@cyanheads/protein-mcp-server 0.1.4 → 0.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +7 -6
- package/changelog/0.2.x/0.2.0.md +25 -0
- package/changelog/0.2.x/0.2.1.md +16 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +6 -1
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts +12 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js +70 -11
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.js +42 -19
- package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js +4 -2
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js +16 -4
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
- package/dist/services/alignment/alignment-service.d.ts +8 -0
- package/dist/services/alignment/alignment-service.d.ts.map +1 -1
- package/dist/services/alignment/alignment-service.js +24 -0
- package/dist/services/alignment/alignment-service.js.map +1 -1
- package/dist/services/foldseek/foldseek-service.d.ts +15 -1
- package/dist/services/foldseek/foldseek-service.d.ts.map +1 -1
- package/dist/services/foldseek/foldseek-service.js +30 -0
- package/dist/services/foldseek/foldseek-service.js.map +1 -1
- package/package.json +4 -4
- package/server.json +3 -3
package/AGENTS.md
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 0.2.1
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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
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**Zod:** ^4.4.3
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package/CLAUDE.md
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 0.2.1
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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
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**Zod:** ^4.4.3
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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| `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. |
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| `protein_find_similar` | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession. |
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| `protein_track_ligands` | Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues. |
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| `protein_compare_structures` | Structurally align
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| `protein_compare_structures` | Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix. |
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| `protein_analyze_collection` | Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs. |
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| `protein_get_annotations` | Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms. |
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- `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases
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- Query from a raw one-letter sequence, a PDB ID, or a UniProt accession
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- Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
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- Async jobs that exceed the poll budget return `status: computing` with a
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- Async jobs that exceed the poll budget return `status: computing` with a `ticketId` — re-call with `ticket_id` set to that value to poll the same job instead of resubmitting
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- Each hit names the engine and source database it came from
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---
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### `protein_compare_structures`
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Structural alignment of
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Structural alignment of multiple structures (up to the configured `PROTEIN_MAX_COMPARE_STRUCTURES` cap) via the RCSB Structural Comparison service.
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- Methods: `tm-align`, `fatcat-rigid`, `fatcat-flexible`
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- `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix
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- Optional per-structure `chain` restricts the alignment to a single chain
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- Each pair is an independent async job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns `status: computing` with its job
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- Each pair is an independent async job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns `status: computing` with its job `uuid`, and a failed pair degrades its row without sinking the others
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- Re-call with a matching `{ a, b, uuid }` entry in `resume[]` (copied from a prior response's `pairs[]`) to poll a computing pair's job instead of resubmitting
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- Returns TM-score, RMSD, and aligned-residue count per pair
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---
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- One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same
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- Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision
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- Corpus analytics run server-side on RCSB's facet engine — distributions, histograms, and cross-tabs in one call, no row pull and no SQL workspace
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- Async alignment and Foldseek jobs poll within a bounded budget and hand back a
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- 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
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Agent-friendly output:
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---
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summary: "Resume protein_find_similar and protein_compare_structures jobs by ticket/UUID instead of resubmitting; compare_structures structures cap widened to the configured 2–25 range with a truncation notice; dependency refresh clears a moderate js-yaml advisory."
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breaking: false
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security: true
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---
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# 0.2.0 — 2026-07-03
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## Added
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- **`protein_find_similar`** — new optional `ticket_id` input. When set on a `by:"structure"` call, polls the existing Foldseek job instead of resolving coordinates and submitting a new search; `pdb_id`/`uniprot`/`databases` are ignored. New error reason `ticket_not_found` when the ticket is invalid or expired. ([#8](https://github.com/cyanheads/protein-mcp-server/issues/8))
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- **`protein_compare_structures`** — new optional `resume` input: an array of `{ a, b, uuid }` entries copied from a prior response's `pairs[]`. A pair whose labels match a `resume` entry (order- and case-insensitive) polls the given UUID instead of submitting a fresh alignment job; unmatched pairs still submit fresh. New error reason `resume_pair_unmatched` when a `resume` entry's labels don't match any pair generated from `structures` + `reference`. ([#8](https://github.com/cyanheads/protein-mcp-server/issues/8))
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- **`AlignmentService.resumePair`** / **`FoldseekService.resume`** — service-level resume methods backing the two tools above. Both reuse the existing polling step and never throw; `resumePair` treats a `404` as `computing` (the RCSB alignment API returns the same 404 for an expired UUID and a job still in flight, so it can't safely report not-found), while `resume` distinguishes a Foldseek `400 "invalid ID"` as a genuine `not_found`.
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## Changed
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- **`protein_compare_structures`** — `structures` cap widened from a hardcoded `.max(10)` to `.max(25)`, matching the existing `PROTEIN_MAX_COMPARE_STRUCTURES` config ceiling (2–25, default 10). A request exceeding the configured cap now surfaces a truncation notice (previously silent). Tool and field descriptions reworded off the hardcoded "2–10" language to describe the configured cap. ([#11](https://github.com/cyanheads/protein-mcp-server/issues/11))
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- **Dependencies:**
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- `@cyanheads/mcp-ts-core` ^0.10.9 → ^0.10.10
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- `@biomejs/biome` 2.5.1 → 2.5.2 (dev)
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- `@types/node` 26.0.0 → 26.1.0 (dev)
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## Security
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- **`js-yaml`** — the dependency refresh (`@cyanheads/mcp-ts-core` bump + lockfile re-resolve) moves the transitive `js-yaml` resolution from 3.14.2 to 3.15.0, clearing [GHSA-h67p-54hq-rp68](https://github.com/advisories/GHSA-h67p-54hq-rp68) (quadratic-complexity ReDoS in `js-yaml < 3.15.0`). `bun audit`: 1 moderate → 0.
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---
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summary: "Nested cross-tab facet children now carry a truncated flag; declared error recovery hints reach the wire; protein_track_ligands binding_site honors limit."
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breaking: false
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security: false
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---
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# 0.2.1 — 2026-07-03
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## Added
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- **`protein_analyze_collection` / `protein_search_structures`** — nested cross-tab facet child dimensions now carry a `truncated` boolean when their bucket list is capped by `bucket_limit`; `renderFacets` appends `(truncated)` to the nested line in `content[]`. ([#13](https://github.com/cyanheads/protein-mcp-server/issues/13))
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## Fixed
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- **`protein_track_ligands` `binding_site`** — now caps returned instances to `limit` and emits a truncation notice, instead of returning every instance regardless of `limit`. ([#9](https://github.com/cyanheads/protein-mcp-server/issues/9))
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- **Declared recovery hints** — `errors[].recovery` now reaches the wire (`data.recovery.hint`, mirrored into `content[]`) at throw sites across `protein_search_structures`, `protein_get_annotations`, `protein_get_structure`, `protein_find_similar`, `protein_track_ligands`, and `protein_analyze_collection`. ([#10](https://github.com/cyanheads/protein-mcp-server/issues/10))
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{"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;
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{"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"}
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.object({
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dimension: z.string().describe('Nested dimension name.'),
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buckets: z.array(leafBucketSchema).describe('Nested buckets within the parent bucket.'),
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truncated: z
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.boolean()
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.optional()
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.describe('True when this nested bucket list was capped by the per-dimension bucket limit.'),
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/** A top-level facet bucket, optionally carrying a nested cross-tab dimension. */
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{"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;
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{"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"}
|
|
@@ -45,6 +45,7 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
|
|
|
45
45
|
label: z.ZodString;
|
|
46
46
|
count: z.ZodNumber;
|
|
47
47
|
}, z.core.$strip>>;
|
|
48
|
+
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
48
49
|
}, z.core.$strip>>>;
|
|
49
50
|
}, z.core.$strip>>;
|
|
50
51
|
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB
|
|
1
|
+
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyH5B,CAAC"}
|
|
@@ -86,7 +86,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
|
|
|
86
86
|
: 'experimental';
|
|
87
87
|
const [primary, secondary] = input.group_by;
|
|
88
88
|
if (!primary)
|
|
89
|
-
throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.'
|
|
89
|
+
throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.', {
|
|
90
|
+
...ctx.recoveryFor('unknown_dimension'),
|
|
91
|
+
});
|
|
90
92
|
const spec = buildFacetSpec(primary, input.interval, secondary);
|
|
91
93
|
const { total, facets } = await rcsb.analyzeFacets({
|
|
92
94
|
...(input.query ? { text: input.query } : {}),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,CAAC;iBACE,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;
|
|
1
|
+
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,CAAC;iBACE,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;YACV,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,2CAA2C,EAAE;gBAC/E,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,MAAM,IAAI,GAAG,cAAc,CAAC,OAAO,EAAE,KAAK,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QAEhE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAChD;YACE,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,aAAa,EAAE,KAAK,CAAC,cAAc,EAAE;gBACzC,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxC,EACD,CAAC,IAAI,CAAC,EACN,GAAG,CACJ,CAAC;QAEF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;QACrD,IAAI,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,mCAAmC,GAAG,sEAAsE,CAC7G,CAAC;QACJ,CAAC;QACD,MAAM,SAAS,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC9E,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAChC,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,2BAA2B,MAAM,CAAC,KAAK,UAAU,CAAC,CAAC;QAC5E,KAAK,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QAC3C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -6,6 +6,7 @@
|
|
|
6
6
|
* @module mcp-server/tools/definitions/compare-structures.tool
|
|
7
7
|
*/
|
|
8
8
|
import { z } from '@cyanheads/mcp-ts-core';
|
|
9
|
+
import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
|
|
9
10
|
export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
|
|
10
11
|
structures: z.ZodArray<z.ZodObject<{
|
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pdb_id: z.ZodString;
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@@ -21,6 +22,11 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
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"fatcat-flexible": "fatcat-flexible";
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}>>;
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timeout_s: z.ZodOptional<z.ZodNumber>;
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resume: z.ZodOptional<z.ZodArray<z.ZodObject<{
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a: z.ZodString;
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b: z.ZodString;
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uuid: z.ZodString;
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}, z.core.$strip>>>;
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}, z.core.$strip>, z.ZodObject<{
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method: z.ZodString;
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reference: z.ZodEnum<{
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@@ -41,7 +47,12 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
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uuid: z.ZodOptional<z.ZodString>;
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error: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>>;
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}, z.core.$strip>,
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}, z.core.$strip>, readonly [{
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readonly reason: "resume_pair_unmatched";
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readonly code: JsonRpcErrorCode.InvalidParams;
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readonly when: "A resume entry's a/b labels don't match any pair generated from structures + reference.";
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readonly recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.";
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}], {
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readonly pairsTotal: z.ZodNumber;
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readonly computing: z.ZodNumber;
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readonly notice: z.ZodOptional<z.ZodString>;
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@@ -1 +1 @@
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1
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-
{"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;
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1
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{"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;AAgGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgI5B,CAAC"}
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@@ -6,6 +6,7 @@
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* @module mcp-server/tools/definitions/compare-structures.tool
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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import { getServerConfig } from '../../../config/server-config.js';
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import { getAlignmentService } from '../../../services/alignment/alignment-service.js';
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import { mapWithConcurrency } from '../../../services/shared/async.js';
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@@ -21,8 +22,8 @@ const inputSchema = z.object({
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})
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.describe('A structure to align, by PDB entry ID with optional chain.'))
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.min(2)
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.max(
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.describe('The
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.max(25)
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.describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice).'),
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reference: z
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.enum(['first', 'all_pairs'])
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.default('first')
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@@ -38,6 +39,25 @@ const inputSchema = z.object({
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.max(120)
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.optional()
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.describe('Poll budget per pair in seconds before returning "computing". Defaults to the server setting.'),
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resume: z
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.array(z
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.object({
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a: z
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.string()
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.min(1)
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.describe('First structure label (entry or entry.chain) of a pair from a prior response.'),
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b: z
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.string()
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.min(1)
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.describe('Second structure label (entry or entry.chain) of a pair from a prior response.'),
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uuid: z
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.string()
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.min(1)
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.describe('Alignment job UUID returned for that pair by a prior call.'),
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})
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.describe('A prior pair to resume by UUID instead of resubmitting.'))
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.optional()
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.describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures and reference unchanged."),
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});
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const outputSchema = z.object({
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method: z.string().describe('Alignment method used.'),
|
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@@ -62,13 +82,22 @@ const outputSchema = z.object({
|
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});
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|
export const compareStructures = tool('protein_compare_structures', {
|
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title: 'protein-mcp-server: compare structures',
|
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65
|
-
description: 'Structurally align
|
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66
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-
'reference:"first" aligns every structure to the first;
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'matrix. Each pair is an independent async alignment
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'partial success — a pair still computing when the
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'
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-
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+
description: 'Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural ' +
|
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+
'Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; ' +
|
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87
|
+
'reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment ' +
|
|
88
|
+
'job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the ' +
|
|
89
|
+
'budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without ' +
|
|
90
|
+
"sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead " +
|
|
91
|
+
'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair.',
|
|
71
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|
annotations: { readOnlyHint: true, openWorldHint: true },
|
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|
+
errors: [
|
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|
+
{
|
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+
reason: 'resume_pair_unmatched',
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|
+
code: JsonRpcErrorCode.InvalidParams,
|
|
97
|
+
when: "A resume entry's a/b labels don't match any pair generated from structures + reference.",
|
|
98
|
+
recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.",
|
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|
+
},
|
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100
|
+
],
|
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|
input: inputSchema,
|
|
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|
output: outputSchema,
|
|
74
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|
enrichment: {
|
|
@@ -79,12 +108,33 @@ export const compareStructures = tool('protein_compare_structures', {
|
|
|
79
108
|
async handler(input, ctx) {
|
|
80
109
|
const cfg = getServerConfig();
|
|
81
110
|
const structures = input.structures.slice(0, cfg.maxCompareStructures);
|
|
111
|
+
const notices = [];
|
|
112
|
+
if (input.structures.length > cfg.maxCompareStructures) {
|
|
113
|
+
notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${input.structures.length - cfg.maxCompareStructures} ignored.`);
|
|
114
|
+
}
|
|
82
115
|
const timeoutMs = input.timeout_s ? input.timeout_s * 1000 : cfg.asyncPollTimeoutMs;
|
|
83
116
|
const method = input.method;
|
|
84
117
|
const pairs = buildPairs(structures, input.reference);
|
|
118
|
+
// Map each supplied resume ticket to a pair. A ticket that matches no pair in
|
|
119
|
+
// the current structures/reference set is a client error — fail loudly rather
|
|
120
|
+
// than silently resubmit and burn a fresh alignment job.
|
|
121
|
+
const resumeByPair = new Map();
|
|
122
|
+
if (input.resume?.length) {
|
|
123
|
+
const validKeys = new Set(pairs.map(([a, b]) => pairKey(label(a), label(b))));
|
|
124
|
+
for (const r of input.resume) {
|
|
125
|
+
const key = pairKey(r.a, r.b);
|
|
126
|
+
if (!validKeys.has(key)) {
|
|
127
|
+
throw ctx.fail('resume_pair_unmatched', `Resume entry ${r.a} ↔ ${r.b} matches no pair in the current structures/reference set.`, { ...ctx.recoveryFor('resume_pair_unmatched') });
|
|
128
|
+
}
|
|
129
|
+
resumeByPair.set(key, r.uuid);
|
|
130
|
+
}
|
|
131
|
+
}
|
|
85
132
|
const alignment = getAlignmentService();
|
|
86
133
|
const rows = await mapWithConcurrency(pairs, cfg.fanoutConcurrency, async ([a, b]) => {
|
|
87
|
-
const
|
|
134
|
+
const resumeUuid = resumeByPair.get(pairKey(label(a), label(b)));
|
|
135
|
+
const outcome = resumeUuid
|
|
136
|
+
? await alignment.resumePair(resumeUuid, timeoutMs, ctx)
|
|
137
|
+
: await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
|
|
88
138
|
const base = { a: label(a), b: label(b) };
|
|
89
139
|
if (outcome.status === 'complete') {
|
|
90
140
|
return {
|
|
@@ -109,9 +159,11 @@ export const compareStructures = tool('protein_compare_structures', {
|
|
|
109
159
|
const failed = rows.filter((r) => r.status === 'failed').length;
|
|
110
160
|
ctx.enrich({ pairsTotal: rows.length, computing });
|
|
111
161
|
if (computing > 0 || failed > 0) {
|
|
112
|
-
|
|
113
|
-
`Re-call
|
|
162
|
+
notices.push(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
|
|
163
|
+
`Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s.`);
|
|
114
164
|
}
|
|
165
|
+
if (notices.length > 0)
|
|
166
|
+
ctx.enrich.notice(notices.join(' '));
|
|
115
167
|
return { method, reference: input.reference, pairs: rows };
|
|
116
168
|
},
|
|
117
169
|
format: (result) => {
|
|
@@ -165,4 +217,11 @@ function toCompare(s) {
|
|
|
165
217
|
function label(s) {
|
|
166
218
|
return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
|
|
167
219
|
}
|
|
220
|
+
/**
|
|
221
|
+
* Canonical, order- and case-insensitive key for a pair of structure labels, so a
|
|
222
|
+
* resume entry matches its pair regardless of which side the client copied first.
|
|
223
|
+
*/
|
|
224
|
+
function pairKey(a, b) {
|
|
225
|
+
return [a.toUpperCase(), b.toUpperCase()].sort().join('');
|
|
226
|
+
}
|
|
168
227
|
//# sourceMappingURL=compare-structures.tool.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"compare-structures.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAE5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,2CAA2C,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAEhE,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,UAAU,EAAE,CAAC;SACV,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,eAAe,CAAC;QACnD,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;KAClF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC,CAC1E;SACA,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,QAAQ,
|
|
1
|
+
{"version":3,"file":"compare-structures.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAE5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,2CAA2C,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAEhE,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,UAAU,EAAE,CAAC;SACV,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,eAAe,CAAC;QACnD,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;KAClF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC,CAC1E;SACA,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,QAAQ,CACP,8FAA8F,CAC/F;IACH,SAAS,EAAE,CAAC;SACT,IAAI,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;SAC5B,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,CAAC,wEAAwE,CAAC;IACrF,MAAM,EAAE,CAAC;SACN,IAAI,CAAC,CAAC,UAAU,EAAE,cAAc,EAAE,iBAAiB,CAAC,CAAC;SACrD,OAAO,CAAC,UAAU,CAAC;SACnB,QAAQ,CAAC,kEAAkE,CAAC;IAC/E,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;IACH,MAAM,EAAE,CAAC;SACN,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,CAAC,EAAE,CAAC;aACD,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,+EAA+E,CAChF;QACH,CAAC,EAAE,CAAC;aACD,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,gFAAgF,CACjF;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;SACD,QAAQ,CAAC,yDAAyD,CAAC,CACvE;SACA,QAAQ,EAAE;SACV,QAAQ,CACP,4PAA4P,CAC7P;CACJ,CAAC,CAAC;AAEH,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACrD,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAC3E,KAAK,EAAE,CAAC;SACL,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACtE,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACvE,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACtF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAClF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACxE,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACnF,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;KACxE,CAAC;SACD,QAAQ,CAAC,2CAA2C,CAAC,CACzD;SACA,QAAQ,CAAC,2BAA2B,CAAC;CACzC,CAAC,CAAC;AAIH,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,kGAAkG;QAClG,uGAAuG;QACvG,wGAAwG;QACxG,0GAA0G;QAC1G,wGAAwG;QACxG,8EAA8E;IAChF,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,uBAAuB;YAC/B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,yFAAyF;YAC/F,QAAQ,EACN,8IAA8I;SACjJ;KACF;IAED,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IAEpB,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC5D,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAClE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;KACnF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,UAAU,GAAG,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,oBAAoB,CAAC,CAAC;QACvE,MAAM,OAAO,GAAa,EAAE,CAAC;QAC7B,IAAI,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,GAAG,CAAC,oBAAoB,EAAE,CAAC;YACvD,OAAO,CAAC,IAAI,CACV,aAAa,GAAG,CAAC,oBAAoB,gBAAgB,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,GAAG,CAAC,oBAAoB,WAAW,CACnH,CAAC;QACJ,CAAC;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;QACpF,MAAM,MAAM,GAAG,KAAK,CAAC,MAAyB,CAAC;QAE/C,MAAM,KAAK,GAAG,UAAU,CAAC,UAAU,EAAE,KAAK,CAAC,SAAS,CAAC,CAAC;QAEtD,8EAA8E;QAC9E,8EAA8E;QAC9E,yDAAyD;QACzD,MAAM,YAAY,GAAG,IAAI,GAAG,EAAkB,CAAC;QAC/C,IAAI,KAAK,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC;YACzB,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC9E,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;gBAC7B,MAAM,GAAG,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC9B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxB,MAAM,GAAG,CAAC,IAAI,CACZ,uBAAuB,EACvB,gBAAgB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,2DAA2D,EACvF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,uBAAuB,CAAC,EAAE,CAChD,CAAC;gBACJ,CAAC;gBACD,YAAY,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC;YAChC,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAG,mBAAmB,EAAE,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,kBAAkB,CAAC,KAAK,EAAE,GAAG,CAAC,iBAAiB,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;YACnF,MAAM,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACjE,MAAM,OAAO,GAAG,UAAU;gBACxB,CAAC,CAAC,MAAM,SAAS,CAAC,UAAU,CAAC,UAAU,EAAE,SAAS,EAAE,GAAG,CAAC;gBACxD,CAAC,CAAC,MAAM,SAAS,CAAC,WAAW,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,CAAC,CAAC;YACpF,MAAM,IAAI,GAAG,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;YAC1C,IAAI,OAAO,CAAC,MAAM,KAAK,UAAU,EAAE,CAAC;gBAClC,OAAO;oBACL,GAAG,IAAI;oBACP,MAAM,EAAE,UAAmB;oBAC3B,IAAI,EAAE,OAAO,CAAC,IAAI;oBAClB,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,OAAO,KAAK,QAAQ;wBAC5C,CAAC,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,OAAO,EAAE;wBACrC,CAAC,CAAC,EAAE,CAAC;oBACP,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;oBACjF,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,eAAe,KAAK,QAAQ;wBACpD,CAAC,CAAC,EAAE,eAAe,EAAE,OAAO,CAAC,MAAM,CAAC,eAAe,EAAE;wBACrD,CAAC,CAAC,EAAE,CAAC;iBACR,CAAC;YACJ,CAAC;YACD,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBACnC,OAAO,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,WAAoB,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,CAAC;YACvE,CAAC;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,QAAiB,EAAE,KAAK,EAAE,OAAO,CAAC,KAAK,EAAE,CAAC;QACtE,CAAC,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,WAAW,CAAC,CAAC,MAAM,CAAC;QACtE,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QAChE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;QACnD,IAAI,SAAS,GAAG,CAAC,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,IAAI,CACV,GAAG,SAAS,2BAA2B,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,MAAM,SAAS,CAAC,CAAC,CAAC,EAAE,IAAI;gBAC/E,0JAA0J,CAC7J,CAAC;QACJ,CAAC;QACD,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QAE7D,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;IAC7D,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,MAAM,KAAK,MAAM,CAAC,SAAS,GAAG,CAAC,CAAC;QAC5F,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;QAClE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACpC,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YACtE,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YAClE,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,eAAe,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YACxF,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,MAAM,EAAE,MAAM,IAAI,MAAM,OAAO,IAAI,CAAC,CAAC;QACjF,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC;QAC5D,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;gBACtB,IAAI,CAAC,CAAC,KAAK;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBACzD,IAAI,CAAC,CAAC,IAAI;oBACR,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,MAAM,KAAK,WAAW,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CACpF,CAAC;YACN,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC;AAEH,SAAS,UAAU,CACjB,UAAyB,EACzB,SAAgC;IAEhC,MAAM,KAAK,GAAsC,EAAE,CAAC;IACpD,IAAI,SAAS,KAAK,OAAO,EAAE,CAAC;QAC1B,MAAM,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,GAAG,UAAU,CAAC;QAClC,IAAI,GAAG;YAAE,KAAK,MAAM,CAAC,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;IACtD,CAAC;SAAM,CAAC;QACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;YACxB,IAAI,CAAC,CAAC;gBAAE,SAAS;YACjB,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;gBACxB,IAAI,CAAC;oBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,SAAS,CAAC,CAAc;IAC/B,OAAO,EAAE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC;AACxE,CAAC;AAED,SAAS,KAAK,CAAC,CAAc;IAC3B,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,WAAW,EAAE,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;AACnF,CAAC;AAED;;;GAGG;AACH,SAAS,OAAO,CAAC,CAAS,EAAE,CAAS;IACnC,OAAO,CAAC,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAC7D,CAAC"}
|
|
@@ -15,6 +15,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
|
|
|
15
15
|
sequence: z.ZodOptional<z.ZodString>;
|
|
16
16
|
pdb_id: z.ZodOptional<z.ZodString>;
|
|
17
17
|
uniprot: z.ZodOptional<z.ZodString>;
|
|
18
|
+
ticket_id: z.ZodOptional<z.ZodString>;
|
|
18
19
|
databases: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
19
20
|
max_evalue: z.ZodOptional<z.ZodNumber>;
|
|
20
21
|
min_identity: z.ZodOptional<z.ZodNumber>;
|
|
@@ -60,6 +61,11 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
|
|
|
60
61
|
readonly when: "The Foldseek search service rejected or failed the structure job.";
|
|
61
62
|
readonly retryable: true;
|
|
62
63
|
readonly recovery: "Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.";
|
|
64
|
+
}, {
|
|
65
|
+
readonly reason: "ticket_not_found";
|
|
66
|
+
readonly code: JsonRpcErrorCode.NotFound;
|
|
67
|
+
readonly when: "The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.";
|
|
68
|
+
readonly recovery: "Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.";
|
|
63
69
|
}], {
|
|
64
70
|
totalCount: z.ZodOptional<z.ZodNumber>;
|
|
65
71
|
notice: z.ZodOptional<z.ZodString>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuEtB,CAAC"}
|
|
@@ -26,6 +26,10 @@ const inputSchema = z.object({
|
|
|
26
26
|
.describe('One-letter amino-acid sequence to search from (by:sequence).'),
|
|
27
27
|
pdb_id: z.string().optional().describe('PDB entry ID to derive the query from.'),
|
|
28
28
|
uniprot: z.string().optional().describe('UniProt accession to derive the query from.'),
|
|
29
|
+
ticket_id: z
|
|
30
|
+
.string()
|
|
31
|
+
.optional()
|
|
32
|
+
.describe('Foldseek ticket ID from a prior by:structure response whose status was "computing". When set, polls that existing job instead of submitting a new search (by:structure only) — pdb_id/uniprot/databases are ignored.'),
|
|
29
33
|
databases: z
|
|
30
34
|
.array(z.string())
|
|
31
35
|
.optional()
|
|
@@ -48,7 +52,7 @@ const outputSchema = z.object({
|
|
|
48
52
|
engine: z.string().describe('The engine that answered (e.g. "RCSB mmseqs2", "Foldseek").'),
|
|
49
53
|
status: z
|
|
50
54
|
.enum(['complete', 'computing'])
|
|
51
|
-
.describe('complete with hits, or computing (async
|
|
55
|
+
.describe('complete with hits, or computing (async — re-call with ticket_id to resume).'),
|
|
52
56
|
ticketId: z
|
|
53
57
|
.string()
|
|
54
58
|
.optional()
|
|
@@ -93,8 +97,8 @@ export const findSimilar = tool('protein_find_similar', {
|
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'sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID ' +
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'or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against ' +
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'experimental and predicted databases; if the job is still computing when the poll budget elapses, the ' +
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'response reports status "computing" with a ticket — re-call
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'database each hit came from.',
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'response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume ' +
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'the same job instead of resubmitting. Output names the engine and database each hit came from.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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errors: [
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{
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@@ -116,6 +120,12 @@ export const findSimilar = tool('protein_find_similar', {
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retryable: true,
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recovery: 'Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.',
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},
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{
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reason: 'ticket_not_found',
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code: JsonRpcErrorCode.NotFound,
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when: 'The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.',
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recovery: 'Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.',
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},
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],
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input: inputSchema,
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output: outputSchema,
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@@ -129,7 +139,7 @@ export const findSimilar = tool('protein_find_similar', {
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format: (result) => {
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const lines = [`## ${result.engine} (by:${result.by}) — ${result.status}`];
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if (result.ticketId)
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lines.push(`**Ticket:** ${result.ticketId} — re-call to resume.`);
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lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id to resume.`);
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for (const h of result.hits) {
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lines.push(`\n### ${h.id} _(${h.source})_`);
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if (h.title)
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@@ -182,15 +192,26 @@ async function runSequence(input, enrichLimit, ctx) {
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};
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}
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async function runStructure(input, timeoutMs, ctx) {
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const
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+
const foldseek = getFoldseekService();
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+
let outcome;
|
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|
+
if (input.ticket_id) {
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|
+
// Resume path: poll the existing ticket, skipping coordinate resolution + submit.
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|
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|
+
outcome = await foldseek.resume({ ticketId: input.ticket_id, limit: input.limit, timeoutMs }, ctx);
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|
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|
+
}
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|
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+
else {
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|
+
const { content, fileName } = await resolveCoordinateFile(input, ctx);
|
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|
+
outcome = await foldseek.search({
|
|
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|
+
fileContent: content,
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|
+
fileName,
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|
+
databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
|
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|
+
mode: FOLDSEEK_MODE,
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|
+
limit: input.limit,
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|
+
timeoutMs,
|
|
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|
+
}, ctx);
|
|
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|
+
}
|
|
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|
+
if (outcome.status === 'not_found') {
|
|
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|
+
throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`, { ...ctx.recoveryFor('ticket_not_found') });
|
|
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|
+
}
|
|
194
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|
if (outcome.status === 'failed') {
|
|
195
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|
throw ctx.fail('search_failed', `Foldseek search failed: ${outcome.error}`, {
|
|
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|
recovery: {
|
|
@@ -199,7 +220,7 @@ async function runStructure(input, timeoutMs, ctx) {
|
|
|
199
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|
});
|
|
200
221
|
}
|
|
201
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|
if (outcome.status === 'computing') {
|
|
202
|
-
ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar to resume.`);
|
|
223
|
+
ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}" to resume.`);
|
|
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224
|
return {
|
|
204
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|
by: 'structure',
|
|
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|
engine: 'Foldseek',
|
|
@@ -232,16 +253,18 @@ async function resolveSequence(input, ctx) {
|
|
|
232
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|
if (input.pdb_id) {
|
|
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254
|
const seq = await getRcsbService().getSequence(input.pdb_id, ctx);
|
|
234
255
|
if (!seq)
|
|
235
|
-
throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}
|
|
256
|
+
throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
236
257
|
return seq.sequence;
|
|
237
258
|
}
|
|
238
259
|
if (input.uniprot) {
|
|
239
260
|
const seq = await getUniProtService().getSequence(input.uniprot, ctx);
|
|
240
261
|
if (!seq)
|
|
241
|
-
throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}
|
|
262
|
+
throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
242
263
|
return seq;
|
|
243
264
|
}
|
|
244
|
-
throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.'
|
|
265
|
+
throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.', {
|
|
266
|
+
...ctx.recoveryFor('missing_query'),
|
|
267
|
+
});
|
|
245
268
|
}
|
|
246
269
|
/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
|
|
247
270
|
async function resolveCoordinateFile(input, ctx) {
|
|
@@ -254,14 +277,14 @@ async function resolveCoordinateFile(input, ctx) {
|
|
|
254
277
|
if (input.uniprot && isUniProtAccession(input.uniprot)) {
|
|
255
278
|
const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);
|
|
256
279
|
if (!model?.pdbUrl) {
|
|
257
|
-
throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}
|
|
280
|
+
throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
258
281
|
}
|
|
259
282
|
return {
|
|
260
283
|
content: await fetchCoordinateText(model.pdbUrl, ctx),
|
|
261
284
|
fileName: `${input.uniprot.toUpperCase()}.pdb`,
|
|
262
285
|
};
|
|
263
286
|
}
|
|
264
|
-
throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.');
|
|
287
|
+
throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.', { ...ctx.recoveryFor('missing_query') });
|
|
265
288
|
}
|
|
266
289
|
function fetchCoordinateText(url, ctx) {
|
|
267
290
|
return fetchText(url, ctx, {
|