npm - @cyanheads/protein-mcp-server - Versions diffs - 0.8.5 → 0.8.6 - Mend

@cyanheads/protein-mcp-server 0.8.5 → 0.8.6

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@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.8.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.8.6-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.2.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.2%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -29,120 +29,98 @@
 ## Overview
-Experimental (PDB) and predicted (AlphaFold) protein structures, federated behind one surface. Search, fetch, align, compare, and annotate structures and their ligands across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek — all keyless. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
+Experimental (PDB) and predicted (AlphaFold) protein structures behind one surface. Search, fetch, align, and annotate structures and their ligands across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, all keyless. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
 ### Tools
 | Tool | Description |
 |:---|:---|
-| `protein_search_structures` | Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns. |
-| `protein_get_structure` | Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining. |
-| `protein_find_similar` | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession. |
-| `protein_track_ligands` | Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues. |
-| `protein_compare_structures` | Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix. |
-| `protein_analyze_collection` | Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs. |
-| `protein_get_annotations` | Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms. |
+| `protein_search_structures` | Search experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets |
+| `protein_get_structure` | Fetch metadata and coordinate URLs for experimental, predicted, or best-available structures |
+| `protein_find_similar` | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) |
+| `protein_track_ligands` | Resolve ligands to component IDs, find structures containing one, or map its binding site |
+| `protein_compare_structures` | Align structures with TM-align or jFATCAT, against a reference or all pairs |
+| `protein_analyze_collection` | Profile the PDB as counts, histograms, timelines, and cross-tabs |
+| `protein_get_annotations` | Fetch UniProt features and variants plus InterPro domains with GO terms |
 ### Resources
 | Resource | Description |
 |:---|:---|
-| `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces. |
-| `af://{uniprot}` | Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version. |
+| `pdb://{entry_id}` | Experimental structure summary for a PDB entry |
+| `af://{uniprot}` | AlphaFold DB predicted-structure summary for a UniProt accession |
-All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `protein_get_structure` for `source: experimental`, and `af://{uniprot}` mirrors it for `source: predicted`. Many MCP clients are tool-only and don't surface resources; the summaries remain reachable through the tools.
+Both resources are also reachable through `protein_get_structure`, for clients that don't surface resources.
 ## Capability reference
 ### `protein_search_structures` <sub>tool</sub>
-- Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
-- `content_type` scopes the search to `experimental`, `predicted`, or `all` (default) — `all` is a genuine union, so computed models appear alongside PDB entries
-- Every hit names its `source`; sequence hits in either universe expose a chainable entry `id` plus the matched polymer `entityId`; experimental hits carry title, method, resolution, and organism enrichment, and AlphaFold models their parsed UniProt accession
-- `start` and `limit` page through ranked results; `nextStart` is returned while another page remains, and an empty page past the end names the offset in `notice` rather than reporting no matches
-- Optional `facets` return a method / organism / release-year breakdown alongside the hits — each dimension may be listed once and reports how many matches carry no value for it; a capped dimension is named in `notice`, with `protein_analyze_collection` (larger `bucket_limit`) as the route to the long tail
-- Chain hit IDs straight into `protein_get_structure`
+- At least one of `query`, `sequence` (an mmseqs2 search; `min_identity` / `max_evalue` apply only with it), `organism`, `method`, or `max_resolution`; `content_type` is `experimental`, `predicted`, or `all` (default); up to 100 hits per page (default 25) via `limit` / `start`
+- Each hit names its `source` and a chainable entry `id` (sequence hits add `entityId`); experimental hits carry title, method, resolution, and organism, AlphaFold models their `uniprotAccession`
+- Optional `facets` (`method`, `organism`, `polymer_type`, `resolution`, `release_year`, `molecular_weight`) add a flat breakdown capped at `PROTEIN_FACET_BUCKET_CAP` buckets per dimension; for non-sequence searches, `protein_analyze_collection` reaches the long tail
 ---
 ### `protein_get_structure` <sub>tool</sub>
-- `source: experimental` batches PDB entry IDs (also resolving computed-model IDs like `AF_*`/`MA_*` from search, tagged `source: predicted` with their provider); `source: predicted` takes UniProt accessions for AlphaFold models with pLDDT/PAE; `source: best_available` takes UniProt accessions and returns the top federated model (highest-resolution experimental if one exists, else the best prediction)
-- Per-ID partial success — unresolved IDs land in `failed[]`; `requested`/`processed` disclose IDs dropped beyond the batch cap, and every advisory (cap, failure, overflow) joins into one `notice`
-- Records fetched with `source: experimental`, computed models included, also carry `polymerEntities` (both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`
-- `coordinateUrls` lists only files that exist: BinaryCIF comes from RCSB's ModelServer, the PDB format is omitted for large mmCIF-only entries, and a computed model's files come from its provider (all three formats from AlphaFold DB, mmCIF from ModelArchive) — an AlphaFold model whose provider lookup fails keeps only its RCSB BinaryCIF, named in `notice`
-- `include_coords` inlines coordinate content, subject to a response budget — an over-budget batch returns a per-structure size outline (re-call with `sections: [ids]`), and a single oversized file is withheld with a pointer to its `coordinateUrls`
-- Every response carries an `attribution` block naming upstream data licenses and citations
+- `source: experimental` (default) takes PDB entry IDs and the `AF_*` / `MA_*` computed-model IDs search returns (these come back as `source: predicted`); `predicted` takes UniProt accessions for AlphaFold models with pLDDT/PAE; `best_available` takes UniProt accessions and returns the highest-resolution experimental structure, else the best prediction. Up to `PROTEIN_MAX_BATCH_IDS` IDs per call (default 25)
+- Unresolved IDs land in `failed[]`, and `requested` / `processed` show IDs dropped past the cap; the call fails as `all_failed` when nothing resolves and `mixed_id_types` when the IDs don't fit `source`. Experimental-source records add `polymerEntities`, `ligands`, `molecularWeight`, and `releaseDate`, and `coordinateUrls` lists only files that exist
+- `include_coords` inlines coordinate text within a response budget; an over-budget batch returns an `overflow` size outline to re-call with `sections: [ids]`, and a lone oversized file is withheld in favor of its `coordinateUrls`
 ---
 ### `protein_find_similar` <sub>tool</sub>
-- `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases — query from a raw sequence, a PDB ID, or a UniProt accession
-- Both modes accept `start`/`limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains; an empty page past the end names the offset in `notice`, distinct from a search with no matches
-- Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
-- An async job that exceeds the poll budget returns `status: computing` with a `ticketId` — re-call with `ticket_id` to resume; a completed structure search returns the same ticket so a new `start` pages the finished job
-- Foldseek searches each chain of a multichain structure as its own query: a structure response covers one query (`query`, 0-based, default `0`) and reports `queryCount`, with a `notice` naming the other queries; pass `query` with `ticket_id` to read another chain's hits from the same job. An out-of-range `query` is rejected (`query_out_of_range`), not answered with an empty list
-- Structure hits are ranked best first by `score` across every searched database (hits without a score last, ties by database then target) before `start`/`limit` paging
-- Each mode reads only its own controls (`sequence`, `max_evalue`, `min_identity` under `by: sequence`; `ticket_id`, `databases`, `query` under `by: structure`) — a field the selected mode can't consume is rejected, not ignored
-- Each hit names the engine and source database it came from
+- `by: sequence` runs a synchronous RCSB mmseqs2 search from `sequence`, `pdb_id`, or `uniprot`, filtered by `max_evalue` / `min_identity`; `by: structure` runs an async Foldseek search from `pdb_id` or `uniprot` against `pdb100` + `afdb50` unless `databases` says otherwise. A field only the other mode reads fails as `mode_mismatched_field`; up to 100 hits per page (default 25)
+- Hits name their `source` and, for structure hits, the `database`, ranked by `score` across all searched databases; responses report `totalCount` and `nextStart`
+- A structure job still running at the poll budget returns `status: computing` with a `ticketId`; re-call with `ticket_id` to resume it or re-page a finished job. A multichain structure is one query per chain: each response covers `query` (0-based, default 0) out of `queryCount`
 ---
 ### `protein_track_ligands` <sub>tool</sub>
-- `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey — ranked by deposition frequency, most-common match first
-- `totalCount` and `candidatesConsidered` report how many components matched and how many were ranked; a broad name whose matches exceed the candidate pool gets a `notice` to narrow the query
-- A formula-shaped `query` matches on exact composition, spaced (`C29 H31 N7 O`) or unspaced; anything else (a component ID included) matches on name and synonyms
-- `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID, with `start`/`limit` paging and `nextStart` while another page remains; a page past the end names the offset in `notice` instead of reporting no entries
-- `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances; ligand instances page with `start`/`limit` like `structures_with_ligand`
-- Pocket residues carry both mmCIF label numbering (`asymId`, `seqId`) and author numbering (`authAsymId`, `authSeqId`) — 1IEP's imatinib pocket lists label THR93 as author THR315; the ligand instance reports its own author chain and residue number
-- Binding sites are experimental-only — computed from deposited coordinates; predicted models carry no bound ligands
+- `mode` is `find_ligand` (`query`: a name or formula), `structures_with_ligand` (`comp_id`), or `binding_site` (`pdb_id`, optional `comp_id`); a missing mode input fails as `missing_param`. `limit` is 1–100 (default 25), and `start` pages the last two modes
+- `find_ligand` returns component IDs with formula, weight, SMILES, and InChIKey, ranked by `depositionCount`, with `totalCount` and `candidatesConsidered` showing when the candidate pool was cut short; `structures_with_ligand` lists entries highest resolution first
+- `binding_site` returns pocket residues with contact distances, numbered in both label (`asymId`, `seqId`) and author (`authAsymId`, `authSeqId`) namespaces; it works on experimental structures only
 ---
 ### `protein_compare_structures` <sub>tool</sub>
-- Aligns 2 to the configured cap (default 10, max 25) structures per call, via `tm-align`, `fatcat-rigid`, or `fatcat-flexible`; optional per-structure `chain` restricts the alignment to a single mmCIF label chain
-- `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix; a structure repeated in `structures[]` is compared once
-- Each pair is an independent async job with per-pair partial success — a pair still computing when the poll budget elapses returns `status: computing` with a job `uuid`; a failed pair degrades only its own row
-- Re-call with a matching `{ a, b, uuid }` entry in `resume[]` to poll a computing pair instead of resubmitting; a resumed pair reports `a`/`b` in the order its job was submitted, whatever the current `structures[]` order, and a resume under a different `method` is rejected
-- Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's `modeledResidues` and 0–100 `coverage`, ordered `[a, b]`; TM-score is normalized by `a`'s length, so the same pair scores differently when reversed
+- 2 structures up to `PROTEIN_MAX_COMPARE_STRUCTURES` (default 10, max 25), each a `pdb_id` with an optional label-namespace `chain`; `method` is `tm-align` (default), `fatcat-rigid`, or `fatcat-flexible`; `reference` is `first` (default) or `all_pairs`; `timeout_s` (5–120) sets the per-pair poll budget
+- Each pair row has a `status` (`complete`, `computing`, `failed`), `tmScore`, `rmsd`, `alignedResidues`, and `[a, b]`-ordered `modeledResidues` and `coverage`; TM-score is normalized by `a`'s length, so reversing a pair changes it
+- A computing pair returns its job `uuid`; re-call with `{ a, b, uuid }` in `resume[]` to poll it instead of resubmitting. A resume under a different `method` or for another pair fails as `resume_method_mismatch` or `resume_job_mismatch`
 ---
 ### `protein_analyze_collection` <sub>tool</sub>
-- Group by `method`, `organism`, `polymer_type`, `resolution`, `release_year`, or `molecular_weight`
-- One `group_by` dimension for a breakdown, or two distinct dimensions for a cross-tab (the first nests the second); a repeated dimension is rejected
-- `interval` sets a histogram bin width (a number, for `resolution` or `molecular_weight`) or date-histogram period (`year`, the only one RCSB accepts) — applies to whichever requested dimension can consume that type; rejected when neither can
-- Scope with a free-text `query`, `organism`, `method`, or `max_resolution`; `content_type` selects the structure universe
-- `bucket_limit` caps buckets per dimension level, not per response — a cross-tab applies it separately to the parent and each nested child, up to `bucket_limit × (1 + bucket_limit)` buckets; `notice` names every capped position and `bucketsReturned` gives the realized total
-- Every dimension reports `missingValueCount` — matches carrying no value for that attribute (e.g. a `resolution` breakdown excludes NMR entries; computed models have neither `method` nor `resolution`)
+- `group_by` takes one of `method`, `organism`, `polymer_type`, `resolution`, `release_year`, `molecular_weight`, or two distinct ones for a cross-tab; scope with `query`, `organism`, `method`, `max_resolution`, and `content_type` (default `experimental`). `interval` sets a numeric bin width for `resolution` / `molecular_weight` or `"year"` for `release_year`
+- Returns `total` and `bucketsReturned`; buckets carry `label` and `count` (numeric bins add `rangeFrom` / `rangeTo`), and every dimension reports `missingValueCount`
+- `bucket_limit` (1–500, default `PROTEIN_FACET_BUCKET_CAP`) caps each dimension level separately, so a cross-tab can return `bucket_limit × (1 + bucket_limit)` buckets; `truncated` and `notice` name the capped positions
 ---
 ### `protein_get_annotations` <sub>tool</sub>
-- UniProt features (domains, binding sites, PTMs) and natural variants, plus InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
-- Provide a UniProt accession directly, or a PDB ID — resolved via the structure's sequence cross-reference
-- A multi-chain PDB entry can map to several accessions; the default is the deterministic lowest-author-chain pick, with alternatives listed under `ambiguity` — pass `chain` (an author chain ID) to select a specific one
-- `include` scopes which classes are fetched (`features`, `domains`, `variants`, `all`); `limit` caps each class independently (1–200, default 50), with a truncated class disclosed in `notice`
-- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
+- A `uniprot` accession, or a `pdb_id` resolved through its UniProt cross-reference (author `chain` picks one accession); `include` is `features`, `domains`, `variants`, or `all` (default); `limit` caps each class separately (1–200, default 50)
+- Returns UniProt features and natural variants plus InterPro domains with GO terms; a PDB entry mapping to several accessions defaults to the lowest author chain and lists the rest in `ambiguity`
+- Capped classes set `truncated` and are named in `notice`; failures are typed as `missing_identifier`, `invalid_accession`, `no_uniprot_mapping`, or `chain_not_found`
 ---
 ### `pdb://{entry_id}` <sub>resource</sub>
-- Experimental structure summary as `application/json` — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces
-- Mirrors `protein_get_structure` for `source: experimental`; `entry_id` is a PDB entry ID (e.g. `4HHB`)
+- `entry_id` is a PDB entry ID (e.g. `4HHB`); returns `application/json` with title, methods, resolution, organisms, ligands, and `polymerEntities` carrying both `authAsymIds` and `labelAsymIds`
+- Same data as `protein_get_structure` with `source: experimental`
 ---
 ### `af://{uniprot}` <sub>resource</sub>
-- Predicted-structure summary as `application/json` — mean pLDDT, confidence-band fractions, model URLs (`cif`/`pdb`/`bcif`), and AlphaFold model version
-- `uniprot` accepts a UniProt accession or an AlphaFold DB entry ID (e.g. `AF-P69905-F1`); mirrors `protein_get_structure` for `source: predicted`
+- `uniprot` is a UniProt accession or an AlphaFold DB entry ID (e.g. `AF-P69905-F1`); returns `application/json` with `meanPlddt`, `confidenceBuckets`, `cifUrl` / `pdbUrl` / `bcifUrl`, and `modelVersion`
+- Same data as `protein_get_structure` with `source: predicted`
 ## Features
@@ -150,27 +128,28 @@ Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): s
 PDB / AlphaFold-specific:
-- One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same
-- Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision
-- Corpus analytics run on RCSB's facet engine — distributions, histograms, and cross-tabs come back as compact bucket counts, not the matching entries
-- Async alignment and Foldseek jobs poll within a bounded budget and hand back a job ticket (`ticketId` / per-pair `uuid`) instead of blocking — re-call with `ticket_id` or a `resume[]` entry to poll the same job instead of resubmitting
+- Search, fetch, and comparison treat experimental (PDB) and predicted (AlphaFold DB, ModelArchive, 3D-Beacons providers) structures the same way
+- Keyless across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek
+- Collection analytics run on RCSB's facet engine and return bucket counts, not matching entries
+- Foldseek and alignment jobs poll for up to `PROTEIN_ASYNC_POLL_TIMEOUT_MS` (default 30 s), then hand back a resume handle (`ticketId`, per-pair `uuid`) instead of blocking
+- Chain namespaces stay separate: `authAsymIds` feed `protein_get_annotations` `chain`, `labelAsymIds` feed `protein_compare_structures` `chain`
 Agent-friendly output:
-- Provenance on every response — each hit carries a `source` (`experimental` / `predicted`), the engine and database that produced it, and effective-query / total-count echoes so agents can reason about coverage
-- Graceful partial failure — batch fetches and pairwise comparisons return per-item rows (`failed[]`, per-pair `status`) instead of failing the whole request, each with actionable recovery text
-- Discriminated output contracts — typed `source` and `status` unions, `computing` results with resume tickets, and budget-overflow outlines let callers branch on data, not string parsing
+- Provenance: every hit names its `source` (`experimental` / `predicted`) and the engine or database behind it, and `protein_get_structure` and `protein_get_annotations` carry an `attribution` block (see [Upstream data licensing](#upstream-data-licensing))
+- Graceful partial failure: `failed[]` rows and per-pair `status` keep one bad ID or pair from failing the request
+- Paging and advisories: paged tools return `totalCount` and `nextStart`, a `start` past the end is flagged in `notice` separately from zero matches, and every advisory joins into that one `notice`
 ## Getting started
 ### Public Hosted Instance
-A public instance is available at `https://protein.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:
+A public instance is available at `https://protein.caseyjhand.com/mcp`, no installation required. Point any MCP client at it via Streamable HTTP:
 ```json
 {
   "mcpServers": {
-    "protein": {
+    "protein-mcp-server": {
       "type": "streamable-http",
       "url": "https://protein.caseyjhand.com/mcp"
     }
@@ -180,7 +159,7 @@ A public instance is available at `https://protein.caseyjhand.com/mcp` — no in
 ### Self-Hosted / Local
-Add the following to your MCP client configuration file. No API key is required — every upstream provider is keyless.
+Add the following to your MCP client configuration file. No API key is needed.
 ```json
 {
@@ -240,7 +219,7 @@ MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
 ### Prerequisites
 - [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).
-- No accounts or API keys — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek are all public and keyless.
+- No accounts or API keys: every upstream is public.
 ### Installation
@@ -262,28 +241,32 @@ cd protein-mcp-server
 bun install
 ```
+4. **Configure environment (optional):**
+```sh
+cp .env.example .env
+# every variable has a working default
+```
 ## Configuration
-All upstream providers are keyless, so the server runs out of the box with no configuration. Every variable below is optional.
+Every variable is optional.
 | Variable | Description | Default |
 |:---|:---|:---|
-| `PROTEIN_ASYNC_POLL_TIMEOUT_MS` | Max wall-clock to poll an async job (alignment / Foldseek) before returning a `computing` result. | `30000` |
-| `PROTEIN_MAX_BATCH_IDS` | Cap on IDs accepted by `protein_get_structure` in one batch (1–100). | `25` |
-| `PROTEIN_MAX_COMPARE_STRUCTURES` | Cap on structures per `protein_compare_structures` call (2–25). | `10` |
-| `PROTEIN_FACET_BUCKET_CAP` | Default cap on buckets per `protein_analyze_collection` dimension (1–500). | `50` |
-| `PROTEIN_FANOUT_CONCURRENCY` | Max concurrent upstream requests for per-ID / per-pair fan-out (1–16). | `5` |
-| `RCSB_SEARCH_BASE_URL` | Base URL for the RCSB Search API v2. | `https://search.rcsb.org` |
-| `ALPHAFOLD_BASE_URL` | Base URL for the AlphaFold Protein Structure Database API. | `https://alphafold.ebi.ac.uk` |
-| `FOLDSEEK_BASE_URL` | Base URL for the Foldseek structural-similarity search service. | `https://search.foldseek.com` |
+| `PROTEIN_ASYNC_POLL_TIMEOUT_MS` | Poll budget for an async alignment or Foldseek job before it returns `computing` (min 1000). | `30000` |
+| `PROTEIN_MAX_BATCH_IDS` | Max IDs per `protein_get_structure` call (1–100). | `25` |
+| `PROTEIN_MAX_COMPARE_STRUCTURES` | Max structures per `protein_compare_structures` call (2–25). | `10` |
+| `PROTEIN_FACET_BUCKET_CAP` | Buckets per dimension for `protein_search_structures` facets, and the `protein_analyze_collection` default (1–500). | `50` |
+| `PROTEIN_FANOUT_CONCURRENCY` | Max concurrent upstream requests for per-ID and per-pair fan-out (1–16). | `5` |
 | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
-| `MCP_HTTP_PORT` | Port for the HTTP server. | `3010` |
-| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto`. The server declares `stateless` in code; set this to override it. | `stateless` |
-| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
+| `MCP_HTTP_PORT` | HTTP server port. | `3010` |
+| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto`. Overrides the `stateless` mode the server declares in code. | `stateless` |
+| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth`. | `none` |
 | `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
-| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |
+| `OTEL_ENABLED` | Enable [OpenTelemetry](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |
-See [`.env.example`](./.env.example) for the full list of provider base-URL overrides and tuning limits.
+Each upstream's base URL can also be pointed at a mirror: `RCSB_SEARCH_BASE_URL`, `RCSB_DATA_BASE_URL`, `RCSB_FILES_BASE_URL`, `RCSB_MODELS_BASE_URL`, `RCSB_ALIGNMENT_BASE_URL`, `BEACONS_BASE_URL`, `ALPHAFOLD_BASE_URL`, `MODELARCHIVE_BASE_URL`, `FOLDSEEK_BASE_URL`, `UNIPROT_BASE_URL`, `INTERPRO_BASE_URL`. See [`.env.example`](./.env.example) for their defaults and the full list of optional overrides.
 ## Running the server
@@ -313,20 +296,20 @@ See [`.env.example`](./.env.example) for the full list of provider base-URL over
 ```sh
 docker build -t protein-mcp-server .
-docker run --rm -e MCP_TRANSPORT_TYPE=http -p 3010:3010 protein-mcp-server
+docker run --rm -p 3010:3010 protein-mcp-server
 ```
-The Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/protein-mcp-server`. OpenTelemetry peer dependencies are installed by default — build with `--build-arg OTEL_ENABLED=false` to omit them.
+The Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/protein-mcp-server`. OpenTelemetry peer dependencies are installed by default; build with `--build-arg OTEL_ENABLED=false` to omit them.
 ## Project structure
 | Directory | Purpose |
 |:---|:---|
-| `src/index.ts` | `createApp()` entry point — registers tools/resources and inits the provider services. |
+| `src/index.ts` | `createApp()` entry point: registers tools and resources, inits the provider services. |
 | `src/config` | Server-specific environment variable parsing and validation with Zod. |
-| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). |
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`) and shared schemas (`_schemas.ts`). |
 | `src/mcp-server/resources` | Resource definitions (`*.resource.ts`). |
-| `src/services` | Provider service layer — RCSB (search, data, facets), AlphaFold, 3D-Beacons (best-available), UniProt (incl. InterPro/GO), Structural Comparison alignment, Foldseek, and shared HTTP/identifier/concurrency helpers. |
+| `src/services` | Upstream clients: `rcsb/` (search, data, facets), `alphafold/`, `beacons/` (3D-Beacons), `uniprot/` (UniProt, InterPro, GO), `alignment/` (RCSB Structural Comparison), `foldseek/`, and `shared/` HTTP, concurrency, identifier, and attribution helpers. |
 | `tests/` | Unit and integration tests mirroring `src/`. |
 ## Development guide
@@ -335,12 +318,12 @@ See [`CLAUDE.md`/`AGENTS.md`](./CLAUDE.md) for development guidelines and archit
 - Handlers throw, framework catches — no `try/catch` in tool logic
 - Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage
-- Register new tools and resources via the barrels in `src/mcp-server/*/definitions/index.ts`
+- Export new definitions from the barrels in `src/mcp-server/*/definitions/index.ts` and register them in the `createApp()` arrays in `src/index.ts`
 - Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields
 ## Upstream data licensing
-Structure and annotation data comes from public upstream databases, each under its own license. `protein_get_structure` and `protein_get_annotations` carry an `attribution` block on every response — the license, citation, and homepage for each source that contributed to that specific response — so the attribution obligation travels with the data to downstream consumers rather than living only here. CC BY / CC BY-SA sources require attribution on redistribution; CC0 sources are citation-only (attribution encouraged, not required).
+Structure and annotation data comes from public databases, each under its own license. `protein_get_structure` and `protein_get_annotations` return an `attribution` block with the license, citation, and homepage of every source that contributed to that response. CC BY and CC BY-SA sources require attribution on redistribution; CC0 sources ask only for citation.
 | Source | Contributes to | License |
 |:---|:---|:---|
@@ -353,7 +336,7 @@ Structure and annotation data comes from public upstream databases, each under i
 | [InterPro](https://www.ebi.ac.uk/interpro/) | `protein_get_annotations` — domain/family data | CC0 1.0 Universal |
 | [GO](https://geneontology.org/) | `protein_get_annotations` — GO terms | CC BY 4.0 |
-`best_available` federates predicted models through [3D-Beacons](https://3d-beacons.org/), so the `attribution` block credits the actual contributing provider (AlphaFold DB, SWISS-MODEL, BFVD, …); a provider without a curated license entry carries a `See provider terms` fallback pointing back to 3D-Beacons rather than a fabricated license. InterPro's own domain/family classifications are CC0; the GO terms carried alongside them are separately CC BY 4.0, so each is credited independently only when it actually contributes. Full citations for each source travel in the `attribution` block of the relevant tool responses. This covers upstream *data* licensing — the server's own code is licensed separately (see [License](#license)).
+`best_available` models arrive through [3D-Beacons](https://3d-beacons.org/), so the block credits the provider that actually supplied the model; a provider with no curated entry gets a `See provider terms` fallback instead of a guessed license. InterPro and GO are credited separately, each only when it contributes. This table covers upstream data; the server's own code is licensed separately (see [License](#license)).
 ## Contributing

package/changelog/0.8.x/0.8.6.md ADDED Viewed

@@ -0,0 +1,22 @@
+---
+summary: "Framework ^0.13.6 → ^0.13.13: tool errors carry a request ID, declared recovery hints are filled in by the framework, and error data no longer carries stacks or request context; Docker builds install in a build-platform deps stage, and the registry's npm entries launch through npx with the HTTP entry pinned to HTTP."
+breaking: false
+security: false
+---
+# 0.8.6 — 2026-10-07
+## Changed
+- **Framework `@cyanheads/mcp-ts-core` ^0.13.6 → ^0.13.13** — tool error results carry `data.requestId` and end with `request <id>` (0.13.10); declared recovery hints are filled by the framework, hint text unchanged (0.13.10); a JSON-stringified object or an integer sent for a string field is repaired before validation (0.13.9); stack traces, request context, and `rootCause` no longer reach error `data` (0.13.7, 0.13.8, 0.13.13); MCP SDK `@modelcontextprotocol/server` ^2.0.0 → ^2.2.0 (0.13.9, 0.13.11).
+- **Tool error recovery forwards** — the `ctx.recoveryFor(...)` arguments are gone from every `ctx.fail` call in the seven tool definitions, because the framework now attaches the declared hint itself. The recovery hints shipped before 0.8.6 too; what callers see is unchanged except for the added request ID.
+- **Dockerfile** (0.13.10, 0.13.11) — production dependencies install in a `deps` stage on the build platform, cross-installing for the target architecture, so multi-arch builds no longer run Bun under QEMU. Musl-only packages are pruned from the glibc image, the production stage no longer carries `bunfig.toml` or an install step, and the unread `ENV MCP_FORCE_CONSOLE_LOGGING` is gone. Bun base images 1.4.0 → 1.4.2.
+- **`server.json`** (0.13.11) — npm entries drop the `run start:*` arguments a registry client would hand the bin and set `runtimeHint: "npx"`; the `streamable-http` entry sets `MCP_TRANSPORT_TYPE` `value: "http"`, so a registry client launching it gets the HTTP transport.
+- **Packaging and docs** — `.env.example` documents the newer framework variables; `.env*` ignore rules, `!dist/*.mcpb` in `files`, and `/.cache/` and `/logs/` in `.mcpbignore` follow the 0.13.11 scaffold; the README tool and resource sections are condensed.
+- **Framework skills and scripts** resynced; `.github/workflows/codeql.yml` updated to the template's per-language jobs.
+## Dependencies
+- `@cyanheads/mcp-ts-core` ^0.13.6 → ^0.13.13
+- `@biomejs/biome` 2.5.14 → 2.5.15, `@socketsecurity/bun-security-scanner` ^1.1.2 → ^1.1.3, `@types/node` 26.6.2 → 26.6.4, `ignore` ^7.0.9 → ^7.0.12, `tsc-alias` ^1.9.5 → ^1.9.7, `vitest` ^5.0.1 → ^5.0.3 (all dev)
+- Bun 1.4.0 → 1.4.2 (`packageManager`, Docker base images)

package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/analyze-collection.tool.js CHANGED Viewed

@@ -124,11 +124,11 @@ export const analyzeCollection = tool('protein_analyze_collection', {
         // an undocumented shape no caller can read, so reject before the call.
         const duplicate = input.group_by.find((d, i, all) => all.indexOf(d) !== i);
         if (duplicate)
-            throw ctx.fail('duplicate_dimension', `group_by lists "${duplicate}" twice; a cross-tab needs two distinct dimensions.`, { ...ctx.recoveryFor('duplicate_dimension') });
+            throw ctx.fail('duplicate_dimension', `group_by lists "${duplicate}" twice; a cross-tab needs two distinct dimensions.`);
         // An override no requested position can consume would reach RCSB as nothing at
         // all — the call would succeed with default bins, looking like a filtered result.
         if (input.interval !== undefined && !intervalTarget(input.interval, primary, secondary))
-            throw ctx.fail('interval_not_applicable', `interval ${input.interval} does not apply to ${input.group_by.join(' or ')}; only ${INTERVAL_DIMENSION_NAMES.join(', ')} bin by an interval, and a numeric width needs resolution or molecular_weight while "year" needs release_year.`, { ...ctx.recoveryFor('interval_not_applicable') });
+            throw ctx.fail('interval_not_applicable', `interval ${input.interval} does not apply to ${input.group_by.join(' or ')}; only ${INTERVAL_DIMENSION_NAMES.join(', ')} bin by an interval, and a numeric width needs resolution or molecular_weight while "year" needs release_year.`);
         const spec = buildFacetSpec(primary, input.interval, secondary);
         const { total, facets } = await rcsb.analyzeFacets({
             ...(input.query ? { text: input.query } : {}),

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package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6HjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA0L5B~~,CAAC"}
1	+ {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6HjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsL5B,CAAC"}

package/dist/mcp-server/tools/definitions/compare-structures.tool.js CHANGED Viewed

@@ -144,7 +144,7 @@ export const compareStructures = tool('protein_compare_structures', {
         }
         if (unique.length < 2) {
             const [only] = unique;
-            throw ctx.fail('no_distinct_pair', `Every entry in structures[] denotes ${only ? label(only) : 'one structure'}; there is no second structure to align it against.`, { ...ctx.recoveryFor('no_distinct_pair') });
+            throw ctx.fail('no_distinct_pair', `Every entry in structures[] denotes ${only ? label(only) : 'one structure'}; there is no second structure to align it against.`);
         }
         const structures = unique.slice(0, cfg.maxCompareStructures);
         if (unique.length > cfg.maxCompareStructures) {
@@ -162,7 +162,7 @@ export const compareStructures = tool('protein_compare_structures', {
             for (const r of input.resume) {
                 const key = pairKey(r.a, r.b);
                 if (!validKeys.has(key)) {
-                    throw ctx.fail('resume_pair_unmatched', `Resume entry ${r.a} ↔ ${r.b} matches no pair in the current structures/reference set.`, { ...ctx.recoveryFor('resume_pair_unmatched') });
+                    throw ctx.fail('resume_pair_unmatched', `Resume entry ${r.a} ↔ ${r.b} matches no pair in the current structures/reference set.`);
                 }
                 resumeByPair.set(key, r.uuid);
             }
@@ -209,9 +209,7 @@ export const compareStructures = tool('protein_compare_structures', {
             return { ...base, status: 'failed', error: outcome.error };
         });
         if (rejection) {
-            throw ctx.fail(rejection.reason, rejection.message, {
-                ...ctx.recoveryFor(rejection.reason),
-            });
+            throw ctx.fail(rejection.reason, rejection.message);
         }
         const computing = rows.filter((r) => r.status === 'computing').length;
         const failed = rows.filter((r) => r.status === 'failed').length;

package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/find-similar.tool.js CHANGED Viewed

@@ -299,7 +299,7 @@ async function runStructure(input, timeoutMs, ctx) {
         });
     }
     if (outcome.status === 'not_found') {
-        throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`, { ...ctx.recoveryFor('ticket_not_found') });
+        throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`);
     }
     if (outcome.status === 'failed') {
         throw ctx.fail('search_failed', `Foldseek search failed: ${outcome.error}`, {
@@ -403,18 +403,16 @@ async function resolveSequence(input, ctx) {
     if (input.pdb_id) {
         const seq = await getRcsbService().getSequence(input.pdb_id, ctx);
         if (!seq)
-            throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
+            throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`);
         return seq.sequence;
     }
     if (input.uniprot) {
         const seq = await getUniProtService().getSequence(input.uniprot, ctx);
         if (!seq)
-            throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
+            throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`);
         return seq;
     }
-    throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.', {
-        ...ctx.recoveryFor('missing_query'),
-    });
+    throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.');
 }
 /** Resolve a query coordinate file (mmCIF or PDB-format text) from a PDB ID or UniProt accession. */
 async function resolveCoordinateFile(input, ctx) {
@@ -428,7 +426,7 @@ async function resolveCoordinateFile(input, ctx) {
     if (input.uniprot && isUniProtAccession(input.uniprot)) {
         const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);
         if (!model?.pdbUrl) {
-            throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
+            throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`);
         }
         return {
             content: await fetchCoordinateText(model.pdbUrl, ctx),