{
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{
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{
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],
"adaptations": [
"Tasks select run.py design or the two score.py modes; model_type independently selects the five official model families. Legacy model-valued task and renamed field aliases remain accepted.",
"PDB and JSON file options accept uploaded contents or bundled references. Multi-input JSON maps caller names to contents or references; the adapter creates job-local native paths and rekeys constraint dictionaries.",
"Checkpoint selectors accept only installed official filenames; checkpoint_path_sc and output directories are managed by the service.",
"The README fast packing example requests zero packs. Current run.py loops range(number_of_packs_per_design), so the runnable preset requests one pack.",
"Scoring presets bundle the official previously generated backbone used by the README.",
"score.py expects parse_these_chains_only as concatenated single-character IDs, unlike the comma-separated run.py flag. The adapter translates it. score.py multi-residue constraints receive arrays because that entry point does not split the README string format.",
"The installer replaces removed np.int dtype aliases in bundled OpenFold with explicit np.int64 indices for Python 3.12 and NumPy 1.26.4."
],
"validation": {
"date": "2026-09-05",
"runtime": "Python 3.12, PyTorch 2.7.1 CPU, NumPy 1.26.4, ProDy 2.6.1",
"official_examples": 43,
"checks": [
"All 34 design, 4 scoring and 5 packing examples completed actual CPU inference through the adapter.",
"Verified output sequence counts, finite normalized scoring probabilities, and packed structure counts.",
"Bundled PDB residue selections matched the official ProDy parser.",
"All presets passed browser form submission and official argument-parser checks.",
"Representative adapter calls passed the actual bio_tools subprocess runner and durable result archiving."
],
"limits": "CUDA and Ubuntu deployment were not exercised on this Windows host."
}
}