(by claude) Fix PDB sequence clusters: migrate off deprecated RCSB bc-*.out files#2239
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jamesmkrieger merged 2 commits intoJun 19, 2026
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RCSB removed the legacy bc-{sqid}.out cluster files (now HTTP 404), so
fetchPDBClusters retrieved no usable data and a subsequent loadPDBClusters
crashed in os.path.getmtime with FileNotFoundError.
- fetchPDBClusters: download from the current clusters-by-entity-{sqid}.txt
endpoint, and refuse to save empty bodies or HTML error pages (so a failed
download is never reported as success).
- loadPDBClusters: re-check the cache file after fetching and raise a clear
IOError instead of crashing in getmtime; parse on the last underscore so
identifiers containing underscores (computed structure models, e.g.
AF_AFP12345F1) still yield clean (identifier, entity) pairs.
- listPDBCluster: the data now clusters by polymer entity rather than chain, so
the second argument is an entity id; update matching and docstrings.
- Add tests for fetch/list and the failed-download error path.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
In a fresh environment prody's package path is unset, so getPackagePath() (reached via fetchPDBClusters) prompts with input(); under pytest's captured output this raised "OSError: reading from stdin while output is captured!". Point the package path at the writable test TEMPDIR in setUpModule and restore it in tearDownModule. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
karolamik13
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Jun 19, 2026
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I have tested it. Everything is working fine.
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Fixes #2238 (discovered and written by claude too)
RCSB removed the legacy bc-{sqid}.out cluster files (now HTTP 404), so fetchPDBClusters retrieved no usable data and a subsequent loadPDBClusters crashed in os.path.getmtime with FileNotFoundError.