@cyanheads/pubchem-mcp-server 0.5.1 → 0.5.2

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Files changed (21) hide show
  1. package/README.md +3 -1
  2. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts +14 -0
  3. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +101 -12
  5. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/index.d.ts +17 -0
  7. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +3 -0
  9. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +65 -33
  11. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  12. package/dist/services/pubchem/pubchem-client.d.ts +29 -8
  13. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  14. package/dist/services/pubchem/pubchem-client.js +102 -37
  15. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  16. package/dist/services/pubchem/types.d.ts +51 -0
  17. package/dist/services/pubchem/types.d.ts.map +1 -1
  18. package/dist/services/pubchem/types.js.map +1 -1
  19. package/manifest.json +1 -1
  20. package/package.json +1 -1
  21. package/server.json +3 -3
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.5.1-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/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-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-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.5.2-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/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-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-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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  </div>
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@@ -52,6 +52,7 @@ Search PubChem for chemical compounds across five search modes.
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  - **Formula search** — find compounds by molecular formula in Hill notation
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  - **Substructure/superstructure** — find compounds containing or contained within a query structure
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  - **2D similarity** — find structurally similar compounds by Tanimoto similarity (configurable threshold)
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+ - Caps at 200 CIDs per page; `offset` pages further, to a ceiling of 10,000. Identifier lookups page over the set already resolved; formula and structure searches widen their bounded upstream request to reach a page, so deep pages cost more upstream
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  - Optionally hydrate results with properties to avoid a follow-up details call
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  ---
@@ -96,6 +97,7 @@ Get a compound's interaction data by CID.
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  - Drug-drug interactions (DrugBank), drug-food interactions, and chemical-target binding/activity (BindingDB, ChEMBL, and others)
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  - Select which interaction kinds to fetch and cap entries per kind
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+ - Paged per kind: each reports its source-record total and its own `nextOffset`, and `offset` reaches the records past a page
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  - Each entry carries its originating source — coverage is richest for approved drugs
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  ---
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts CHANGED
@@ -10,6 +10,7 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
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  "drug-food": "drug-food";
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  target: "target";
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  }>>>;
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+ offset: z.ZodDefault<z.ZodNumber>;
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  maxEntries: z.ZodDefault<z.ZodNumber>;
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  }, z.core.$strip>, z.ZodObject<{
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  cid: z.ZodNumber;
@@ -23,9 +24,22 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
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  source: z.ZodString;
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  text: z.ZodString;
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  }, z.core.$strip>>;
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+ paging: z.ZodArray<z.ZodObject<{
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+ kind: z.ZodEnum<{
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+ "drug-drug": "drug-drug";
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+ "drug-food": "drug-food";
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+ target: "target";
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+ }>;
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+ returnedCount: z.ZodNumber;
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+ totalRecords: z.ZodNumber;
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+ nextOffset: z.ZodOptional<z.ZodNumber>;
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+ truncated: z.ZodBoolean;
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+ }, z.core.$strip>>;
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  }, z.core.$strip>, undefined, {
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  readonly requestedKinds: z.ZodString;
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  readonly returnedCount: z.ZodNumber;
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+ readonly offset: z.ZodNumber;
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+ readonly nextOffset: z.ZodOptional<z.ZodNumber>;
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  readonly failedKinds: z.ZodOptional<z.ZodString>;
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  readonly notice: z.ZodOptional<z.ZodString>;
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  }>;
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;EA+HlC,CAAC"}
1
+ {"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+OlC,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js CHANGED
@@ -7,7 +7,7 @@ import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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  import { inlineData, quoteData } from './untrusted-text.js';
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  export const getCompoundInteractions = tool('pubchem_get_compound_interactions', {
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  title: 'Get Compound Interactions',
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- description: "Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Richest for approved drugs; many compounds have no deposited interaction records.",
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+ description: "Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.",
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  annotations: {
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  readOnlyHint: true,
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  idempotentHint: true,
@@ -24,13 +24,23 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  .min(1)
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  .default(['drug-drug'])
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  .describe('Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"].'),
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+ offset: z
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+ .number()
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+ .int()
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+ .min(0)
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+ // PubChem's record cursor is a signed 32-bit integer; a larger start makes the upstream
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+ // query fail outright, which would surface as a retryable kind failure that no retry can
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+ // clear. Rejecting it here names the bound instead.
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+ .max(2147483646)
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+ .default(0)
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+ .describe("Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0."),
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  maxEntries: z
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  .number()
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  .int()
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  .min(1)
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  .max(50)
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  .default(10)
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- .describe('Max entries per kind (1-50). Well-studied drugs have a long tail of interactions. Default: 10.'),
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+ .describe('Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10.'),
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  }),
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  output: z.object({
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  cid: z.number().describe('PubChem Compound ID.'),
@@ -47,12 +57,38 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  })
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  .describe('A single interaction entry.'))
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  .describe('Interaction entries across the requested kinds.'),
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+ paging: z
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+ .array(z
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+ .object({
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+ kind: z
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+ .enum(['drug-drug', 'drug-food', 'target'])
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+ .describe('Interaction category this page covers.'),
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+ returnedCount: z.number().describe('Interaction entries returned for this kind.'),
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+ totalRecords: z
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+ .number()
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+ .describe('Source records available for this kind, across all pages. Entries are derived from these records and can be fewer: a "target" record naming no molecular target and a "drug-drug" record carrying no statement both yield nothing, and duplicate measurements collapse within a page. Pages divide the records, not the entries, so a duplicate split across two pages is reported on both.'),
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+ nextOffset: z
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+ .number()
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+ .optional()
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+ .describe('Offset to pass on the next call to continue this kind past the current page. Omitted when no records remain.'),
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+ truncated: z
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+ .boolean()
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+ .describe('True when source records remain for this kind past the current page.'),
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+ })
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+ .describe('Page position for one interaction kind.'))
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+ .describe('Per-kind page position, one entry per requested kind that was retrieved. A kind listed in failedKinds is absent — its position is unknown, not exhausted.'),
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  }),
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- // Agent-facing context — kind echo, total returned, failed kinds, and an empty-result notice.
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- // Reaches structuredContent and content[]; keys disjoint from output (cid/entries).
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+ // Agent-facing context — kind echo, total returned, the page boundary, failed kinds, and
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+ // an empty-result notice. Reaches structuredContent and content[]; keys disjoint from
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+ // output (cid/entries/paging).
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  enrichment: {
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  requestedKinds: z.string().describe('Interaction kinds requested (comma-separated).'),
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  returnedCount: z.number().describe('Total interaction entries returned across all kinds.'),
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+ offset: z.number().describe('Zero-based start position read within each requested kind.'),
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+ nextOffset: z
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+ .number()
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+ .optional()
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+ .describe('Offset to pass on the next call, reported when exactly one requested kind has records remaining. Omitted when none do, and when several do — those advance to different positions, so read paging[].nextOffset instead.'),
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  failedKinds: z
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  .string()
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  .optional()
@@ -60,11 +96,11 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  notice: z
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  .string()
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  .optional()
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- .describe('Guidance when no interaction data was found for the requested kinds.'),
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+ .describe('Guidance when a kind failed, when no interaction data was found, when the offset runs past every requested kind, or when further pages remain. Absent when this page is complete and every kind resolved.'),
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  },
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  async handler(input, ctx) {
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  const client = getPubChemClient();
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- const { entries, failedKinds } = await client.getInteractions(input.cid, input.kinds, input.maxEntries);
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+ const { entries, pages, failedKinds } = await client.getInteractions(input.cid, input.kinds, input.maxEntries, input.offset);
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  for (const f of failedKinds) {
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  ctx.log.warning('Interaction kind failed', {
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  cid: input.cid,
@@ -75,25 +111,78 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  ctx.log.info('Interactions fetched', {
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  cid: input.cid,
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  kinds: input.kinds,
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+ offset: input.offset,
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  returned: entries.length,
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  failed: failedKinds.length,
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  });
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- ctx.enrich({ requestedKinds: input.kinds.join(', '), returnedCount: entries.length });
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+ // Each kind advances by the records it actually read, never by maxEntries — a kind that
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+ // stopped early (or whose window ran short) would otherwise emit a next offset that skips
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+ // records, and a cap-derived stride can also land off an integer boundary.
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+ const paging = pages.map((p) => {
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+ const next = input.offset + p.recordsConsumed;
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+ const truncated = next < p.totalRecords;
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+ return {
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+ kind: p.kind,
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+ returnedCount: p.returnedCount,
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+ totalRecords: p.totalRecords,
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+ truncated,
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+ ...(truncated ? { nextOffset: next } : {}),
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+ };
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+ });
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+ ctx.enrich({
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+ requestedKinds: input.kinds.join(', '),
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+ returnedCount: entries.length,
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+ offset: input.offset,
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+ });
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+ const remaining = paging.filter((p) => p.truncated);
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+ // A single scalar nextOffset only means something when one kind is still going; with two
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+ // it would have to pick one and silently skip the other's records.
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+ const soleNextOffset = remaining.length === 1 ? remaining[0]?.nextOffset : undefined;
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+ if (soleNextOffset !== undefined)
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+ ctx.enrich({ nextOffset: soleNextOffset });
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+ // Notice is last-wins, so every applicable signal composes into one string.
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+ const noticeParts = [];
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  if (failedKinds.length > 0) {
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  const names = failedKinds.map((f) => f.kind).join(', ');
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  const plural = failedKinds.length > 1;
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  ctx.enrich({ failedKinds: names });
86
- ctx.enrich.notice(`Could not retrieve ${names} interaction${plural ? 's' : ''} for CID ${input.cid}.${entries.length > 0 ? ' Returned the kinds that succeeded.' : ''} Retry to re-attempt ${plural ? 'them' : 'it'}.`);
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+ noticeParts.push(`Could not retrieve ${names} interaction${plural ? 's' : ''} for CID ${input.cid}.${entries.length > 0 ? ' Returned the kinds that succeeded.' : ''} Retry to re-attempt ${plural ? 'them' : 'it'}.`);
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+ }
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+ const largestTotal = paging.reduce((max, p) => Math.max(max, p.totalRecords), 0);
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+ if (entries.length === 0 && paging.length > 0) {
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+ if (largestTotal === 0) {
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+ noticeParts.push(`No ${paging.map((p) => p.kind).join('/')} interaction data found for CID ${input.cid}. PubChem has no deposited interaction records for this compound — coverage is richest for approved drugs.`);
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+ }
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+ else if (input.offset >= largestTotal) {
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+ noticeParts.push(`offset ${input.offset} is past every requested kind — the largest has ${largestTotal} record(s). Pass an offset below ${largestTotal}.`);
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+ }
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+ else {
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+ noticeParts.push(`CID ${input.cid} has ${largestTotal} record(s) for the requested kind(s), but none read on this page carried a reportable interaction.`);
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+ }
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162
  }
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- else if (entries.length === 0) {
89
- ctx.enrich.notice(`No ${input.kinds.join('/')} interaction data found for CID ${input.cid}. PubChem has no deposited interaction records for this compound — coverage is richest for approved drugs.`);
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+ if (remaining.length > 0) {
164
+ noticeParts.push(`More records remain — ${remaining
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+ .map((p) => `${p.kind}: pass offset=${p.nextOffset} of ${p.totalRecords} total`)
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+ .join('; ')}.`);
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  }
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- return { cid: input.cid, entries };
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+ if (noticeParts.length > 0)
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+ ctx.enrich.notice(noticeParts.join(' '));
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+ return { cid: input.cid, entries, paging };
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  },
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  format(result) {
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  const lines = [`## Interactions — CID ${result.cid}`, ''];
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+ for (const p of result.paging) {
175
+ const summary = `${p.returnedCount} entr${p.returnedCount === 1 ? 'y' : 'ies'} from ${p.totalRecords} source record(s)`;
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+ lines.push(`- **${p.kind}** — ${summary}${p.truncated ? ' — truncated' : ''}`);
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+ if (p.nextOffset !== undefined)
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+ lines.push(` Next offset: ${p.nextOffset}`);
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+ }
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+ if (result.paging.length > 0)
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+ lines.push('');
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  if (result.entries.length === 0) {
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- lines.push('No interaction data found.');
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+ // Neutral wording: an empty page is "no data", "offset past the end", or "the records
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+ // read named no interaction" — the enrichment trailer's notice says which.
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+ lines.push('No interaction entries returned.');
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  return [{ type: 'text', text: lines.join('\n') }];
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  }
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  for (const e of result.entries) {
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -125,6 +125,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
125
125
  smiles: "smiles";
126
126
  }>>;
127
127
  threshold: import("zod").ZodDefault<import("zod").ZodNumber>;
128
+ offset: import("zod").ZodDefault<import("zod").ZodNumber>;
128
129
  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
129
130
  properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
130
131
  [x: string]: string;
@@ -160,6 +161,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
160
161
  readonly searchType: import("zod").ZodString;
161
162
  readonly totalFound: import("zod").ZodOptional<import("zod").ZodNumber>;
162
163
  readonly totalFoundAtLeast: import("zod").ZodOptional<import("zod").ZodNumber>;
164
+ readonly offset: import("zod").ZodNumber;
165
+ readonly nextOffset: import("zod").ZodOptional<import("zod").ZodNumber>;
163
166
  readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
164
167
  readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
165
168
  readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
@@ -298,6 +301,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
298
301
  "drug-food": "drug-food";
299
302
  target: "target";
300
303
  }>>>;
304
+ offset: import("zod").ZodDefault<import("zod").ZodNumber>;
301
305
  maxEntries: import("zod").ZodDefault<import("zod").ZodNumber>;
302
306
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
303
307
  cid: import("zod").ZodNumber;
@@ -311,9 +315,22 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
311
315
  source: import("zod").ZodString;
312
316
  text: import("zod").ZodString;
313
317
  }, import("zod/v4/core").$strip>>;
318
+ paging: import("zod").ZodArray<import("zod").ZodObject<{
319
+ kind: import("zod").ZodEnum<{
320
+ "drug-drug": "drug-drug";
321
+ "drug-food": "drug-food";
322
+ target: "target";
323
+ }>;
324
+ returnedCount: import("zod").ZodNumber;
325
+ totalRecords: import("zod").ZodNumber;
326
+ nextOffset: import("zod").ZodOptional<import("zod").ZodNumber>;
327
+ truncated: import("zod").ZodBoolean;
328
+ }, import("zod/v4/core").$strip>>;
314
329
  }, import("zod/v4/core").$strip>, undefined, {
315
330
  readonly requestedKinds: import("zod").ZodString;
316
331
  readonly returnedCount: import("zod").ZodNumber;
332
+ readonly offset: import("zod").ZodNumber;
333
+ readonly nextOffset: import("zod").ZodOptional<import("zod").ZodNumber>;
317
334
  readonly failedKinds: import("zod").ZodOptional<import("zod").ZodString>;
318
335
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
319
336
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -27,6 +27,7 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
27
27
  smiles: "smiles";
28
28
  }>>;
29
29
  threshold: z.ZodDefault<z.ZodNumber>;
30
+ offset: z.ZodDefault<z.ZodNumber>;
30
31
  maxResults: z.ZodDefault<z.ZodNumber>;
31
32
  properties: z.ZodOptional<z.ZodArray<z.ZodEnum<{
32
33
  [x: string]: string;
@@ -62,6 +63,8 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
62
63
  readonly searchType: z.ZodString;
63
64
  readonly totalFound: z.ZodOptional<z.ZodNumber>;
64
65
  readonly totalFoundAtLeast: z.ZodOptional<z.ZodNumber>;
66
+ readonly offset: z.ZodNumber;
67
+ readonly nextOffset: z.ZodOptional<z.ZodNumber>;
65
68
  readonly truncated: z.ZodOptional<z.ZodBoolean>;
66
69
  readonly shown: z.ZodOptional<z.ZodNumber>;
67
70
  readonly cap: z.ZodOptional<z.ZodNumber>;
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8Y1B,CAAC"}
1
+ {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAob1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -19,7 +19,7 @@ const queryTypeEnum = z.enum(['smiles', 'cid']);
19
19
  const propertyEnum = z.enum(COMPOUND_PROPERTIES);
20
20
  export const searchCompounds = tool('pubchem_search_compounds', {
21
21
  title: 'Search Compounds',
22
- description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
22
+ description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
23
23
  annotations: {
24
24
  readOnlyHint: true,
25
25
  idempotentHint: true,
@@ -60,12 +60,19 @@ export const searchCompounds = tool('pubchem_search_compounds', {
60
60
  .max(100)
61
61
  .default(90)
62
62
  .describe('Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.'),
63
+ offset: z
64
+ .number()
65
+ .int()
66
+ .min(0)
67
+ .max(10000)
68
+ .default(0)
69
+ .describe('Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.'),
63
70
  maxResults: z
64
71
  .number()
65
72
  .min(1)
66
73
  .max(200)
67
74
  .default(20)
68
- .describe('Maximum CIDs to return (1-200). Default: 20.'),
75
+ .describe('Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20.'),
69
76
  properties: z
70
77
  .array(propertyEnum)
71
78
  .optional()
@@ -92,8 +99,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
92
99
  .optional()
93
100
  .describe('Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.'),
94
101
  }),
95
- // Agent-facing context — search strategy echo, total before cap, and an empty-result
96
- // notice. Reaches structuredContent and content[] automatically; not in the domain return.
102
+ // Agent-facing context — search strategy echo, total, the page boundary, and a notice
103
+ // covering unresolved identifiers, an empty page, and further pages. Reaches
104
+ // structuredContent and content[] automatically; not in the domain return.
97
105
  //
98
106
  // Bounded-total convention: a reported total states only what the server actually
99
107
  // observed. `totalFound` carries a true count and appears only when the whole match set
@@ -108,21 +116,23 @@ export const searchCompounds = tool('pubchem_search_compounds', {
108
116
  totalFound: z
109
117
  .number()
110
118
  .optional()
111
- .describe('Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
119
+ .describe('Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
112
120
  totalFoundAtLeast: z
113
121
  .number()
114
122
  .optional()
115
- .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more.'),
116
- truncated: z
117
- .boolean()
123
+ .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; page further with offset to observe more.'),
124
+ offset: z.number().describe('Zero-based index of the first CID returned.'),
125
+ nextOffset: z
126
+ .number()
118
127
  .optional()
119
- .describe('True when CIDs were capped at maxResults — more matches exist than returned.'),
120
- shown: z.number().optional().describe('CIDs returned after the maxResults cap.'),
128
+ .describe('Offset to pass on the next call to continue past this page. Omitted when no further matches remain.'),
129
+ truncated: z.boolean().optional().describe('True when matching CIDs remain past this page.'),
130
+ shown: z.number().optional().describe('CIDs returned on this page.'),
121
131
  cap: z.number().optional().describe('The maxResults cap that was applied.'),
122
132
  notice: z
123
133
  .string()
124
134
  .optional()
125
- .describe('Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.'),
135
+ .describe('Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and every identifier resolved.'),
126
136
  },
127
137
  errors: [
128
138
  {
@@ -153,10 +163,12 @@ export const searchCompounds = tool('pubchem_search_compounds', {
153
163
  async handler(input, ctx) {
154
164
  const client = getPubChemClient();
155
165
  let allCids = [];
156
- // Formula and structure searches are bounded server-side. One record past the cap is
157
- // enough to prove more matches exist without moving the rest of PubChem's match set,
158
- // which for a common substructure runs to 16.3 MB of CIDs.
159
- const recordCap = input.maxResults + 1;
166
+ // Formula and structure searches are bounded server-side. One record past the requested
167
+ // page is enough to prove more matches exist without moving the rest of PubChem's match
168
+ // set, which for a common substructure runs to 16.3 MB of CIDs. The window has to cover
169
+ // the offset too — these endpoints take a record count, not a start position, and their
170
+ // ordering is a stable prefix, so reaching page N means asking for everything up to it.
171
+ const recordCap = input.offset + input.maxResults + 1;
160
172
  let boundedSearch = false;
161
173
  const identifierMap = new Map();
162
174
  // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
@@ -243,23 +255,33 @@ export const searchCompounds = tool('pubchem_search_compounds', {
243
255
  break;
244
256
  }
245
257
  }
246
- // Deduplicate and cap
258
+ // Deduplicate, then take the requested page.
247
259
  const uniqueCids = [...new Set(allCids)];
248
260
  const observedTotal = uniqueCids.length;
249
- const cappedCids = uniqueCids.slice(0, input.maxResults);
261
+ const pagedCids = uniqueCids.slice(input.offset, input.offset + input.maxResults);
250
262
  // A bounded search that came back short of its cap returned everything PubChem had, so
251
263
  // the count is exact. A saturated one only proves a floor.
252
264
  const totalIsExact = !boundedSearch || allCids.length < recordCap;
265
+ // The stride comes from the page that was returned, never from maxResults — that input
266
+ // accepts a fractional value, which would emit a nextOffset this tool's own integer
267
+ // offset validator then rejects.
268
+ const nextOffset = input.offset + pagedCids.length;
269
+ // A saturated bounded search proved a record beyond the window it asked for, so more
270
+ // remain even though observedTotal cannot say how many.
271
+ const hasMore = !totalIsExact || nextOffset < observedTotal;
253
272
  ctx.log.info('Search completed', {
254
273
  searchType: input.searchType,
255
274
  observedTotal,
256
275
  totalIsExact,
257
- returned: cappedCids.length,
276
+ offset: input.offset,
277
+ returned: pagedCids.length,
258
278
  });
259
- // Agent-facing context: search strategy echo, total, and empty-result notice.
279
+ // Agent-facing context: search strategy echo, total, page boundary, and notices.
260
280
  ctx.enrich(totalIsExact
261
- ? { searchType: input.searchType, totalFound: observedTotal }
262
- : { searchType: input.searchType, totalFoundAtLeast: observedTotal });
281
+ ? { searchType: input.searchType, totalFound: observedTotal, offset: input.offset }
282
+ : { searchType: input.searchType, totalFoundAtLeast: observedTotal, offset: input.offset });
283
+ if (hasMore)
284
+ ctx.enrich({ nextOffset });
263
285
  // Identifier-mode signals (#29): name inputs that did not resolve and flag CID
264
286
  // collisions, so a partial miss is never silent. Empty for other search types.
265
287
  const noticeParts = [];
@@ -270,20 +292,30 @@ export const searchCompounds = tool('pubchem_search_compounds', {
270
292
  for (const c of collisions) {
271
293
  noticeParts.push(`Identifiers ${c.identifiers.join(', ')} all resolved to CID ${c.cid}; the result row echoes only "${identifierMap.get(c.cid)}" for it.`);
272
294
  }
273
- if (cappedCids.length === 0) {
274
- ctx.enrich.notice(noticeParts.length > 0
275
- ? noticeParts.join(' ')
276
- : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
295
+ if (pagedCids.length === 0) {
296
+ // An empty page is either "nothing matched" or "the offset ran past the matches" —
297
+ // say which, and name the bound the caller can page back inside.
298
+ if (observedTotal === 0) {
299
+ if (noticeParts.length === 0) {
300
+ noticeParts.push(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
301
+ }
302
+ }
303
+ else {
304
+ // Reachable only with an exact total: a saturated bounded search observed
305
+ // offset + maxResults + 1 records, so its page is never empty.
306
+ noticeParts.push(`offset ${input.offset} is past the ${observedTotal} match(es) found. Pass an offset below ${observedTotal}.`);
307
+ }
308
+ ctx.enrich.notice(noticeParts.join(' '));
277
309
  }
278
- else if (observedTotal > cappedCids.length) {
310
+ else if (hasMore) {
279
311
  // Truncated: fold any identifier notice into the truncation guidance (notice is
280
312
  // last-wins, so compose rather than emit two). Without an exact total there is no
281
- // "of N" to quote — say more exist and stop.
313
+ // "of N" to quote — say more exist, and still hand over the next offset.
282
314
  const truncationGuidance = totalIsExact
283
- ? `Showing ${cappedCids.length} of ${observedTotal} matches — raise maxResults (max 200) for more.`
284
- : `Showing ${cappedCids.length} matches; more exist, but PubChem reports no match count for a ${input.searchType} search — raise maxResults (max 200) for more.`;
315
+ ? `Showing matches ${input.offset + 1}-${nextOffset} of ${observedTotal}. Pass offset=${nextOffset} for the next page.`
316
+ : `Showing matches ${input.offset + 1}-${nextOffset}; more exist, but PubChem reports no match count for a ${input.searchType} search. Pass offset=${nextOffset} for the next page.`;
285
317
  ctx.enrich.truncated({
286
- shown: cappedCids.length,
318
+ shown: pagedCids.length,
287
319
  cap: input.maxResults,
288
320
  guidance: noticeParts.length > 0
289
321
  ? `${noticeParts.join(' ')} ${truncationGuidance}`
@@ -295,11 +327,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
295
327
  }
296
328
  // Optionally hydrate with properties
297
329
  let propsMap;
298
- if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
299
- const rows = await client.getProperties(cappedCids, input.properties);
330
+ if (input.properties && input.properties.length > 0 && pagedCids.length > 0) {
331
+ const rows = await client.getProperties(pagedCids, input.properties);
300
332
  propsMap = new Map(rows.map((r) => [r.CID, r]));
301
333
  }
302
- const results = cappedCids.map((cid) => {
334
+ const results = pagedCids.map((cid) => {
303
335
  const result = { cid };
304
336
  const identifier = identifierMap.get(cid);
305
337
  if (identifier)
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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