Folddisco Release 2-9375a2d

Folddisco Release 2 at a glance: new sparse index format, E‑value statistics for hits, structure-similarity metrics with better sorting and filtering, new `analyze` command, column‑based output formatting, and faster hashing/retrieval. Folddisco has its own Marv now and was published:

Kim H, Kim RS, Mirdita M, Yoon J, Steinegger M. Structural motif search across the protein-universe with Folddisco. Nature Biotechnology, (2026)

Breaking changes

• New unified index format. The old SimpleHashMap/alloc indexing modes were replaced by a single FolddiscoIndex (built on the new SparseIndex). Not compatible with older indices (cb099b5, 157497d, ac1e91e, 9dd06f1).
• New hashes are limited to 30 bits, changing the on‑disk hash layout (21300eb).
• Default sort strategy is now IDF+RMSD (1a33f06, 4579cff).

New features and enhancements

• E‑value estimation for matches based on the IDF score, with per‑match IDF and multiple fitting functions (#32, d395c8a, c452eca, fdfeadb, 5ab3881, 3043123, de68e15) by @jwyoon05.
• Structure‑similarity metrics exposed to the CLI, enabling result filtering and metric‑aware sorting (16696a4, 408ffa9, a99e45a, 013f5c8).
• Column‑based TSV/CSV output formatting and updated match‑result header (88dc390, 1e115a9, f92169f).
• mmap type now handles index files larger than available memory (765aeeb).
• Version handling via environment variable for build environments without git (716f25f).
• Two new binning schemes, including shift binning for higher sensitivity (217bb7d, d3700a8, c708dea).
• Improved foldcomp path resolution (95abc73, 8d7a776).

Performance

• Faster hashing with FxHasher (23133c0).
• Accelerated residue mapping (5f3796b).
• Residue retrieval checks distances first, then fetches features, and drops an unnecessary distance‑map copy (c6f57e5, 60a70e0).
• Query residues are no longer sorted unnecessarily (d589728).

Bug fixes

• Fixed CIF parsing for structures with numeric values (e.g. ligand code 919) and relative paths; no longer truncates multi‑char chain IDs (#41, 1bab90c) by @adobles96.
• Fixed duplicated entry issue in the index (82cd989).
• Fixed a benchmark bug (#29, 3392bf2).

Documentation & developer notes

• Add analyze command for index distribution analysis: reports total/empty/density and amino‑acid pair counts, with a --top-n option (10d42cb, c28c502, 58aa0f7, 7d6c911, 10eb601).
• Add docker containers and conda/docker install instructions to README (9c13b9d, c6ee2ef).
• Updated preprint version, download links, and pre‑built indices; added Cargo and PDB dataset links (f928970, 335a295, 9375a2d).
• Removed obsolete doctests and the foldcomp feature test; test cleanup (2ebad32, 0f1d715, 5fedfb4).