lingyuzeng
3e07402f4e
Add a public numbering module and route fragmenting, validation, and scaffold preparation through the canonical numbering entry. Rewrite the repository entry docs around the fixed numbering contract, add MkDocs landing pages, and document the mirror mapping used for medicinal-chemistry comparisons. Also refresh the validation analysis reports to explain the canonical-versus-mirrored numbering relationship.
53 lines
1.7 KiB
Python
53 lines
1.7 KiB
Python
from __future__ import annotations
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from macro_lactone_toolkit import (
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MacrolactoneFragmenter,
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mirror_macrolactone_position,
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mirror_macrolactone_positions,
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number_macrolactone,
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)
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from macro_lactone_toolkit.splicing.scaffold_prep import prepare_macrolactone_scaffold
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from .helpers import build_macrolactone
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def test_number_macrolactone_matches_fragmenter_numbering() -> None:
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built = build_macrolactone(16, {5: "methyl"})
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api_result = number_macrolactone(built.smiles, ring_size=16)
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fragmenter_result = MacrolactoneFragmenter(ring_size=16).number_molecule(built.smiles)
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assert api_result.position_to_atom == fragmenter_result.position_to_atom
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assert api_result.atom_to_position == fragmenter_result.atom_to_position
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def test_mirror_macrolactone_position_for_ring16() -> None:
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assert mirror_macrolactone_position(6, 16) == 13
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assert mirror_macrolactone_position(7, 16) == 12
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assert mirror_macrolactone_position(15, 16) == 4
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assert mirror_macrolactone_position(16, 16) == 3
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def test_mirror_macrolactone_positions_returns_stable_mapping() -> None:
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assert mirror_macrolactone_positions([6, 7, 15, 16], 16) == {
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6: 13,
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7: 12,
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15: 4,
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16: 3,
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}
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def test_prepare_scaffold_keeps_requested_position_label() -> None:
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built = build_macrolactone(16, {5: "ethyl"})
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scaffold, dummy_map = prepare_macrolactone_scaffold(
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built.mol,
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positions=[5],
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ring_size=16,
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)
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numbering = number_macrolactone(built.mol, ring_size=16)
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assert 5 in dummy_map
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assert numbering.position_to_atom[5] == built.position_to_atom[5]
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assert numbering.position_to_atom[5] == scaffold.GetAtomWithIdx(dummy_map[5]).GetNeighbors()[0].GetIdx()
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