v2.4.0

Features

• Keep AlphaFold's AlphaMissense url on each model (87c0129)

Other Changes

• Remove timeout's abort listener once it resolves (9f6717b)
• Stop a Foldseek wait as soon as the caller aborts (3511c3d)
• Escape ids in the RCSB GraphQL queries; share the JSON guards (84e5ff9)
• Skip pickStructureSequence's alignment when a chain matches exactly (1b11222)
• Let an abort of UniProt's descendant search reach the caller (90c1fad)
• Share the residue walk; drop duplicated counting and padding helpers (a17933a)

Full changelog: v2.3.0...v2.4.0

v2.3.0

Other Changes

• Split the Foldseek search into steps and keep every field of a hit (725541b)

Full changelog: v2.2.0...v2.3.0

v2.2.0

Other Changes

• Update README.md (0bf5a2d)
• Update README.md (21d8a9d)
• Rewrite AI-writing tropes in README and docs (1d928e4)
• Restore claims changed by the tropes rewrite (ea8bccd)
• Fold short verdict sentences into their neighbours (3fbeb14)
• Restore wording the tropes rewrite changed without a trope (6dc489f)
• Tighten README docs list and pipeline intro (3bf4617)
• Add a Foldseek search, an entry-name search and label chains (8a53fff)

Full changelog: v2.1.0...v2.2.0

v2.1.0

Bug Fixes

• Stop searchUniProtEntries logging failed lookups to the console (0a75861)

Documentation

• Turn the README intro into short bullets (00a7a83)
• Rewrite README and api.md prose that reads as generated (2c72922)
• Second trope pass; sweep coordinates, pipeline and faq too (9432a35)
• Rewrite source comments that describe the JBrowse plugin (61e07fd)

Features

• Rename runLocalAlignment to alignSequences (d4a853c)

Full changelog: v2.0.0...v2.1.0

v2.0.0

Bug Fixes

• Name the package as user agent outside a browser (474b7b2)

Documentation

• Rewrite README with usage; give api.md signatures, types and examples (acf49b9)

Features

• BREAKING Read PDB entries and entry lists from RCSB instead of PDBe (93f618a)

Full changelog: v1.4.0...v2.0.0

v1.4.0

Features

• Search UniProt by NCBI GeneID; keep AlphaFold's model id and mean pLDDT (50907c1)

Full changelog: v1.3.0...v1.4.0

v1.3.0

Documentation

• Restructure README into bullets, add docs/ with pipeline and coordinate diagrams (efa26d2)
• Add FAQ on mapping trust, link g2p_mapper, plain-language flowchart (c94c2d4)
• Split the pipeline flowchart into two lanes that meet at chain choice (ca19a3c)
• Replace pipeline flowchart with the two-side version, and correct SIFTS's role (aa36a8e)
• Restyle the pipeline flowchart after the other repos' dataflow charts (976d736)
• Cut the pipeline flowchart to the main path (631f6af)
• Say what 'best match' means for chain choice (94d7b76)

Features

• Keep only shared stretches between two isoforms; ask 3D-Beacons unfiltered (1a9f711)

Full changelog: v1.2.2...v1.3.0

v1.2.2

Bug Fixes

• Look up YP_ and AP_ RefSeq proteins, and keep an empty answer when the wider taxon search fails (f8d35e4)

Full changelog: v1.2.1...v1.2.2

v1.2.1

Bug Fixes

• Search a taxon's descendants when the taxon itself has no entry (d8f74a0)

Documentation

• Fix anti-AI writing tropes in README (84005ab)

Full changelog: v1.2.0...v1.2.1

v1.2.0

Bug Fixes

• Do not retry a 4xx, which repeats the same answer (1a13936)

Full changelog: v1.1.0...v1.2.0