@cyanheads/protein-mcp-server 0.5.1 → 0.5.3

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Files changed (26) hide show
  1. package/AGENTS.md +8 -8
  2. package/CLAUDE.md +8 -8
  3. package/Dockerfile +2 -2
  4. package/README.md +7 -2
  5. package/changelog/0.5.x/0.5.2.md +22 -0
  6. package/changelog/0.5.x/0.5.3.md +20 -0
  7. package/dist/index.js +15 -0
  8. package/dist/index.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts +3 -0
  10. package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/find-similar.tool.js +20 -3
  12. package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +6 -2
  14. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/search-structures.tool.js +36 -8
  16. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts +3 -0
  18. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/track-ligands.tool.js +21 -2
  20. package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
  21. package/dist/services/rcsb/rcsb-service.d.ts +2 -0
  22. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  23. package/dist/services/rcsb/rcsb-service.js +5 -5
  24. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  25. package/package.json +6 -6
  26. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,10 +1,10 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.5.1
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
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+ **Version:** 0.5.3
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
6
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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- **MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0
7
+ **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
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  **Zod:** ^4.4.3
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  **TypeScript:** ^7.0.2
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@@ -36,7 +36,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
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  - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
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  - **Use `ctx.log`** for request-scoped logging. No `console` calls.
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  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
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- - **Check `ctx.elicit`** for presence before calling.
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+ - **Need input the caller didn't supply?** `return ctx.requestInput(...)` and read `ctx.inputs` when the handler is re-entered. Never `await` for user input mid-handler.
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  - **Secrets in env vars only** — never hardcoded.
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  - **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
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@@ -188,13 +188,13 @@ Handlers receive a unified `ctx` object. Key properties:
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  | Property | Description |
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  |:---------|:------------|
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- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
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+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
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  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
193
- | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
193
+ | `ctx.requestInput` | Suspend and ask the caller for more input — `return ctx.requestInput({ inputRequests: { key: inputRequired.elicit({ message, requestedSchema }) } })`. Never returns; the handler is re-entered with the answers. Always present. |
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+ | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. Empty on the first round. |
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  | `ctx.enrich` | Success-path agent context (empty-result notices, query echo, pagination totals) — `ctx.enrich(...)` or `.notice()` / `.total()` / `.echo()` / `.truncated()`. Reaches `structuredContent` and `content[]`; lands only when the definition declares an `enrichment` block (no-op otherwise). |
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  | `ctx.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
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  | `ctx.signal` | `AbortSignal` for cancellation. |
197
- | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
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  | `ctx.requestId` | Unique request ID. |
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  | `ctx.tenantId` | Tenant ID from JWT; `'default'` for stdio or HTTP with auth off. |
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@@ -313,7 +313,7 @@ Available skills:
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  | `api-auth` | Auth modes, scopes, JWT/OAuth |
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  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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  | `api-config` | AppConfig, parseConfig, env vars |
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- | `api-context` | Context interface, logger, state, progress |
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+ | `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
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  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
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  | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
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  | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
package/CLAUDE.md CHANGED
@@ -1,10 +1,10 @@
1
1
  # Developer Protocol
2
2
 
3
3
  **Server:** protein-mcp-server
4
- **Version:** 0.5.1
5
- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
4
+ **Version:** 0.5.3
5
+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
6
6
  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
7
- **MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0
7
+ **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
8
8
  **Zod:** ^4.4.3
9
9
  **TypeScript:** ^7.0.2
10
10
 
@@ -36,7 +36,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
36
36
  - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
37
37
  - **Use `ctx.log`** for request-scoped logging. No `console` calls.
38
38
  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
39
- - **Check `ctx.elicit`** for presence before calling.
39
+ - **Need input the caller didn't supply?** `return ctx.requestInput(...)` and read `ctx.inputs` when the handler is re-entered. Never `await` for user input mid-handler.
40
40
  - **Secrets in env vars only** — never hardcoded.
41
41
  - **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
42
42
 
@@ -188,13 +188,13 @@ Handlers receive a unified `ctx` object. Key properties:
188
188
 
189
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  | Property | Description |
190
190
  |:---------|:------------|
191
- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
191
+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
192
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  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
193
- | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
193
+ | `ctx.requestInput` | Suspend and ask the caller for more input — `return ctx.requestInput({ inputRequests: { key: inputRequired.elicit({ message, requestedSchema }) } })`. Never returns; the handler is re-entered with the answers. Always present. |
194
+ | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. Empty on the first round. |
194
195
  | `ctx.enrich` | Success-path agent context (empty-result notices, query echo, pagination totals) — `ctx.enrich(...)` or `.notice()` / `.total()` / `.echo()` / `.truncated()`. Reaches `structuredContent` and `content[]`; lands only when the definition declares an `enrichment` block (no-op otherwise). |
195
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  | `ctx.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
196
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  | `ctx.signal` | `AbortSignal` for cancellation. |
197
- | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
198
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  | `ctx.requestId` | Unique request ID. |
199
199
  | `ctx.tenantId` | Tenant ID from JWT; `'default'` for stdio or HTTP with auth off. |
200
200
 
@@ -313,7 +313,7 @@ Available skills:
313
313
  | `api-auth` | Auth modes, scopes, JWT/OAuth |
314
314
  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
315
315
  | `api-config` | AppConfig, parseConfig, env vars |
316
- | `api-context` | Context interface, logger, state, progress |
316
+ | `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
317
317
  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
318
318
  | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
319
319
  | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
package/Dockerfile CHANGED
@@ -4,7 +4,7 @@
4
4
  # This stage installs all dependencies (including dev), builds the TypeScript
5
5
  # source code into JavaScript, and prepares the production assets.
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  # ==============================================================================
7
- FROM oven/bun:1.3.14 AS build
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+ FROM --platform=$BUILDPLATFORM oven/bun:1.4.0 AS build
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  WORKDIR /usr/src/app
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@@ -30,7 +30,7 @@ RUN bun run build
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  # application. It uses a slim base image and only includes production
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  # dependencies and build artifacts.
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  # ==============================================================================
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- FROM oven/bun:1.3.14-slim AS production
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+ FROM oven/bun:1.4.0-slim AS production
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  WORKDIR /usr/src/app
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package/README.md CHANGED
@@ -7,7 +7,7 @@
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8
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.5.1-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-^1.30.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
10
+ [![Version](https://img.shields.io/badge/Version-0.5.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
11
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12
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  </div>
13
13
 
@@ -47,7 +47,8 @@ Federated search across experimental (PDB) and predicted (computed-model) struct
47
47
 
48
48
  - Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
49
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  - `content_type` scopes the search to `experimental`, `predicted`, or `all` — the default `all` is a genuine union of both universes, so computed models appear alongside PDB entries
50
- - Every hit names its `source`; experimental hits are enriched with title, method, resolution, and organism, while computed models carry the UniProt accession parsed from their ID
50
+ - Every hit names its `source`; experimental sequence hits expose a chainable PDB entry `id` plus the matched polymer `entityId`, with title, method, resolution, and organism enrichment, while computed models retain their complete model ID and parsed UniProt accession
51
+ - `start` and `limit` page through ranked results; `nextStart` is returned while another page remains
51
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  - Optional `facets` return a method / organism / release-year breakdown alongside the hits at no extra call, each reporting how many matches carry no value for that dimension; each dimension may be listed once
52
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  - Chain hit IDs straight into `protein_get_structure`
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@@ -72,6 +73,7 @@ Find structurally or evolutionarily related proteins, by sequence or by fold.
72
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73
74
  - `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
76
+ - Sequence searches accept `start` with `limit` and return `nextStart` while another page remains
75
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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 `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
@@ -84,9 +86,12 @@ Ligand discovery and binding-site analysis across the PDB.
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85
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  - `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey
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  - `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID
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+ - `mode: structures_with_ligand` accepts `start` with `limit` and returns `nextStart` while another page remains
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  - `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances
88
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  - Binding sites are experimental-only — computed from deposited coordinates (predicted models carry no bound ligands)
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93
+ Paged RCSB results preserve the upstream order within each response. Resolution ties and changes in the live corpus mean traversal is best-effort across calls, not a stable export snapshot.
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+
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95
  ---
91
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92
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  ### `protein_compare_structures`
package/changelog/0.5.x/0.5.2.md ADDED
@@ -0,0 +1,22 @@
1
+ ---
2
+ summary: "Tool inputs are strict now — an unrecognized argument key is rejected instead of stripped — and cache hints let 2026-07-28 clients hold listings and resource reads for up to an hour; HTTP session mode is pinned to stateless."
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+ breaking: true
4
+ security: false
5
+ ---
6
+
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+ # 0.5.2 — 2026-08-25
8
+
9
+ ## Added
10
+
11
+ - **Cache hints**: `tools/list`, `resources/list`, `resources/templates/list`, `server/discover`, and `resources/read` all advertise `ttlMs: 3_600_000` (1 hour) at `cacheScope: 'public'` to protocol-revision-2026-07-28 clients — every listing is static per build, and the PDB/AlphaFold summary resources tolerate an hour of staleness.
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+
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+ ## Changed
14
+
15
+ - **Tool inputs are strict**: an unrecognized top-level argument key is now rejected by name (`-32602`) instead of silently stripped, and every tool's advertised `inputSchema` carries `additionalProperties: false` under JSON Schema 2020-12 (previously draft-07). A key nested inside an input object still strips.
16
+ - **`outputSchema` now declares the error envelope**: success fields advertise as optional and `error` is declared, so a client that validates `structuredContent` without checking `isError` no longer misreads an error result as schema-invalid.
17
+ - **HTTP session mode pinned to `stateless`**: `.env.example`'s `MCP_SESSION_MODE` is now set explicitly instead of left on the schema's `auto` default, which resolves to `stateful` — this server holds no per-session state.
18
+ - **Dependencies:**
19
+ - `@cyanheads/mcp-ts-core` ^0.11.5 → ^0.12.3 — adopts the framework's SDK v2 migration ([mcp-ts-core#305](https://github.com/cyanheads/mcp-ts-core/issues/305))
20
+ - `@modelcontextprotocol/sdk` ^1.30.0 → `@modelcontextprotocol/server` / `@modelcontextprotocol/client` ^2.0.0 (transitive via mcp-ts-core)
21
+ - Bun `1.3.14` → `1.4.0` — both `Dockerfile` stages and the `packageManager` pin; the build stage now targets `--platform=$BUILDPLATFORM` for the multi-arch image
22
+ - `@biomejs/biome` `2.5.8` → `2.5.10`, `tsc-alias` `^1.9.1` → `^1.9.2`, `vitest` `^4.1.10` → `^4.1.11` (dev)
package/changelog/0.5.x/0.5.3.md ADDED
@@ -0,0 +1,20 @@
1
+ ---
2
+ summary: "RCSB-backed tools support offset pagination; structure searches accept method or resolution criteria alone, retain chainable sequence-hit IDs, and enrich every entry on a returned sequence page."
3
+ breaking: false
4
+ security: false
5
+ ---
6
+
7
+ # 0.5.3 — 2026-08-30
8
+
9
+ ## Added
10
+
11
+ - **RCSB result pagination**: `protein_search_structures`, sequence-mode `protein_find_similar`, and `structures_with_ligand` mode in `protein_track_ligands` accept `start` and return `nextStart` while more results remain ([#41](https://github.com/cyanheads/protein-mcp-server/issues/41)).
12
+
13
+ ## Changed
14
+
15
+ - **Experimental sequence hits**: `protein_search_structures` exposes the chainable PDB entry as `id` and retains the matched polymer entity as `entityId` ([#39](https://github.com/cyanheads/protein-mcp-server/issues/39)).
16
+ - **Filter-only structure searches**: experimental `method` and `max_resolution` now form valid RCSB search criteria without text, sequence, or organism input ([#40](https://github.com/cyanheads/protein-mcp-server/issues/40)).
17
+
18
+ ## Fixed
19
+
20
+ - **Sequence-result enrichment**: `protein_find_similar` enriches every distinct entry returned on a sequence page instead of limiting metadata by the facet bucket cap ([#44](https://github.com/cyanheads/protein-mcp-server/issues/44)).
package/dist/index.js CHANGED
@@ -31,6 +31,21 @@ await createApp({
31
31
  prompts: [],
32
32
  // Public, keyless data server — serve the full inventory to unauthenticated callers.
33
33
  landing: { requireAuth: false },
34
+ /**
35
+ * Cache hints for protocol revision 2026-07-28. Every listing is static per
36
+ * build and identical for every caller — no auth-gated definitions, no
37
+ * per-tenant filtering — so a shared cache may hold them. `resources/read`
38
+ * serves PDB and AlphaFold summaries, whose upstreams publish on a weekly
39
+ * (PDB) and per-release (AlphaFold) cadence; an hour of staleness sits well
40
+ * inside both. 2025-era responses are unaffected either way.
41
+ */
42
+ cacheHints: {
43
+ 'tools/list': { ttlMs: 3_600_000, cacheScope: 'public' },
44
+ 'resources/list': { ttlMs: 3_600_000, cacheScope: 'public' },
45
+ 'resources/templates/list': { ttlMs: 3_600_000, cacheScope: 'public' },
46
+ 'server/discover': { ttlMs: 3_600_000, cacheScope: 'public' },
47
+ 'resources/read': { ttlMs: 3_600_000, cacheScope: 'public' },
48
+ },
34
49
  instructions: 'protein-mcp-server federates experimental (PDB) and predicted (AlphaFold) protein structures: search structures by text, sequence, or organism/method/resolution (protein_search_structures); fetch metadata and coordinate URLs for PDB IDs or UniProt accessions (protein_get_structure); find sequence or fold homologs via mmseqs2 or Foldseek (protein_find_similar); resolve ligands and map binding-site residues (protein_track_ligands); align 2–10 structures with TM-align or jFATCAT (protein_compare_structures); profile the PDB with server-side facet distributions and trends (protein_analyze_collection); and pull UniProt features plus InterPro domains and GO terms (protein_get_annotations).',
35
50
  setup(core) {
36
51
  const serverConfig = getServerConfig();
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,YAAY,EACV,srBAAsrB;IACxrB,KAAK,CAAC,IAAI;QACR,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;QACvC,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,mBAAmB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;IAC/D,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B;;;;;;;OAOG;IACH,UAAU,EAAE;QACV,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACxD,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KAC7D;IACD,YAAY,EACV,srBAAsrB;IACxrB,KAAK,CAAC,IAAI;QACR,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;QACvC,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,mBAAmB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;IAC/D,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts CHANGED
@@ -20,6 +20,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
20
20
  max_evalue: z.ZodOptional<z.ZodNumber>;
21
21
  min_identity: z.ZodOptional<z.ZodNumber>;
22
22
  limit: z.ZodDefault<z.ZodNumber>;
23
+ start: z.ZodDefault<z.ZodNumber>;
23
24
  }, z.core.$strip>, z.ZodObject<{
24
25
  by: z.ZodEnum<{
25
26
  sequence: "sequence";
@@ -69,6 +70,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
69
70
  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.";
70
71
  }], {
71
72
  totalCount: z.ZodOptional<z.ZodNumber>;
73
+ start: z.ZodOptional<z.ZodNumber>;
74
+ nextStart: z.ZodOptional<z.ZodNumber>;
72
75
  notice: z.ZodOptional<z.ZodString>;
73
76
  }>;
74
77
  //# sourceMappingURL=find-similar.tool.d.ts.map
package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map CHANGED
@@ -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;AAkHjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwEtB,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;AA6HjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwEtB,CAAC"}
package/dist/mcp-server/tools/definitions/find-similar.tool.js CHANGED
@@ -46,6 +46,12 @@ const inputSchema = z.object({
46
46
  .optional()
47
47
  .describe('Minimum sequence identity 0–1 (by:sequence). Default 0.'),
48
48
  limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
49
+ start: z
50
+ .number()
51
+ .int()
52
+ .min(0)
53
+ .default(0)
54
+ .describe('Zero-based result offset (by:sequence only).'),
49
55
  });
50
56
  const outputSchema = z.object({
51
57
  by: z.enum(['sequence', 'structure']).describe('Echoed similarity axis.'),
@@ -95,6 +101,11 @@ const enrichmentShape = {
95
101
  .number()
96
102
  .optional()
97
103
  .describe('Total upstream matches before pagination (by:sequence).'),
104
+ start: z.number().optional().describe('Zero-based offset of the sequence-result page.'),
105
+ nextStart: z
106
+ .number()
107
+ .optional()
108
+ .describe('Offset for the next sequence-result page; absent on the final or past-end page.'),
98
109
  notice: z.string().optional().describe('Advisory note (still computing, empty results).'),
99
110
  };
100
111
  export const findSimilar = tool('protein_find_similar', {
@@ -139,7 +150,7 @@ export const findSimilar = tool('protein_find_similar', {
139
150
  handler(input, ctx) {
140
151
  const cfg = getServerConfig();
141
152
  if (input.by === 'sequence')
142
- return runSequence(input, cfg.facetBucketCap, ctx);
153
+ return runSequence(input, ctx);
143
154
  return runStructure(input, cfg.asyncPollTimeoutMs, ctx);
144
155
  },
145
156
  format: (result) => {
@@ -165,21 +176,27 @@ export const findSimilar = tool('protein_find_similar', {
165
176
  return [{ type: 'text', text: lines.join('\n') }];
166
177
  },
167
178
  });
168
- async function runSequence(input, enrichLimit, ctx) {
179
+ async function runSequence(input, ctx) {
169
180
  const rcsb = getRcsbService();
170
181
  const sequence = await resolveSequence(input, ctx);
171
182
  const result = await rcsb.searchSequence(sequence, {
172
183
  ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
173
184
  ...(typeof input.min_identity === 'number' ? { minIdentity: input.min_identity } : {}),
174
185
  limit: input.limit,
186
+ start: input.start,
175
187
  }, ctx);
176
- const entryIds = [...new Set(result.hits.map((h) => entryIdOf(h.id)))].slice(0, enrichLimit);
188
+ const entryIds = [...new Set(result.hits.map((h) => entryIdOf(h.id)))];
177
189
  const metaById = new Map();
178
190
  if (entryIds.length > 0) {
179
191
  for (const meta of await rcsb.getEntries(entryIds, ctx))
180
192
  metaById.set(meta.id, meta);
181
193
  }
182
194
  ctx.enrich.total(result.total);
195
+ const nextStart = input.start + result.hits.length;
196
+ ctx.enrich({
197
+ start: input.start,
198
+ ...(nextStart < result.total ? { nextStart } : {}),
199
+ });
183
200
  if (result.hits.length === 0)
184
201
  ctx.enrich.notice('No sequence-similar entries found. Lower min_identity or raise max_evalue.');
185
202
  return {
package/dist/mcp-server/tools/definitions/find-similar.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts CHANGED
@@ -29,9 +29,11 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
29
29
  resolution: "resolution";
30
30
  }>>>;
31
31
  limit: z.ZodDefault<z.ZodNumber>;
32
+ start: z.ZodDefault<z.ZodNumber>;
32
33
  }, z.core.$strip>, z.ZodObject<{
33
34
  hits: z.ZodArray<z.ZodObject<{
34
35
  id: z.ZodString;
36
+ entityId: z.ZodOptional<z.ZodString>;
35
37
  source: z.ZodEnum<{
36
38
  experimental: "experimental";
37
39
  predicted: "predicted";
@@ -57,8 +59,8 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
57
59
  }, z.core.$strip>, readonly [{
58
60
  readonly reason: "no_criteria";
59
61
  readonly code: JsonRpcErrorCode.InvalidParams;
60
- readonly when: "No query, sequence, or organism was provided — nothing to search on.";
61
- readonly recovery: "Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).";
62
+ readonly when: "No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.";
63
+ readonly recovery: "Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.";
62
64
  }, {
63
65
  readonly reason: "duplicate_dimension";
64
66
  readonly code: JsonRpcErrorCode.InvalidParams;
@@ -66,6 +68,8 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
66
68
  readonly recovery: "List each facet dimension at most once; drop the repeated value and re-call.";
67
69
  }], {
68
70
  readonly totalCount: z.ZodNumber;
71
+ readonly start: z.ZodNumber;
72
+ readonly nextStart: z.ZodOptional<z.ZodNumber>;
69
73
  readonly effectiveQuery: z.ZodOptional<z.ZodString>;
70
74
  readonly notice: z.ZodOptional<z.ZodString>;
71
75
  }>;
package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoN3B,CAAC"}
1
+ {"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsP3B,CAAC"}
package/dist/mcp-server/tools/definitions/search-structures.tool.js CHANGED
@@ -46,8 +46,8 @@ export const searchStructures = tool('protein_search_structures', {
46
46
  {
47
47
  reason: 'no_criteria',
48
48
  code: JsonRpcErrorCode.InvalidParams,
49
- when: 'No query, sequence, or organism was provided — nothing to search on.',
50
- recovery: 'Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).',
49
+ when: 'No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.',
50
+ recovery: 'Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.',
51
51
  },
52
52
  {
53
53
  reason: 'duplicate_dimension',
@@ -98,12 +98,22 @@ export const searchStructures = tool('protein_search_structures', {
98
98
  .optional()
99
99
  .describe('Optional dimensions to summarize as a facet breakdown alongside the hits. Each dimension at most once; repeating one is rejected.'),
100
100
  limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
101
+ start: z
102
+ .number()
103
+ .int()
104
+ .min(0)
105
+ .default(0)
106
+ .describe('Zero-based result offset. Combine with limit to retrieve later pages.'),
101
107
  }),
102
108
  output: z.object({
103
109
  hits: z
104
110
  .array(z
105
111
  .object({
106
112
  id: z.string().describe('Structure identifier (PDB entry ID or computed-model ID).'),
113
+ entityId: z
114
+ .string()
115
+ .optional()
116
+ .describe('Matched polymer-entity ID for experimental sequence hits; id remains the chainable PDB entry ID.'),
107
117
  source: z
108
118
  .enum(['experimental', 'predicted'])
109
119
  .describe('Which universe the hit came from.'),
@@ -135,6 +145,11 @@ export const searchStructures = tool('protein_search_structures', {
135
145
  }),
136
146
  enrichment: {
137
147
  totalCount: z.number().describe('Total matches upstream before pagination.'),
148
+ start: z.number().describe('Zero-based offset of the returned page.'),
149
+ nextStart: z
150
+ .number()
151
+ .optional()
152
+ .describe('Offset for the next page; absent on the final or past-end page.'),
138
153
  effectiveQuery: z.string().optional().describe('Echoed text query for follow-up calls.'),
139
154
  notice: z
140
155
  .string()
@@ -142,8 +157,12 @@ export const searchStructures = tool('protein_search_structures', {
142
157
  .describe('Advisory note (empty results, predicted-search caveats, truncation, facet dimensions whose buckets cover materially less than totalCount). Carries every applicable advisory in one string.'),
143
158
  },
144
159
  async handler(input, ctx) {
145
- if (!input.query && !input.sequence && !input.organism) {
146
- throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.', {
160
+ if (!input.query &&
161
+ !input.sequence &&
162
+ !input.organism &&
163
+ !input.method &&
164
+ typeof input.max_resolution !== 'number') {
165
+ throw ctx.fail('no_criteria', 'Provide a query, sequence, organism, method, or maximum resolution to search on.', {
147
166
  ...ctx.recoveryFor('no_criteria'),
148
167
  });
149
168
  }
@@ -168,6 +187,7 @@ export const searchStructures = tool('protein_search_structures', {
168
187
  ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
169
188
  contentType: CONTENT_TYPE_SCOPES[input.content_type],
170
189
  limit: input.limit,
190
+ start: input.start,
171
191
  }, ctx, facetSpecs);
172
192
  const experimentalIds = [
173
193
  ...new Set(result.hits.filter((h) => !isPredictedId(h.id)).map((h) => entryIdOf(h.id))),
@@ -177,9 +197,14 @@ export const searchStructures = tool('protein_search_structures', {
177
197
  for (const meta of await rcsb.getEntries(experimentalIds, ctx))
178
198
  metaById.set(meta.id, meta);
179
199
  }
180
- const hits = result.hits.map((h) => toHit(h, metaById));
200
+ const hits = result.hits.map((h) => toHit(h, metaById, Boolean(input.sequence)));
181
201
  const facets = result.facets?.map((f) => toFacetOutput(f, cfg.facetBucketCap, result.total));
182
202
  ctx.enrich.total(result.total);
203
+ const nextStart = input.start + hits.length;
204
+ ctx.enrich({
205
+ start: input.start,
206
+ ...(nextStart < result.total ? { nextStart } : {}),
207
+ });
183
208
  if (input.query)
184
209
  ctx.enrich.echo(input.query);
185
210
  // `notice` is a single last-wins field, so the zero-hit advice and one
@@ -200,6 +225,7 @@ export const searchStructures = tool('protein_search_structures', {
200
225
  if (h.title)
201
226
  lines.push(h.title);
202
227
  const meta = [
228
+ h.entityId ? `**Entity:** ${h.entityId}` : null,
203
229
  h.method ? `**Method:** ${h.method}` : null,
204
230
  typeof h.resolution === 'number' ? `**Resolution:** ${h.resolution} Å` : null,
205
231
  h.organism ? `**Organism:** ${h.organism}` : null,
@@ -217,7 +243,7 @@ export const searchStructures = tool('protein_search_structures', {
217
243
  },
218
244
  });
219
245
  /** Build one output hit, folding in enrichment metadata when available. */
220
- function toHit(hit, metaById) {
246
+ function toHit(hit, metaById, sequenceSearch) {
221
247
  if (isPredictedId(hit.id)) {
222
248
  const accession = accessionFromCsm(hit.id);
223
249
  return {
@@ -227,9 +253,11 @@ function toHit(hit, metaById) {
227
253
  ...(accession ? { uniprotAccession: accession } : {}),
228
254
  };
229
255
  }
230
- const meta = metaById.get(entryIdOf(hit.id));
256
+ const entryId = entryIdOf(hit.id);
257
+ const meta = metaById.get(entryId);
231
258
  return {
232
- id: hit.id,
259
+ id: sequenceSearch ? entryId : hit.id,
260
+ ...(sequenceSearch ? { entityId: hit.id } : {}),
233
261
  source: 'experimental',
234
262
  score: hit.score,
235
263
  ...(meta?.title ? { title: meta.title } : {}),
package/dist/mcp-server/tools/definitions/search-structures.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts CHANGED
@@ -17,6 +17,7 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
17
17
  comp_id: z.ZodOptional<z.ZodString>;
18
18
  pdb_id: z.ZodOptional<z.ZodString>;
19
19
  limit: z.ZodDefault<z.ZodNumber>;
20
+ start: z.ZodDefault<z.ZodNumber>;
20
21
  }, z.core.$strip>, z.ZodObject<{
21
22
  mode: z.ZodEnum<{
22
23
  binding_site: "binding_site";
@@ -59,6 +60,8 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
59
60
  readonly recovery: "Use mode \"find_ligand\" to resolve a name to a component ID first, then confirm the ligand is present in the structure via protein_get_structure.";
60
61
  }], {
61
62
  readonly totalCount: z.ZodOptional<z.ZodNumber>;
63
+ readonly start: z.ZodOptional<z.ZodNumber>;
64
+ readonly nextStart: z.ZodOptional<z.ZodNumber>;
62
65
  readonly resolvedCompId: z.ZodOptional<z.ZodString>;
63
66
  readonly notice: z.ZodOptional<z.ZodString>;
64
67
  }>;
package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuOvB,CAAC"}
1
+ {"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgQvB,CAAC"}
package/dist/mcp-server/tools/definitions/track-ligands.tool.js CHANGED
@@ -82,6 +82,12 @@ export const trackLigands = tool('protein_track_ligands', {
82
82
  .max(100)
83
83
  .default(25)
84
84
  .describe('Maximum results to return (1–100).'),
85
+ start: z
86
+ .number()
87
+ .int()
88
+ .min(0)
89
+ .default(0)
90
+ .describe('Zero-based result offset (mode structures_with_ligand only).'),
85
91
  }),
86
92
  output: z.object({
87
93
  mode: z
@@ -113,6 +119,14 @@ export const trackLigands = tool('protein_track_ligands', {
113
119
  .number()
114
120
  .optional()
115
121
  .describe('Total upstream matches before pagination (structures_with_ligand).'),
122
+ start: z
123
+ .number()
124
+ .optional()
125
+ .describe('Zero-based offset of the structures_with_ligand result page.'),
126
+ nextStart: z
127
+ .number()
128
+ .optional()
129
+ .describe('Offset for the next structures_with_ligand page; absent on the final or past-end page.'),
116
130
  resolvedCompId: z.string().optional().describe('The chemical component ID used to query.'),
117
131
  notice: z
118
132
  .string()
@@ -161,9 +175,14 @@ export const trackLigands = tool('protein_track_ligands', {
161
175
  throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".', {
162
176
  ...ctx.recoveryFor('missing_param'),
163
177
  });
164
- const result = await rcsb.searchByLigand(compId, { limit: input.limit }, ctx);
178
+ const result = await rcsb.searchByLigand(compId, { limit: input.limit, start: input.start }, ctx);
165
179
  ctx.enrich.total(result.total);
166
- ctx.enrich({ resolvedCompId: compId });
180
+ const nextStart = input.start + result.hits.length;
181
+ ctx.enrich({
182
+ resolvedCompId: compId,
183
+ start: input.start,
184
+ ...(nextStart < result.total ? { nextStart } : {}),
185
+ });
167
186
  // A valid component with zero containing structures is an empty result set,
168
187
  // not a not-found — mirrors protein_search_structures' empty-hits behavior.
169
188
  if (result.hits.length === 0) {
package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/dist/services/rcsb/rcsb-service.d.ts CHANGED
@@ -40,6 +40,7 @@ export declare class RcsbService {
40
40
  maxEvalue?: number;
41
41
  minIdentity?: number;
42
42
  limit?: number;
43
+ start?: number;
43
44
  contentType?: ContentType[];
44
45
  }, ctx: Context): Promise<SearchResult>;
45
46
  /**
@@ -51,6 +52,7 @@ export declare class RcsbService {
51
52
  */
52
53
  searchByLigand(compId: string, opts: {
53
54
  limit?: number;
55
+ start?: number;
54
56
  contentType?: ContentType[];
55
57
  }, ctx: Context): Promise<SearchResult>;
56
58
  /**
package/dist/services/rcsb/rcsb-service.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/rcsb/rcsb-service.js CHANGED
@@ -64,7 +64,7 @@ export class RcsbService {
64
64
  return_type: 'polymer_entity',
65
65
  request_options: {
66
66
  ...contentTypeOption(opts.contentType),
67
- paginate: { start: 0, rows: opts.limit ?? 25 },
67
+ paginate: { start: opts.start ?? 0, rows: opts.limit ?? 25 },
68
68
  scoring_strategy: 'sequence',
69
69
  },
70
70
  };
@@ -79,7 +79,7 @@ export class RcsbService {
79
79
  * entries, not an arbitrary PDB-ID-ascending slice).
80
80
  */
81
81
  async searchByLigand(compId, opts, ctx) {
82
- const raw = await this.postSearch(ligandContainmentQuery(compId, opts.contentType, opts.limit ?? 25, true), ctx, 'RcsbService.searchByLigand');
82
+ const raw = await this.postSearch(ligandContainmentQuery(compId, opts.contentType, opts.start ?? 0, opts.limit ?? 25, true), ctx, 'RcsbService.searchByLigand');
83
83
  return { total: raw.total_count ?? 0, hits: normalizeHits(raw.result_set) };
84
84
  }
85
85
  /**
@@ -88,7 +88,7 @@ export class RcsbService {
88
88
  * surfaces first — a count-only query (rows 0), no rows or sort pulled.
89
89
  */
90
90
  async countEntriesWithLigand(compId, ctx) {
91
- const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
91
+ const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
92
92
  return raw.total_count ?? 0;
93
93
  }
94
94
  /** Resolve a ligand name/synonym to candidate chemical component IDs. */
@@ -309,7 +309,7 @@ function contentTypeOption(contentTypes) {
309
309
  * `rows` bounds the page (0 for a count-only query), and `sortByResolution`
310
310
  * orders entries best-resolution-first (skip it for counts — order is moot).
311
311
  */
312
- function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
312
+ function ligandContainmentQuery(compId, contentType, start, rows, sortByResolution) {
313
313
  return {
314
314
  query: {
315
315
  type: 'terminal',
@@ -323,7 +323,7 @@ function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
323
323
  return_type: 'entry',
324
324
  request_options: {
325
325
  ...contentTypeOption(contentType ?? ['experimental']),
326
- paginate: { start: 0, rows },
326
+ paginate: { start, rows },
327
327
  ...(sortByResolution
328
328
  ? { sort: [{ sort_by: 'rcsb_entry_info.resolution_combined', direction: 'asc' }] }
329
329
  : {}),
package/dist/services/rcsb/rcsb-service.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/protein-mcp-server",
3
- "version": "0.5.1",
3
+ "version": "0.5.3",
4
4
  "mcpName": "io.github.cyanheads/protein-mcp-server",
5
5
  "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
@@ -82,7 +82,7 @@
82
82
  }
83
83
  ],
84
84
  "license": "Apache-2.0",
85
- "packageManager": "bun@1.3.14",
85
+ "packageManager": "bun@1.4.0",
86
86
  "engines": {
87
87
  "bun": ">=1.3.0",
88
88
  "node": ">=24.0.0"
@@ -91,18 +91,18 @@
91
91
  "access": "public"
92
92
  },
93
93
  "dependencies": {
94
- "@cyanheads/mcp-ts-core": "^0.11.5",
94
+ "@cyanheads/mcp-ts-core": "^0.12.3",
95
95
  "pino-pretty": "^13.1.3",
96
96
  "zod": "^4.4.3"
97
97
  },
98
98
  "devDependencies": {
99
- "@biomejs/biome": "2.5.8",
99
+ "@biomejs/biome": "2.5.10",
100
100
  "@socketsecurity/bun-security-scanner": "^1.1.2",
101
101
  "@types/node": "26.2.0",
102
102
  "depcheck": "^1.4.7",
103
103
  "ignore": "^7.0.6",
104
- "tsc-alias": "^1.9.1",
104
+ "tsc-alias": "^1.9.2",
105
105
  "typescript": "^7.0.2",
106
- "vitest": "^4.1.10"
106
+ "vitest": "^4.1.11"
107
107
  }
108
108
  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/protein-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.5.1",
9
+ "version": "0.5.3",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/protein-mcp-server",
21
21
  "runtimeHint": "node",
22
- "version": "0.5.1",
22
+ "version": "0.5.3",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -48,7 +48,7 @@
48
48
  "registryBaseUrl": "https://registry.npmjs.org",
49
49
  "identifier": "@cyanheads/protein-mcp-server",
50
50
  "runtimeHint": "node",
51
- "version": "0.5.1",
51
+ "version": "0.5.3",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",