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| |
|
|
| import csv |
| import importlib.util |
| import os |
| import subprocess |
| import sys |
| import tempfile |
| import unittest |
| from pathlib import Path |
|
|
| ROOT = Path(__file__).resolve().parents[1] |
| sys.path.insert(0, str(ROOT / "scripts")) |
| from prepare_motifbench import adapt_pdb |
| from validate_release import residues, validate |
|
|
|
|
| class ReleaseTests(unittest.TestCase): |
| def test_reference(self): |
| validate() |
|
|
| def test_corrected_contig_preserves_motif_and_target(self): |
| with (ROOT / "contig_specifications.csv").open(newline="") as handle: |
| row = next(r for r in csv.DictReader(handle) if r["problem"] == "1A22_PS01352_c1") |
| self.assertEqual(row["length"], "75") |
| self.assertEqual(row["contig"], "0-0;A1-5;16-20;B1-3;21-25;C1-30;0-0") |
| self.assertEqual(row["contig_original"], "0-0;B353-357;16-20;B374-376;21-25;B402-431;0-0") |
|
|
| def test_adapter_preserves_backbone_and_masks_redesign(self): |
| case = "1AHD_PS00027_c1" |
| with (ROOT / "test_cases.csv").open(newline="") as handle: |
| row = next(r for r in csv.DictReader(handle) if r["pdb_id"] == case) |
| redesign = residues(row["redesign_idcs"]) |
| with tempfile.TemporaryDirectory() as temp: |
| path = Path(temp) / "adapted.pdb" |
| adapt_pdb(ROOT / "motif_pdbs" / f"{case}.pdb", path, redesign) |
| for line in path.read_text().splitlines(): |
| if line.startswith("ATOM "): |
| key = (line[21], int(line[22:26])) |
| if key in redesign: |
| self.assertEqual(line[17:20], "UNK") |
| self.assertIn(line[12:16].strip(), {"N", "CA", "C", "O"}) |
| else: |
| self.assertNotEqual(line[17:20], "UNK") |
|
|
| def test_reconstruction_rejects_unpinned_prosite(self): |
| with tempfile.TemporaryDirectory() as temp: |
| temp = Path(temp) |
| fake = temp / "prosite.dat" |
| fake.write_text("not the pinned PROSITE release\n") |
| config = temp / "config.yaml" |
| config.write_text(f"input:\n prosite_dat: {fake}\n") |
| result = subprocess.run( |
| [sys.executable, str(ROOT / "scripts/reconstruct.py"), "--config", str(config)], |
| text=True, capture_output=True, |
| ) |
| self.assertNotEqual(result.returncode, 0) |
| self.assertIn("wrong PROSITE input", result.stderr) |
|
|
| @unittest.skipUnless(os.environ.get("MOTIFBENCH_WORK"), "set MOTIFBENCH_WORK for upstream smoke test") |
| def test_upstream_motif_info_and_segment_checker(self): |
| work = Path(os.environ["MOTIFBENCH_WORK"]) |
| with (ROOT / "test_cases.csv").open(newline="") as handle: |
| cases = list(csv.DictReader(handle)) |
| module_spec = importlib.util.spec_from_file_location( |
| "upstream_motif_info", work / "scripts/write_motifInfo_from_scaffoldInfo.py" |
| ) |
| upstream = importlib.util.module_from_spec(module_spec) |
| module_spec.loader.exec_module(upstream) |
| for index, row in enumerate(cases, 1): |
| name = f"{index:02d}_{row['pdb_id']}" |
| chains = upstream.read_pdb_residues(work / "motif_pdbs" / f"{name}.pdb") |
| observed = {(chain, number) for chain, entries in chains.items() |
| for number, name in entries.items() if name == "UNK"} |
| self.assertEqual(observed, residues(row["redesign_idcs"]), row["pdb_id"]) |
| with tempfile.TemporaryDirectory() as temp: |
| info = Path(temp) / "scaffold_info.csv" |
| output = Path(temp) / "motif_info.csv" |
| indices = ( |
| 0, |
| next(i for i, r in enumerate(cases) if ";" in r["motif_residues"]), |
| next(i for i, r in enumerate(cases) if r["pdb_id"] == "1A22_PS01352_c1"), |
| ) |
| for index in indices: |
| row = cases[index] |
| name = f"{index + 1:02d}_{row['pdb_id']}" |
| chains = [segment[0] for segment in row["motif_residues"].split(";")] |
| with info.open("w", newline="") as handle: |
| writer = csv.writer(handle) |
| writer.writerow(["sample_num", "motif_placements"]) |
| placement = "0/A/16/B/21/C/0" if row["pdb_id"] == "1A22_PS01352_c1" else "/".join(["0"] + chains + ["0"]) |
| writer.writerow([0, placement]) |
| subprocess.run([sys.executable, str(work / "scripts/write_motifInfo_from_scaffoldInfo.py"), |
| str(info), str(work / "motif_pdbs" / f"{name}.pdb"), |
| str(output)], check=True) |
| with output.open(newline="") as handle: |
| result = next(csv.DictReader(handle)) |
| self.assertEqual(result["pdb_name"], name) |
| self.assertEqual(result["segment_order"], ";".join(chains)) |
| self.assertEqual(residues(result["redesign_positions"]), residues(row["redesign_idcs"])) |
| subprocess.run([sys.executable, str(work / "scripts/check_segment_validity.py"), |
| "-i", str(work / "test_cases.csv"), "-t", str(output)], check=True) |
| if row["pdb_id"] == "1A22_PS01352_c1": |
| with (work / "example/contig_specifications.csv").open(newline="") as handle: |
| spec = next(r for r in csv.DictReader(handle) if r["problem"] == name) |
| self.assertEqual(spec["contig"], "0-0;A1-5;16-20;B1-3;21-25;C1-30;0-0") |
|
|
| @unittest.skipUnless(os.environ.get("MOTIFBENCH_WORK"), "set MOTIFBENCH_WORK for upstream smoke test") |
| def test_upstream_summary_is_ordered_before_scoring(self): |
| work = Path(os.environ["MOTIFBENCH_WORK"]) |
| with (ROOT / "test_cases.csv").open(newline="") as handle: |
| cases = list(csv.DictReader(handle)) |
| first = f"01_{cases[0]['pdb_id']}" |
| last = f"100_{cases[99]['pdb_id']}" |
| with tempfile.TemporaryDirectory() as temp: |
| result = Path(temp) |
| cluster = result / first / "esm_successful_backbones" / "diversity_cluster.tsv" |
| cluster.parent.mkdir(parents=True) |
| cluster.write_text(f"{first}_0.pdb {first}_0.pdb\n") |
| with (result / "summary_by_problem.csv").open("w", newline="") as handle: |
| writer = csv.writer(handle) |
| writer.writerow(["Problem", "Num_Solutions", "Novelty", "Success_Rate", "Num_Evaluated"]) |
| writer.writerow([last, 0, 0, 0, 100]) |
| writer.writerow([first, 1, 0, 1, 100]) |
| subprocess.run([sys.executable, str(ROOT / "scripts/summarize_motifbench.py"), |
| str(work), str(result)], check=True) |
| with (result / "summary_by_problem_ordered.csv").open(newline="") as handle: |
| scored = list(csv.DictReader(handle)) |
| self.assertEqual([r["Problem"] for r in scored], [first, last]) |
| self.assertGreater(float(scored[0]["overall_score"]), 0) |
| self.assertEqual(float(scored[1]["overall_score"]), 0) |
|
|
|
|
| if __name__ == "__main__": |
| unittest.main() |
|
|
