@cyanheads/protein-mcp-server 0.2.1 → 0.3.1

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Files changed (29) hide show
  1. package/AGENTS.md +3 -2
  2. package/CLAUDE.md +3 -2
  3. package/README.md +21 -2
  4. package/changelog/0.3.x/0.3.0.md +20 -0
  5. package/changelog/0.3.x/0.3.1.md +16 -0
  6. package/dist/mcp-server/tools/definitions/_schemas.d.ts +10 -0
  7. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/_schemas.js +19 -0
  9. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +22 -1
  11. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/get-annotations.tool.js +114 -4
  13. package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +9 -0
  15. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/get-structure.tool.js +72 -13
  17. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  18. package/dist/services/rcsb/rcsb-service.d.ts +9 -3
  19. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  20. package/dist/services/rcsb/rcsb-service.js +24 -11
  21. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  22. package/dist/services/rcsb/types.d.ts +9 -0
  23. package/dist/services/rcsb/types.d.ts.map +1 -1
  24. package/dist/services/shared/attribution.d.ts +42 -0
  25. package/dist/services/shared/attribution.d.ts.map +1 -0
  26. package/dist/services/shared/attribution.js +111 -0
  27. package/dist/services/shared/attribution.js.map +1 -0
  28. package/package.json +1 -1
  29. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.2.1
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+ **Version:** 0.3.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -80,7 +80,8 @@ export const getAnnotations = tool('protein_get_annotations', {
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  async handler(input, ctx) {
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  let accession = input.uniprot?.toUpperCase();
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  if (!accession && input.pdb_id) {
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- accession = (await getRcsbService().resolveUniprot(input.pdb_id, ctx))[0];
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+ // entity-grained; the real handler picks deterministically by author chain
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+ accession = (await getRcsbService().resolveUniprotEntities(input.pdb_id, ctx))[0]?.accession;
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  }
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  if (!accession || !isUniProtAccession(accession)) {
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  throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.2.1
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+ **Version:** 0.3.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -80,7 +80,8 @@ export const getAnnotations = tool('protein_get_annotations', {
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  async handler(input, ctx) {
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  let accession = input.uniprot?.toUpperCase();
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  if (!accession && input.pdb_id) {
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- accession = (await getRcsbService().resolveUniprot(input.pdb_id, ctx))[0];
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+ // entity-grained; the real handler picks deterministically by author chain
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+ accession = (await getRcsbService().resolveUniprotEntities(input.pdb_id, ctx))[0]?.accession;
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  }
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  if (!accession || !isUniProtAccession(accession)) {
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  throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.2.1-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-^1.29.0-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-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.3.1-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-^1.29.0-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-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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  </div>
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@@ -62,6 +62,7 @@ Fetch structures with metadata and coordinate-file URLs, resolving across provid
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  - `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
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  - Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
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  - `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
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+ - Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
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  ---
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@@ -119,8 +120,10 @@ Sequence and functional annotation for a protein.
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  - UniProt features (domains, binding sites, PTMs) and natural sequence variants
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  - InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
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- - Provide a UniProt accession directly, or a PDB ID — resolved to its accession via the structure's sequence cross-reference
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+ - Provide a UniProt accession directly, or a PDB ID — resolved to a UniProt accession via the structure's sequence cross-reference
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+ - A multi-chain PDB entry can map to several accessions; the default is the deterministic lowest-author-chain pick, with the alternatives listed under `ambiguity`. Pass `chain` (an author chain ID, e.g. `A`) to select a specific one
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  - `include` scopes which annotation classes are fetched: `features`, `domains`, `variants`, or `all`
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+ - Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
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  ## Resources
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@@ -340,6 +343,22 @@ bun run devcheck
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  bun run test
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  ```
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+ ## Upstream data licensing
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+
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+ 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).
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+
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+ | Source | Contributes to | License |
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+ |:---|:---|:---|
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+ | [RCSB PDB](https://www.rcsb.org/) | `protein_get_structure` — experimental records | CC0 1.0 Universal |
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+ | [AlphaFold DB](https://alphafold.ebi.ac.uk/) | `protein_get_structure` — predicted models | CC BY 4.0 |
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+ | [SWISS-MODEL](https://swissmodel.expasy.org/) | `protein_get_structure` — `best_available` models | CC BY-SA 4.0 |
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+ | [BFVD](https://bfvd.steineggerlab.workers.dev/) | `protein_get_structure` — `best_available` models | CC BY 4.0 |
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+ | [UniProt](https://www.uniprot.org/) | `protein_get_annotations` | CC BY 4.0 |
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+ | [InterPro](https://www.ebi.ac.uk/interpro/) | `protein_get_annotations` — domain/family data | CC0 1.0 Universal |
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+ | [GO](https://geneontology.org/) | `protein_get_annotations` — GO terms | CC BY 4.0 |
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+
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+ `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)).
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+
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  ## License
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363
 
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  Apache-2.0 — see [LICENSE](LICENSE) for details.
package/changelog/0.3.x/0.3.0.md ADDED
@@ -0,0 +1,20 @@
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+ ---
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+ summary: "protein_get_annotations disambiguates multi-chain PDB entries via a new chain input; protein_get_structure and protein_get_annotations both carry upstream data-source attribution (license + citation)."
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+ breaking: false
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+ security: false
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+ ---
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+
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+ # 0.3.0 — 2026-07-03
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+
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+ ## Added
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+
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+ - **`protein_get_annotations` `chain`** — optional author chain ID (`auth_asym_id`) input disambiguates a multi-chain PDB entry to a specific UniProt accession; ignored when `uniprot` is supplied directly. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
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+ - **`protein_get_annotations` `ambiguity`** — new optional output field listing every distinct UniProt mapping (chains, accession, protein name) and a notice, present when a PDB ID resolves to more than one accession and no `chain` was given. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
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+ - **`chain_not_found`** — new declared error reason on `protein_get_annotations` for a supplied `chain` that matches no UniProt-mapped polymer entity in the resolved entry. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
14
+ - **`attribution`** — new output field on `protein_get_structure` and `protein_get_annotations`: license, citation, and homepage for every upstream source that contributed to the response (RCSB PDB, AlphaFold DB, SWISS-MODEL, BFVD, UniProt, InterPro, GO). `best_available` credits the real federated 3D-Beacons provider; an uncurated provider gets an honest "See provider terms" fallback rather than a fabricated license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
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+ - **README** — "Upstream data licensing" section documenting each source's license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
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+
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+ ## Changed
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+
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+ - **`RcsbService.resolveUniprot()`** → `resolveUniprotEntities()` — returns entity-grained `UniProtXref[]` (chains, accession, protein name) instead of a flat accession list. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
20
+ - **`protein_get_annotations` unqualified PDB resolution** — now picks the deterministic lowest-author-chain accession instead of an order dependent on upstream GraphQL entity ordering. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
package/changelog/0.3.x/0.3.1.md ADDED
@@ -0,0 +1,16 @@
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+ ---
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+ summary: "best_available confidence scores are now scale-correct and self-describing instead of overloading meanPlddt; experimental best_available picks return the full cif/pdb/bcif coordinate set, matching source: experimental."
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+ breaking: false
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+ security: false
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+ ---
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+
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+ # 0.3.1 — 2026-07-03
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+
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+ ## Changed
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+
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+ - **`protein_get_structure` description** — clarifies that `best_available`'s experimental pick optimizes for resolution, not biological representativeness (it can return an engineered mutant over the wild-type entry). ([#16](https://github.com/cyanheads/protein-mcp-server/issues/16))
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+
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+ ## Fixed
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+
15
+ - **`protein_get_structure` (`best_available`)** — a non-pLDDT provider score (e.g. SWISS-MODEL's QMEANDisCo, 0–1 scale) no longer populates the pLDDT-scaled `meanPlddt` field (0–100 scale). New `confidence` + `confidenceType` output fields carry the score on its native scale and name the metric; `meanPlddt` now populates only when `confidenceType` is `pLDDT`. ([#14](https://github.com/cyanheads/protein-mcp-server/issues/14))
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+ - **`protein_get_structure` (`best_available`)** — an experimental pick now returns the full `cif`/`pdb`/`bcif` coordinate-file URL set from RCSB, matching `source: experimental`, instead of the single 3D-Beacons `modelUrl`. ([#16](https://github.com/cyanheads/protein-mcp-server/issues/16))
package/dist/mcp-server/tools/definitions/_schemas.d.ts CHANGED
@@ -29,4 +29,14 @@ export type FacetDimensionOutput = z.infer<typeof facetDimensionSchema>;
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  export declare function toFacetOutput(facet: FacetDimension, cap: number): FacetDimensionOutput;
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  /** Render a list of facet dimensions to markdown lines for `format()` parity. */
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  export declare function renderFacets(facets: FacetDimensionOutput[]): string[];
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+ /** License + citation for one upstream data source that contributed to a response. */
33
+ export declare const attributionSchema: z.ZodObject<{
34
+ source: z.ZodString;
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+ license: z.ZodString;
36
+ citation: z.ZodString;
37
+ homepage: z.ZodString;
38
+ }, z.core.$strip>;
39
+ export type AttributionOutput = z.infer<typeof attributionSchema>;
40
+ /** Render an attribution list to one compact markdown line per source for `format()` parity. */
41
+ export declare function renderAttribution(attributions: AttributionOutput[]): string[];
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  //# sourceMappingURL=_schemas.d.ts.map
package/dist/mcp-server/tools/definitions/_schemas.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAoC/D,yCAAyC;AACzC,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;iBAW4B,CAAC;AAE9D,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,oFAAoF;AACpF,wBAAgB,aAAa,CAAC,KAAK,EAAE,cAAc,EAAE,GAAG,EAAE,MAAM,GAAG,oBAAoB,CAmBtF;AAED,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAarE"}
1
+ {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAoC/D,yCAAyC;AACzC,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;iBAW4B,CAAC;AAE9D,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,oFAAoF;AACpF,wBAAgB,aAAa,CAAC,KAAK,EAAE,cAAc,EAAE,GAAG,EAAE,MAAM,GAAG,oBAAoB,CAmBtF;AAED,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAarE;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E"}
package/dist/mcp-server/tools/definitions/_schemas.js CHANGED
@@ -84,4 +84,23 @@ export function renderFacets(facets) {
84
84
  }
85
85
  return lines;
86
86
  }
87
+ /** License + citation for one upstream data source that contributed to a response. */
88
+ export const attributionSchema = z
89
+ .object({
90
+ source: z
91
+ .string()
92
+ .describe('Contributing data-source display name (e.g. "RCSB PDB", "AlphaFold DB", "SWISS-MODEL", "UniProt"). Open-ended — best_available structures are federated through 3D-Beacons providers.'),
93
+ license: z.string().describe('License the source data is released under (e.g. "CC BY 4.0").'),
94
+ citation: z.string().describe('Primary-literature citation to credit the source.'),
95
+ homepage: z.string().describe('Source homepage (absolute URL).'),
96
+ })
97
+ .describe('Upstream data-source attribution: license, citation, and homepage.');
98
+ /** Render an attribution list to one compact markdown line per source for `format()` parity. */
99
+ export function renderAttribution(attributions) {
100
+ const lines = [];
101
+ for (const a of attributions) {
102
+ lines.push(`- **${a.source}** (${a.license}) — ${a.citation} — ${a.homepage}`);
103
+ }
104
+ return lines;
105
+ }
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  //# sourceMappingURL=_schemas.js.map
package/dist/mcp-server/tools/definitions/_schemas.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/D,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;IACvF,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,iFAAiF,CAAC;CAC/F,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,oBAAoB,CAAC;SAC3B,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F,yCAAyC;AACzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC3F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAI9D,oFAAoF;AACpF,MAAM,UAAU,aAAa,CAAC,KAAqB,EAAE,GAAW;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC;IAC7C,OAAO;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,GAAG,CAAC,CAAC,CAAC,QAAQ;gBACZ,CAAC,CAAC;oBACE,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAC/B,SAAS,EAAE,CAAC,CAAC,SAAS;wBACtB,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;wBACpF,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;qBACvD,CAAC,CAAC;iBACJ;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;QACH,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KAC1C,CAAC;AACJ,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,IAAI,EAAE,EAAE,CAAC;gBACjC,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC3E,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
1
+ {"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/D,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;IACvF,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,iFAAiF,CAAC;CAC/F,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,oBAAoB,CAAC;SAC3B,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F,yCAAyC;AACzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC3F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAI9D,oFAAoF;AACpF,MAAM,UAAU,aAAa,CAAC,KAAqB,EAAE,GAAW;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC;IAC7C,OAAO;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,GAAG,CAAC,CAAC,CAAC,QAAQ;gBACZ,CAAC,CAAC;oBACE,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAC/B,SAAS,EAAE,CAAC,CAAC,SAAS;wBACtB,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;wBACpF,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;qBACvD,CAAC,CAAC;iBACJ;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;QACH,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KAC1C,CAAC;AACJ,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,IAAI,EAAE,EAAE,CAAC;gBACjC,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC3E,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,sFAAsF;AACtF,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,CAAC;IACN,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,CACP,uLAAuL,CACxL;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+DAA+D,CAAC;IAC7F,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CACjE,CAAC;KACD,QAAQ,CAAC,oEAAoE,CAAC,CAAC;AAIlF,gGAAgG;AAChG,MAAM,UAAU,iBAAiB,CAAC,YAAiC;IACjE,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,YAAY,EAAE,CAAC;QAC7B,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,MAAM,OAAO,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;IACjF,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts CHANGED
@@ -2,7 +2,8 @@
2
2
  * @fileoverview protein_get_annotations — sequence & functional annotation for a
3
3
  * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
4
4
  * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
5
- * PDB ID to its accession when needed.
5
+ * PDB ID to its accession when needed — deterministically by default, by author
6
+ * chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
6
7
  * @module mcp-server/tools/definitions/get-annotations.tool
7
8
  */
8
9
  import { z } from '@cyanheads/mcp-ts-core';
@@ -10,6 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
11
  export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
11
12
  uniprot: z.ZodOptional<z.ZodString>;
12
13
  pdb_id: z.ZodOptional<z.ZodString>;
14
+ chain: z.ZodOptional<z.ZodString>;
13
15
  include: z.ZodDefault<z.ZodEnum<{
14
16
  all: "all";
15
17
  features: "features";
@@ -46,11 +48,30 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
46
48
  category: z.ZodOptional<z.ZodString>;
47
49
  }, z.core.$strip>>;
48
50
  }, z.core.$strip>>>;
51
+ ambiguity: z.ZodOptional<z.ZodObject<{
52
+ accessions: z.ZodArray<z.ZodObject<{
53
+ chain: z.ZodArray<z.ZodString>;
54
+ accession: z.ZodString;
55
+ proteinName: z.ZodOptional<z.ZodString>;
56
+ }, z.core.$strip>>;
57
+ notice: z.ZodString;
58
+ }, z.core.$strip>>;
59
+ attribution: z.ZodArray<z.ZodObject<{
60
+ source: z.ZodString;
61
+ license: z.ZodString;
62
+ citation: z.ZodString;
63
+ homepage: z.ZodString;
64
+ }, z.core.$strip>>;
49
65
  }, z.core.$strip>, readonly [{
50
66
  readonly reason: "no_uniprot_mapping";
51
67
  readonly code: JsonRpcErrorCode.NotFound;
52
68
  readonly when: "A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.";
53
69
  readonly recovery: "Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.";
70
+ }, {
71
+ readonly reason: "chain_not_found";
72
+ readonly code: JsonRpcErrorCode.NotFound;
73
+ readonly when: "A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.";
74
+ readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).";
54
75
  }], {
55
76
  readonly resolvedFrom: z.ZodOptional<z.ZodString>;
56
77
  readonly notice: z.ZodOptional<z.ZodString>;
package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4CjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2IzB,CAAC"}
1
+ {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6NzB,CAAC"}
package/dist/mcp-server/tools/definitions/get-annotations.tool.js CHANGED
@@ -2,14 +2,17 @@
2
2
  * @fileoverview protein_get_annotations — sequence & functional annotation for a
3
3
  * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
4
4
  * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
5
- * PDB ID to its accession when needed.
5
+ * PDB ID to its accession when needed — deterministically by default, by author
6
+ * chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
6
7
  * @module mcp-server/tools/definitions/get-annotations.tool
7
8
  */
8
9
  import { tool, z } from '@cyanheads/mcp-ts-core';
9
10
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
11
  import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
12
+ import { attributionsFor } from '../../../services/shared/attribution.js';
11
13
  import { isUniProtAccession } from '../../../services/shared/identifiers.js';
12
14
  import { getUniProtService } from '../../../services/uniprot/uniprot-service.js';
15
+ import { attributionSchema, renderAttribution } from './_schemas.js';
13
16
  const featureSchema = z
14
17
  .object({
15
18
  type: z.string().describe('Feature type (e.g. Domain, Binding site, Modified residue).'),
@@ -40,12 +43,33 @@ const domainSchema = z
40
43
  .describe('Associated GO terms.'),
41
44
  })
42
45
  .describe('An InterPro domain/family membership with GO terms.');
46
+ const ambiguitySchema = z
47
+ .object({
48
+ accessions: z
49
+ .array(z
50
+ .object({
51
+ chain: z
52
+ .array(z.string())
53
+ .describe('Author chain IDs (auth_asym_id) this entity covers (e.g. ["A", "C"]).'),
54
+ accession: z.string().describe('UniProt accession the chains map to.'),
55
+ proteinName: z.string().optional().describe('Polymer entity description.'),
56
+ })
57
+ .describe('One chain-group → UniProt accession mapping within the entry.'))
58
+ .describe('Every distinct UniProt mapping for the entry, lowest-chain first.'),
59
+ notice: z
60
+ .string()
61
+ .describe('Why multiple mappings exist and how to select one via the chain input.'),
62
+ })
63
+ .describe('Present only when a PDB ID mapped to more than one distinct UniProt accession and no chain was supplied. The returned accession is the deterministic lowest-chain pick — re-call with chain set to a specific author chain ID to select another.');
43
64
  export const getAnnotations = tool('protein_get_annotations', {
44
65
  title: 'protein-mcp-server: get annotations',
45
66
  description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
46
67
  'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
47
68
  "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
48
- 'sequence cross-reference. Use the "include" parameter to scope which annotation classes are fetched.',
69
+ 'sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is ' +
70
+ 'deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to ' +
71
+ 'select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries ' +
72
+ 'an "attribution" block with the upstream data licenses and citations.',
49
73
  annotations: { readOnlyHint: true, openWorldHint: true },
50
74
  errors: [
51
75
  {
@@ -54,6 +78,12 @@ export const getAnnotations = tool('protein_get_annotations', {
54
78
  when: 'A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.',
55
79
  recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.',
56
80
  },
81
+ {
82
+ reason: 'chain_not_found',
83
+ code: JsonRpcErrorCode.NotFound,
84
+ when: 'A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.',
85
+ recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).',
86
+ },
57
87
  ],
58
88
  input: z.object({
59
89
  uniprot: z
@@ -64,6 +94,10 @@ export const getAnnotations = tool('protein_get_annotations', {
64
94
  .string()
65
95
  .optional()
66
96
  .describe('PDB entry ID; resolved to a UniProt accession via cross-reference.'),
97
+ chain: z
98
+ .string()
99
+ .optional()
100
+ .describe('Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].chains in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
67
101
  include: z
68
102
  .enum(['features', 'domains', 'variants', 'all'])
69
103
  .default('all')
@@ -79,6 +113,12 @@ export const getAnnotations = tool('protein_get_annotations', {
79
113
  features: z.array(featureSchema).optional().describe('Structural/functional features.'),
80
114
  variants: z.array(featureSchema).optional().describe('Natural sequence variants.'),
81
115
  domains: z.array(domainSchema).optional().describe('InterPro domain/family memberships.'),
116
+ ambiguity: ambiguitySchema
117
+ .optional()
118
+ .describe('Alternative UniProt mappings when a PDB ID resolved ambiguously (no chain given).'),
119
+ attribution: z
120
+ .array(attributionSchema)
121
+ .describe('Upstream data-source licenses and citations for every source that contributed to this response. Always present — the attribution obligation travels with the data.'),
82
122
  }),
83
123
  enrichment: {
84
124
  resolvedFrom: z
@@ -92,10 +132,37 @@ export const getAnnotations = tool('protein_get_annotations', {
92
132
  const rcsb = getRcsbService();
93
133
  let accession = input.uniprot?.toUpperCase();
94
134
  let resolvedFrom;
135
+ let ambiguity;
95
136
  if (!accession && input.pdb_id) {
96
- const accessions = await rcsb.resolveUniprot(input.pdb_id, ctx);
97
- accession = accessions[0];
137
+ const entities = await rcsb.resolveUniprotEntities(input.pdb_id, ctx);
98
138
  resolvedFrom = input.pdb_id.toUpperCase();
139
+ const chain = input.chain?.trim();
140
+ if (chain) {
141
+ const match = entities.find((e) => e.chains.includes(chain));
142
+ if (!match) {
143
+ const available = entities.flatMap((e) => e.chains);
144
+ throw ctx.fail('chain_not_found', `Chain "${chain}" matches no UniProt-mapped polymer entity in ${resolvedFrom}.`, {
145
+ recovery: {
146
+ hint: available.length
147
+ ? `Author chains in ${resolvedFrom}: ${available.join(', ')}. Pass one of these, or omit chain for the deterministic default mapping.`
148
+ : `${resolvedFrom} exposes no UniProt-mapped protein chains. Pass a UniProt accession directly.`,
149
+ },
150
+ });
151
+ }
152
+ accession = match.accession;
153
+ }
154
+ else {
155
+ // Deterministic default: order entities by their lowest author chain ID and
156
+ // take the first, so the same entry always yields the same accession
157
+ // regardless of upstream GraphQL entity ordering. When more than one distinct
158
+ // accession exists, surface the alternatives so the caller can pick a chain.
159
+ const ordered = orderByLowestChain(entities);
160
+ accession = ordered[0]?.accession;
161
+ const distinct = new Set(entities.map((e) => e.accession));
162
+ if (accession && distinct.size > 1) {
163
+ ambiguity = buildAmbiguity(resolvedFrom, accession, ordered, distinct.size);
164
+ }
165
+ }
99
166
  }
100
167
  if (!accession) {
101
168
  throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
@@ -115,6 +182,15 @@ export const getAnnotations = tool('protein_get_annotations', {
115
182
  const variants = entry.features.filter((f) => f.category === 'variant');
116
183
  const wantFeatures = include === 'features' || include === 'all';
117
184
  const wantVariants = include === 'variants' || include === 'all';
185
+ // Attribution rides with the data. UniProt always contributes on success;
186
+ // InterPro only when it returned entries; GO only when a returned entry carries
187
+ // GO terms. InterPro (CC0) and GO (CC BY 4.0) are gated independently — an
188
+ // InterPro entry can exist with zero GO terms.
189
+ const sources = new Set(['UniProt']);
190
+ if (interpro.length > 0)
191
+ sources.add('InterPro');
192
+ if (interpro.some((d) => d.goTerms.length > 0))
193
+ sources.add('GO');
118
194
  if (resolvedFrom)
119
195
  ctx.enrich({ resolvedFrom });
120
196
  return {
@@ -127,6 +203,8 @@ export const getAnnotations = tool('protein_get_annotations', {
127
203
  ...(wantFeatures ? { features: toFeatureOutput(features) } : {}),
128
204
  ...(wantVariants ? { variants: toFeatureOutput(variants) } : {}),
129
205
  ...(wantInterPro ? { domains: interpro } : {}),
206
+ ...(ambiguity ? { ambiguity } : {}),
207
+ attribution: attributionsFor(sources),
130
208
  };
131
209
  },
132
210
  format: (result) => {
@@ -142,6 +220,13 @@ export const getAnnotations = tool('protein_get_annotations', {
142
220
  lines.push(head.join(' | '));
143
221
  if (result.function)
144
222
  lines.push(`\n**Function:** ${result.function}`);
223
+ if (result.ambiguity) {
224
+ lines.push(`\n### Multiple UniProt mappings`);
225
+ lines.push(result.ambiguity.notice);
226
+ for (const m of result.ambiguity.accessions) {
227
+ lines.push(`- **${m.accession}**${m.proteinName ? ` — ${m.proteinName}` : ''} (chains ${m.chain.join(', ') || 'none'})`);
228
+ }
229
+ }
145
230
  if (result.features && result.features.length > 0) {
146
231
  lines.push(`\n### Features (${result.features.length})`);
147
232
  for (const f of result.features)
@@ -160,9 +245,34 @@ export const getAnnotations = tool('protein_get_annotations', {
160
245
  lines.push(` - ${g.id} ${g.name}${g.category ? ` [${g.category}]` : ''}`);
161
246
  }
162
247
  }
248
+ if (result.attribution.length > 0) {
249
+ lines.push(`\n### Attribution`);
250
+ lines.push(...renderAttribution(result.attribution));
251
+ }
163
252
  return [{ type: 'text', text: lines.join('\n') }];
164
253
  },
165
254
  });
255
+ /** Lowest author chain ID for an entity (code-unit order); '' when it has none. */
256
+ function lowestChain(entity) {
257
+ return [...entity.chains].sort()[0] ?? '';
258
+ }
259
+ /** Order UniProt xrefs by their lowest author chain ID — the deterministic default pick. */
260
+ function orderByLowestChain(entities) {
261
+ return [...entities].sort((a, b) => lowestChain(a).localeCompare(lowestChain(b)));
262
+ }
263
+ /** Assemble the ambiguity block: every distinct mapping, lowest-chain first, with a notice. */
264
+ function buildAmbiguity(entryId, chosen, ordered, distinctCount) {
265
+ return {
266
+ accessions: ordered.map((e) => ({
267
+ chain: e.chains,
268
+ accession: e.accession,
269
+ ...(e.proteinName ? { proteinName: e.proteinName } : {}),
270
+ })),
271
+ notice: `${entryId} maps to ${distinctCount} distinct UniProt accessions across its chains. ` +
272
+ `Returning ${chosen}, the deterministic lowest-chain pick. ` +
273
+ 'Re-call with chain set to a specific author chain ID to select another.',
274
+ };
275
+ }
166
276
  function toFeatureOutput(features) {
167
277
  return features.map((f) => ({
168
278
  type: f.type,
package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts CHANGED
@@ -4,6 +4,7 @@
4
4
  * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
5
5
  * coordinate-file content; when that overflows a byte budget it returns a
6
6
  * per-structure section outline for targeted re-call instead of truncating.
7
+ * Carries upstream data attribution (RCSB PDB / AlphaFold DB) per response.
7
8
  * @module mcp-server/tools/definitions/get-structure.tool
8
9
  */
9
10
  import { z } from '@cyanheads/mcp-ts-core';
@@ -30,6 +31,8 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
30
31
  resolution: z.ZodOptional<z.ZodNumber>;
31
32
  organism: z.ZodOptional<z.ZodString>;
32
33
  provider: z.ZodOptional<z.ZodString>;
34
+ confidence: z.ZodOptional<z.ZodNumber>;
35
+ confidenceType: z.ZodOptional<z.ZodString>;
33
36
  meanPlddt: z.ZodOptional<z.ZodNumber>;
34
37
  confidenceBuckets: z.ZodOptional<z.ZodObject<{
35
38
  veryLow: z.ZodNumber;
@@ -54,6 +57,12 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
54
57
  id: z.ZodString;
55
58
  reason: z.ZodString;
56
59
  }, z.core.$strip>>;
60
+ attribution: z.ZodArray<z.ZodObject<{
61
+ source: z.ZodString;
62
+ license: z.ZodString;
63
+ citation: z.ZodString;
64
+ homepage: z.ZodString;
65
+ }, z.core.$strip>>;
57
66
  overflow: z.ZodOptional<z.ZodObject<{
58
67
  sections: z.ZodArray<z.ZodObject<{
59
68
  id: z.ZodString;
package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsQvB,CAAC"}