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| """Make an isolated MotifBench-compatible working copy.""" |
| import argparse |
| import csv |
| import shutil |
| import subprocess |
| import tempfile |
| from pathlib import Path |
|
|
| from validate_release import ROOT, residues, validate |
|
|
| UPSTREAM_COMMIT = "d5a714c6a376c701e29dfa66d42a1b13c5e339e0" |
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|
| def adapt_pdb(source, destination, redesign): |
| with source.open() as inp, destination.open("w") as out: |
| for line in inp: |
| if line.startswith("ATOM "): |
| key = (line[21], int(line[22:26])) |
| if key in redesign: |
| if line[12:16].strip() not in {"N", "CA", "C", "O"}: |
| continue |
| line = line[:17] + "UNK" + line[20:] |
| out.write(line) |
|
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|
|
| def prepare(upstream, dest): |
| upstream = upstream.resolve(strict=True) |
| dest = dest.resolve() |
| if dest.exists() or dest == upstream or upstream in dest.parents: |
| raise ValueError("destination must be a new directory outside the upstream checkout") |
| if not dest.parent.is_dir(): |
| raise ValueError("destination parent directory must already exist") |
| commit = subprocess.check_output( |
| ["git", "-C", str(upstream), "rev-parse", "HEAD"], text=True |
| ).strip() |
| if commit != UPSTREAM_COMMIT: |
| raise ValueError(f"expected MotifBench commit {UPSTREAM_COMMIT}, found {commit}") |
| status = subprocess.check_output( |
| ["git", "-C", str(upstream), "status", "--porcelain"], text=True |
| ) |
| if status: |
| raise ValueError("MotifBench checkout must be clean") |
| validate() |
| with (ROOT / "test_cases.csv").open(newline="") as handle: |
| cases = list(csv.DictReader(handle)) |
| with (ROOT / "contig_specifications.csv").open(newline="") as handle: |
| reader = csv.DictReader(handle) |
| specs = list(reader) |
| names = {row["pdb_id"]: f"{i:02d}_{row['pdb_id']}" for i, row in enumerate(cases, 1)} |
| with tempfile.TemporaryDirectory(prefix=".bilby-motifbench-", dir=dest.parent) as temp: |
| work = Path(temp) / "work" |
| shutil.copytree(upstream, work, ignore=shutil.ignore_patterns(".git", "motif_pdbs")) |
| (work / "motif_pdbs").mkdir() |
| shutil.copy2(ROOT / "test_cases.csv", work / "test_cases.csv") |
| for row in cases: |
| case = row["pdb_id"] |
| adapt_pdb(ROOT / "motif_pdbs" / f"{case}.pdb", |
| work / "motif_pdbs" / f"{names[case]}.pdb", |
| residues(row["redesign_idcs"])) |
| with (work / "example" / "contig_specifications.csv").open("w", newline="") as handle: |
| writer = csv.DictWriter(handle, fieldnames=["problem", "length", "contig"], |
| extrasaction="ignore") |
| writer.writeheader() |
| for row in specs: |
| row["problem"] = names[row["problem"]] |
| writer.writerow(row) |
| work.rename(dest) |
| print(f"Created {dest} with {len(cases)} adapted cases; original checkout unchanged.") |
|
|
|
|
| def main(): |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("upstream", type=Path, help="clean pinned MotifBench checkout") |
| parser.add_argument("destination", type=Path, help="new working directory") |
| args = parser.parse_args() |
| prepare(args.upstream, args.destination) |
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|
|
| if __name__ == "__main__": |
| main() |
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|
