fix: preserve DO_PREPARED stamp on Protein sync and to_pdb - #617
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Prepared proteins already on UFA were re-uploaded via biotite on sync(lazy=True), which dropped REMARK 99 and overwrote the stamped file. Skip upload when remote_path is set, and re-stamp after PDB rewrites.
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Closing — stamp fix belongs on metabolism-async-execution, not a standalone PR from main. |
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Summary
Protein.sync/registerfrom re-uploading whenremote_pathis already set, so Pocket Finder and other tools no longer overwrite stamped Prepared Protein PDBs on UFA.REMARK 99 DO_PREPAREDafter biotiteto_pdbwhen the source had the stamp.toolbox_coredependency), tests, and docs.Test plan
uv run pytest --env local -x tests/test_prepared_protein_stamp.pyREMARK 99 DO_PREPAREDafterpf.run()prepared.sync()with onlyremote_pathset still links/creates a proteins-table row without rewriting the file