File size: 7,244 Bytes
88152cd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 | # Copyright 2026 Emile de Bruyn
# SPDX-License-Identifier: Apache-2.0
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()
|