*]c1ccccc1[2*]
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Fragment: C*
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Target: Splicing at 1 should leave [2*] intact.
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"""
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scaffold = Chem.MolFromSmiles("[1*]c1ccccc1[2*]")
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fragment = Chem.MolFromSmiles("C*")
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# Splice at 1
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product = splice_molecule(scaffold, fragment, position=1)
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# Expected: Cc1ccccc1[2*]
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expected = Chem.MolFromSmiles("Cc1ccccc1[2*]")
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assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)
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