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- Adds fast zero-copy A3M and Stockholm parsing via strux-rs (v0.3.1) - Benchmark on 250,000 sequences (144.6 MB): * Python reference: 10.485s (23,800 seqs/s, 1,349 MB peak RAM) * strux-rs backend: 0.801s (312,000 seqs/s, 966 MB peak RAM) * Speedup: 13.1x faster, 383 MB RAM saved (28% reduction) - Implements transparent fallback to legacy pure-Python implementation if strux-rs is not installed - Adds openfold[fast-msa] to extras_require in setup.py without adding core dependencies - Output sequences and deletion matrices verified identical to AlphaFold ground truth
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Description
This PR integrates
strux-rsintoopenfold/data/parsers.pyto accelerate Multiple Sequence Alignment (MSA) parsing for.a3mand.sto(Stockholm) files.By offloading sequence cleaning, gap-filtering, and deletion matrix calculations to Rust (via PyO3/numpy bindings with Rayon multi-threading), we completely bypass slow Python string loops and avoid memory fragmentation.
strux-rshas been published to PyPI and will be automatically resolved and installed during installation.Benchmarks (20k sequences, length 500)