lingyuzeng
46a438dd36
- skip fused/shared/multi-anchor side systems during extraction - add fragment library schema and fragment_library.csv export - make scaffold prep strict for non-spliceable positions
80 lines
3.2 KiB
Python
80 lines
3.2 KiB
Python
from rdkit import Chem
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from macro_lactone_toolkit import MacrolactoneFragmenter
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from .helpers import (
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build_macrolactone,
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build_macrolactone_with_fused_side_ring,
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build_macrolactone_with_shared_atom_side_ring,
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build_macrolactone_with_single_anchor_side_ring,
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)
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def test_fragmentation_returns_empty_list_without_sidechains():
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built = build_macrolactone(12)
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="plain")
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assert result.fragments == []
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def test_fragmentation_emits_labeled_and_plain_smiles_round_trip():
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built = build_macrolactone(16, {5: "ethyl", 8: "methyl"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="mol_001")
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assert result.parent_id == "mol_001"
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assert result.ring_size == 16
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assert {fragment.cleavage_position for fragment in result.fragments} == {5, 8}
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for fragment in result.fragments:
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labeled = Chem.MolFromSmiles(fragment.fragment_smiles_labeled)
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plain = Chem.MolFromSmiles(fragment.fragment_smiles_plain)
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assert labeled is not None
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assert plain is not None
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assert Chem.MolToSmiles(labeled, isomericSmiles=True)
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assert Chem.MolToSmiles(plain, isomericSmiles=True)
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assert any(
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atom.GetAtomicNum() == 0 and atom.GetIsotope() == fragment.cleavage_position
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for atom in labeled.GetAtoms()
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)
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assert any(
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atom.GetAtomicNum() == 0 and atom.GetIsotope() == 0
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for atom in plain.GetAtoms()
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)
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def test_fragmentation_preserves_attachment_bond_type():
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built = build_macrolactone(16, {6: "exocyclic_alkene"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="bond_type")
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fragment = next(fragment for fragment in result.fragments if fragment.cleavage_position == 6)
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labeled = Chem.MolFromSmiles(fragment.fragment_smiles_labeled)
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plain = Chem.MolFromSmiles(fragment.fragment_smiles_plain)
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for mol in (labeled, plain):
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dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
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neighbor = dummy_atom.GetNeighbors()[0]
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bond = mol.GetBondBetweenAtoms(dummy_atom.GetIdx(), neighbor.GetIdx())
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assert bond.GetBondType() == Chem.BondType.DOUBLE
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def test_fragmentation_skips_fused_side_ring_but_keeps_single_anchor_sidechains():
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built = build_macrolactone_with_fused_side_ring(side_chains={10: "methyl"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="fused")
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assert {fragment.cleavage_position for fragment in result.fragments} == {10}
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def test_fragmentation_skips_shared_atom_multi_anchor_component():
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built = build_macrolactone_with_shared_atom_side_ring(side_chains={11: "ethyl"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="shared_atom")
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assert {fragment.cleavage_position for fragment in result.fragments} == {11}
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def test_fragmentation_allows_single_anchor_side_ring():
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built = build_macrolactone_with_single_anchor_side_ring()
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="single_anchor_ring")
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assert {fragment.cleavage_position for fragment in result.fragments} == {5}
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