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.
308 lines
11 KiB
Python
308 lines
11 KiB
Python
from __future__ import annotations
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import json
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import sqlite3
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import subprocess
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import sys
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from pathlib import Path
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import pandas as pd
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from macro_lactone_toolkit import MacrolactoneFragmenter
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from .helpers import build_ambiguous_smiles, build_macrolactone
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PROJECT_ROOT = Path(__file__).resolve().parents[1]
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ACTIVE_TEXT_ASSETS = [
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PROJECT_ROOT / "scripts" / "README.md",
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PROJECT_ROOT / "docs" / "SUMMARY.md",
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PROJECT_ROOT / "docs" / "project-docs" / "QUICK_COMMANDS.md",
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PROJECT_ROOT / "notebooks" / "README_analyze_ring16.md",
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]
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def run_script(script_name: str, *args: str) -> subprocess.CompletedProcess[str]:
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return subprocess.run(
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[sys.executable, str(PROJECT_ROOT / "scripts" / script_name), *args],
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capture_output=True,
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text=True,
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check=False,
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cwd=PROJECT_ROOT,
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)
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def test_batch_process_script_writes_flat_outputs_and_summary(tmp_path):
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valid = build_macrolactone(14, {4: "methyl"})
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ambiguous = build_ambiguous_smiles()
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input_path = tmp_path / "molecules.csv"
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output_path = tmp_path / "fragments.csv"
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errors_path = tmp_path / "errors.csv"
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summary_path = tmp_path / "summary.json"
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pd.DataFrame(
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[
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{"id": "valid_1", "smiles": valid.smiles},
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{"id": "ambiguous_1", "smiles": ambiguous},
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]
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).to_csv(input_path, index=False)
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completed = run_script(
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"batch_process.py",
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"--input",
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str(input_path),
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"--output",
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str(output_path),
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"--errors-output",
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str(errors_path),
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"--summary-output",
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str(summary_path),
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)
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assert completed.returncode == 0, completed.stderr
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assert output_path.exists()
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assert errors_path.exists()
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assert summary_path.exists()
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summary = json.loads(summary_path.read_text(encoding="utf-8"))
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assert summary["processed"] == 2
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assert summary["successful"] == 1
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assert summary["failed"] == 1
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def test_analyze_fragments_script_generates_reports_and_plot(tmp_path):
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built = build_macrolactone(16, {5: "methyl", 7: "ethyl"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="analysis_1")
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fragments = pd.DataFrame(
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[
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{
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"parent_id": result.parent_id,
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"parent_smiles": result.parent_smiles,
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"ring_size": result.ring_size,
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**fragment.to_dict(),
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}
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for fragment in result.fragments
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]
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)
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input_path = tmp_path / "fragments.csv"
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output_dir = tmp_path / "analysis"
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fragments.to_csv(input_path, index=False)
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completed = run_script(
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"analyze_fragments.py",
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"--input",
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str(input_path),
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"--output-dir",
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str(output_dir),
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)
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assert completed.returncode == 0, completed.stderr
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assert (output_dir / "position_statistics.csv").exists()
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assert (output_dir / "fragment_property_summary.csv").exists()
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assert (output_dir / "position_frequencies.png").exists()
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assert (output_dir / "analysis_summary.txt").exists()
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def test_generate_sdf_and_statistics_script_generates_artifacts(tmp_path):
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built = build_macrolactone(16, {5: "methyl"})
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result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="sdf_1")
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fragments = pd.DataFrame(
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[
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{
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"parent_id": result.parent_id,
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"parent_smiles": result.parent_smiles,
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"ring_size": result.ring_size,
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**fragment.to_dict(),
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}
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for fragment in result.fragments
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]
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)
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input_path = tmp_path / "fragments.csv"
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output_dir = tmp_path / "sdf_output"
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fragments.to_csv(input_path, index=False)
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completed = run_script(
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"generate_sdf_and_statistics.py",
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"--input",
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str(input_path),
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"--output-dir",
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str(output_dir),
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)
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assert completed.returncode == 0, completed.stderr
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assert (output_dir / "cleavage_position_statistics.json").exists()
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assert (output_dir / "sdf" / "sdf_1_3d.sdf").exists()
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def test_analyze_validation_fragment_library_script_generates_reports(tmp_path):
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input_path = tmp_path / "fragment_library.csv"
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db_path = tmp_path / "fragments.db"
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output_dir = tmp_path / "fragment_library_analysis"
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pd.DataFrame(
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[
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{
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"id": 1,
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"source_type": "validation_extract",
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"source_fragment_id": "ML16A_frag_0",
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"source_parent_ml_id": "ML16A",
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"source_parent_chembl_id": None,
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"cleavage_position": 3,
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"fragment_smiles_labeled": "[3*]C",
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"fragment_smiles_plain": "*C",
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"has_dummy_atom": True,
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"dummy_atom_count": 1,
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"splice_ready": True,
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"original_bond_type": "SINGLE",
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"created_at": "2026-03-19 00:00:00",
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},
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{
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"id": 2,
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"source_type": "validation_extract",
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"source_fragment_id": "ML16A_frag_1",
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"source_parent_ml_id": "ML16A",
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"source_parent_chembl_id": None,
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"cleavage_position": 3,
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"fragment_smiles_labeled": "[3*]CC",
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"fragment_smiles_plain": "*CC",
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"has_dummy_atom": True,
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"dummy_atom_count": 1,
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"splice_ready": True,
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"original_bond_type": "SINGLE",
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"created_at": "2026-03-19 00:00:00",
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},
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{
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"id": 3,
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"source_type": "validation_extract",
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"source_fragment_id": "ML16B_frag_0",
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"source_parent_ml_id": "ML16B",
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"source_parent_chembl_id": None,
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"cleavage_position": 4,
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"fragment_smiles_labeled": "[4*]O",
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"fragment_smiles_plain": "*O",
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"has_dummy_atom": True,
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"dummy_atom_count": 1,
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"splice_ready": True,
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"original_bond_type": "SINGLE",
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"created_at": "2026-03-19 00:00:00",
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},
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{
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"id": 4,
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"source_type": "validation_extract",
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"source_fragment_id": "ML14A_frag_0",
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"source_parent_ml_id": "ML14A",
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"source_parent_chembl_id": None,
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"cleavage_position": 3,
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"fragment_smiles_labeled": "[3*]CCC",
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"fragment_smiles_plain": "*CCC",
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"has_dummy_atom": True,
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"dummy_atom_count": 1,
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"splice_ready": True,
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"original_bond_type": "SINGLE",
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"created_at": "2026-03-19 00:00:00",
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},
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]
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).to_csv(input_path, index=False)
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with sqlite3.connect(db_path) as connection:
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connection.execute(
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"""
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CREATE TABLE parent_molecules (
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id INTEGER PRIMARY KEY,
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ml_id TEXT NOT NULL,
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chembl_id TEXT,
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molecule_name TEXT,
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smiles TEXT NOT NULL,
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classification TEXT NOT NULL,
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ring_size INTEGER,
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primary_reason_code TEXT,
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primary_reason_message TEXT,
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processing_status TEXT NOT NULL,
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error_message TEXT,
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num_sidechains INTEGER,
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cleavage_positions TEXT,
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numbered_image_path TEXT,
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created_at TEXT NOT NULL,
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processed_at TEXT
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)
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"""
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)
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connection.executemany(
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"""
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INSERT INTO parent_molecules (
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id, ml_id, chembl_id, molecule_name, smiles, classification, ring_size,
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primary_reason_code, primary_reason_message, processing_status, error_message,
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num_sidechains, cleavage_positions, numbered_image_path, created_at, processed_at
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)
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VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
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""",
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[
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(1, "ML16A", None, None, "C1CCCCCCCCCCCCCC(=O)O1", "standard_macrolactone", 16, None, None, "success", None, 2, "[3]", None, "2026-03-19 00:00:00", None),
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(2, "ML16B", None, None, "C1CCCCCCCCCCCCCC(=O)O1", "standard_macrolactone", 16, None, None, "success", None, 1, "[4]", None, "2026-03-19 00:00:00", None),
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(3, "ML14A", None, None, "C1CCCCCCCCCCCC(=O)O1", "standard_macrolactone", 14, None, None, "success", None, 1, "[3]", None, "2026-03-19 00:00:00", None),
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],
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)
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connection.commit()
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completed = run_script(
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"analyze_validation_fragment_library.py",
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"--input",
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str(input_path),
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"--db",
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str(db_path),
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"--output-dir",
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str(output_dir),
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"--ring-size",
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"16",
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)
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assert completed.returncode == 0, completed.stderr
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assert (output_dir / "fragment_atom_count_distribution.png").exists()
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assert (output_dir / "fragment_atom_count_summary.csv").exists()
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assert (output_dir / "fragment_atom_count_filter_candidates.csv").exists()
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assert (output_dir / "ring16_position_count_comparison.csv").exists()
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assert (output_dir / "ring16_position_count_comparison.png").exists()
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assert (output_dir / "ring16_position_atom_count_distribution.png").exists()
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assert (output_dir / "ring16_position_atom_count_boxplot_gt3.png").exists()
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assert (output_dir / "ring16_position_diversity.csv").exists()
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assert (output_dir / "ring16_position_diversity_gt3.csv").exists()
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assert (output_dir / "ring16_position_diversity_gt3.png").exists()
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assert (output_dir / "ring16_position_ring_sensitivity.csv").exists()
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assert (output_dir / "ring16_position_ring_sensitivity.png").exists()
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assert (output_dir / "ring16_medchem_hotspot_comparison.csv").exists()
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assert (output_dir / "ring16_medchem_hotspot_comparison.png").exists()
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assert (output_dir / "fragment_library_analysis_report.md").exists()
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assert (output_dir / "fragment_library_analysis_report_zh.md").exists()
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assert (output_dir / "analysis_summary.txt").exists()
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diversity = pd.read_csv(output_dir / "ring16_position_diversity.csv")
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assert set(diversity["cleavage_position"]) == {3, 4}
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assert set(diversity["total_fragments"]) == {1, 2}
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diversity_gt3 = pd.read_csv(output_dir / "ring16_position_diversity_gt3.csv")
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assert diversity_gt3.empty
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report_zh = (output_dir / "fragment_library_analysis_report_zh.md").read_text(encoding="utf-8")
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assert "桥连或双锚点侧链不会进入当前片段库" in report_zh
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assert "cyclic single-anchor side chains" in report_zh
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assert "6 → 13" in report_zh
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assert "7 → 12" in report_zh
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assert "15 → 4" in report_zh
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assert "16 → 3" in report_zh
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def test_active_text_assets_do_not_reference_legacy_api():
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forbidden_patterns = [
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"from src.",
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"import src.",
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"process_csv(",
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"batch_to_dataframe(",
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"visualize_molecule(",
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"save_to_json(",
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]
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for path in ACTIVE_TEXT_ASSETS:
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text = path.read_text(encoding="utf-8")
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for pattern in forbidden_patterns:
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assert pattern not in text, f"{path} still contains legacy reference: {pattern}"
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