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
52 lines
1.7 KiB
Python
52 lines
1.7 KiB
Python
import pytest
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from rdkit import Chem
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from macro_lactone_toolkit import MacrolactoneFragmenter
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from macro_lactone_toolkit.splicing.engine import splice_molecule
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from macro_lactone_toolkit.splicing.scaffold_prep import prepare_macrolactone_scaffold
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from .helpers import build_macrolactone, canonicalize
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def test_splice_benzene_methyl():
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scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
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fragment = Chem.MolFromSmiles("C*")
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product = splice_molecule(scaffold, fragment, position=1)
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assert canonicalize(product) == canonicalize("Cc1ccccc1")
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def test_splice_missing_isotope():
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scaffold = Chem.MolFromSmiles("c1ccccc1[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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scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
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fragment = Chem.MolFromSmiles("C")
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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_prepare_scaffold_and_reassemble_fragment():
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built = build_macrolactone(16, {5: "ethyl"})
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result = MacrolactoneFragmenter(ring_size=16).fragment_molecule(built.smiles, parent_id="reassemble")
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fragment = next(fragment for fragment in result.fragments if fragment.cleavage_position == 5)
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scaffold, dummy_map = prepare_macrolactone_scaffold(
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built.smiles,
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positions=[5],
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ring_size=16,
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)
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assert 5 in dummy_map
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product = splice_molecule(scaffold, Chem.MolFromSmiles(fragment.fragment_smiles_labeled), position=5)
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assert canonicalize(product) == canonicalize(built.mol)
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