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
58 lines
2.1 KiB
Python
58 lines
2.1 KiB
Python
from __future__ import annotations
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import json
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import sqlite3
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import pandas as pd
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from macro_lactone_toolkit.validation.validator import MacrolactoneValidator
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from ..helpers import build_macrolactone_with_fused_side_ring
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def test_validator_exports_only_single_anchor_fragments_and_fragment_library(tmp_path):
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built = build_macrolactone_with_fused_side_ring(side_chains={10: "methyl"})
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input_path = tmp_path / "input.csv"
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output_dir = tmp_path / "validation_output"
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pd.DataFrame(
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[
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{
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"ml_id": "ML00000001",
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"IDs": "CHEMBL0001",
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"smiles": built.smiles,
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}
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]
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).to_csv(input_path, index=False)
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validator = MacrolactoneValidator(output_dir=output_dir, sample_ratio=1.0)
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results = validator.run(input_path)
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assert results == {"total": 1, "success": 1, "failed": 0, "skipped": 0}
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with sqlite3.connect(output_dir / "fragments.db") as connection:
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fragments = connection.execute(
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"SELECT cleavage_position, has_dummy_atom, dummy_atom_count FROM side_chain_fragments"
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).fetchall()
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library_entries = connection.execute(
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"""
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SELECT source_type, source_parent_ml_id, source_parent_chembl_id,
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cleavage_position, has_dummy_atom, dummy_atom_count, splice_ready
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FROM fragment_library_entries
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"""
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).fetchall()
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assert fragments == [(10, 1, 1)]
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assert library_entries == [("validation_extract", "ML00000001", "CHEMBL0001", 10, 1, 1, 1)]
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summary = pd.read_csv(output_dir / "summary.csv")
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assert summary.loc[0, "num_sidechains"] == 1
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assert json.loads(summary.loc[0, "cleavage_positions"]) == [10]
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fragment_library = pd.read_csv(output_dir / "fragment_library.csv")
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assert fragment_library.loc[0, "source_type"] == "validation_extract"
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assert int(fragment_library.loc[0, "cleavage_position"]) == 10
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assert bool(fragment_library.loc[0, "has_dummy_atom"]) is True
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assert int(fragment_library.loc[0, "dummy_atom_count"]) == 1
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assert bool(fragment_library.loc[0, "splice_ready"]) is True
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