lingyuzeng
5e7b236f31
Unify macrolactone detection, numbering, fragmentation, and splicing under the installable macro_lactone_toolkit package. - replace legacy src.* modules with the new package layout - add analyze/number/fragment CLI entrypoints and pixi tasks - migrate tests, README, and scripts to the new package API
74 lines
2.3 KiB
Python
74 lines
2.3 KiB
Python
import pytest
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from rdkit import Chem
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from macro_lactone_toolkit import (
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AmbiguousMacrolactoneError,
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MacroLactoneAnalyzer,
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MacrolactoneDetectionError,
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MacrolactoneFragmenter,
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)
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from .helpers import build_ambiguous_smiles, build_macrolactone
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@pytest.mark.parametrize("ring_size", [12, 14, 16, 20])
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def test_analyzer_detects_supported_ring_sizes(ring_size: int):
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built = build_macrolactone(ring_size)
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analyzer = MacroLactoneAnalyzer()
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assert analyzer.get_valid_ring_sizes(built.smiles) == [ring_size]
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def test_analyzer_rejects_non_lactone_macrocycle():
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analyzer = MacroLactoneAnalyzer()
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assert analyzer.get_valid_ring_sizes("C1CCCCCCCCCCC1") == []
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def test_fragmenter_auto_numbers_ring_with_expected_positions():
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built = build_macrolactone(16, {5: "methyl"})
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result = MacrolactoneFragmenter().number_molecule(built.mol)
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assert result.ring_size == 16
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assert result.position_to_atom == built.position_to_atom
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assert set(result.position_to_atom) == set(range(1, 17))
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assert result.atom_to_position == {
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atom_idx: position for position, atom_idx in built.position_to_atom.items()
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}
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carbonyl_atom = built.mol.GetAtomWithIdx(result.position_to_atom[1])
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assert carbonyl_atom.GetSymbol() == "C"
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assert any(
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bond.GetBondType() == Chem.BondType.DOUBLE and bond.GetOtherAtom(carbonyl_atom).GetSymbol() == "O"
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for bond in carbonyl_atom.GetBonds()
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)
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ester_oxygen = built.mol.GetAtomWithIdx(result.position_to_atom[2])
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assert ester_oxygen.GetSymbol() == "O"
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def test_fragmenter_requires_explicit_ring_size_for_ambiguous_molecule():
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ambiguous_smiles = build_ambiguous_smiles()
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with pytest.raises(AmbiguousMacrolactoneError):
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MacrolactoneFragmenter().number_molecule(ambiguous_smiles)
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def test_fragmenter_raises_for_missing_macrolactone():
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with pytest.raises(MacrolactoneDetectionError):
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MacrolactoneFragmenter().number_molecule("CCO")
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def test_explicit_ring_size_selects_requested_ring():
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built = build_macrolactone(14)
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result = MacrolactoneFragmenter(ring_size=14).number_molecule(built.smiles)
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assert result.ring_size == 14
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def test_explicit_ring_size_rejects_wrong_ring():
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built = build_macrolactone(12)
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with pytest.raises(MacrolactoneDetectionError):
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MacrolactoneFragmenter(ring_size=16).number_molecule(built.smiles)
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