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>
96 lines
3.0 KiB
Python
96 lines
3.0 KiB
Python
import pytest
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from rdkit import Chem
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from src.splicing.fragment_prep import activate_fragment
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def test_activate_smart_ethanol():
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"""Test 'smart' activation on Ethanol (CCO). Should attach to Oxygen."""
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smiles = "CCO"
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mol = activate_fragment(smiles, strategy="smart")
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# Check if we have a dummy atom
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assert mol is not None
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assert mol.GetNumAtoms() == 4 # C, C, O, *
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# Check if the dummy atom is attached to Oxygen
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# Find the dummy atom
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dummy_atom = None
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for atom in mol.GetAtoms():
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if atom.GetSymbol() == '*':
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dummy_atom = atom
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break
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assert dummy_atom is not None
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# Check neighbors of dummy atom
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neighbors = dummy_atom.GetNeighbors()
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assert len(neighbors) == 1
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assert neighbors[0].GetSymbol() == 'O'
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# Check output SMILES format
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out_smiles = Chem.MolToSmiles(mol)
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assert '*' in out_smiles
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def test_activate_smart_amine():
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"""Test 'smart' activation on Ethylamine (CCN). Should attach to Nitrogen."""
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smiles = "CCN"
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mol = activate_fragment(smiles, strategy="smart")
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assert mol is not None
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# Find the dummy atom
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dummy_atom = None
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for atom in mol.GetAtoms():
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if atom.GetSymbol() == '*':
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dummy_atom = atom
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break
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assert dummy_atom is not None
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neighbors = dummy_atom.GetNeighbors()
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assert neighbors[0].GetSymbol() == 'N'
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def test_activate_random_pentane():
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"""Test 'random' activation on Pentane (CCCCC). Should attach to a Carbon."""
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smiles = "CCCCC"
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# Seed is not easily passed to the function unless we add it to the signature or fix it inside.
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# For this test, any Carbon is fine.
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mol = activate_fragment(smiles, strategy="random")
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assert mol is not None
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assert mol.GetNumAtoms() == 6 # 5 C + 1 *
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dummy_atom = None
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for atom in mol.GetAtoms():
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if atom.GetSymbol() == '*':
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dummy_atom = atom
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break
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assert dummy_atom is not None
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neighbors = dummy_atom.GetNeighbors()
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assert neighbors[0].GetSymbol() == 'C'
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def test_activate_smart_fallback():
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"""Test 'smart' fallback when no heteroatoms are found (e.g. Propane)."""
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smiles = "CCC"
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# Should fall back to finding a terminal carbon or random
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# The requirement says "fall back to a terminal Carbon" or random.
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# Let's assume the implementation picks a terminal carbon if possible, or just behaves like random on C.
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mol = activate_fragment(smiles, strategy="smart")
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assert mol is not None
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dummy_atom = None
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for atom in mol.GetAtoms():
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if atom.GetSymbol() == '*':
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dummy_atom = atom
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break
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assert dummy_atom is not None
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neighbor = dummy_atom.GetNeighbors()[0]
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assert neighbor.GetSymbol() == 'C'
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# Verify it's a valid molecule
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assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE
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def test_invalid_smiles():
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with pytest.raises(ValueError):
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activate_fragment("NotASmiles", strategy="smart")
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