Folddisco Release 3-3e193e3

Folddisco Release 3 improves default ranking, adds geometry- and substitution-tolerant search and novelty screening, and loads large indices much faster. On M-CSA catalytic sites, Sens@1FP rises from 0.45 to 0.5 (report).

New features

• --sensitive (= --expand-radius 2): also searches neighbouring distance and angle bins, recovering motifs whose geometry deviates from the query.
• --aa-subst blosum62|group|size, or :* per residue: allows similar amino acids, ranked below exact matches.
• --confident: reports only matches covering most of the query within 1 Å RMSD.
• --novelty-mode: reports one KNOWN, PARTIAL or NOVEL verdict per query, with the best hit as evidence.
• index --expand-radius, --aa-subst: Optional index-time expansion for small databases.
• Multi-character and numeric chain IDs (AA_250, 10_250, --chain-sep), suggested by @adobles96 (#44), with thanks to @Immortals-33 (#48) and @kamurani (#33).

Changes

• Results are now sorted by match_score per match and structure_score per structure instead of idf. Use --sort-by idf:desc,rmsd:asc to restore the previous order.

Performance

• Index lookups are memory-mapped and cached on first use, so the AFDB50 lookup loads in about 18 ms instead of 3 s.

Bug fixes

• Substituted residues (:H, :ND) are no longer dropped during matching.
• Malformed -q strings now produce an error message instead of a panic.

Full Changelog: 2-9375a2d...3-3e193e3