@cyanheads/pubchem-mcp-server 0.1.17 → 0.1.19
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/Dockerfile +2 -2
- package/README.md +2 -2
- package/dist/index.js +1 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +7 -6
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +15 -31
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js +6 -2
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +6 -4
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +11 -9
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts +1 -2
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.js +3 -9
- package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +3 -3
- package/dist/mcp-server/tools/definitions/search-assays.tool.js +6 -8
- package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +3 -3
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js +14 -23
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
- package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
- package/dist/services/pubchem/pubchem-client.js +38 -65
- package/dist/services/pubchem/pubchem-client.js.map +1 -1
- package/dist/services/pubchem/types.d.ts +0 -4
- package/dist/services/pubchem/types.d.ts.map +1 -1
- package/dist/services/pubchem/types.js +0 -5
- package/dist/services/pubchem/types.js.map +1 -1
- package/package.json +7 -7
- package/server.json +3 -3
package/Dockerfile
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@@ -4,7 +4,7 @@
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# This stage installs all dependencies (including dev), builds the TypeScript
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# source code into JavaScript, and prepares the production assets.
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# ==============================================================================
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FROM oven/bun:1 AS build
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FROM oven/bun:1.3 AS build
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WORKDIR /usr/src/app
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@@ -28,7 +28,7 @@ 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-slim AS production
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FROM oven/bun:1.3-slim AS production
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WORKDIR /usr/src/app
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/) [](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -131,7 +131,7 @@ Add to your MCP client config (e.g., `claude_desktop_config.json`):
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### Prerequisites
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-
- [Bun v1.
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- [Bun v1.3.0](https://bun.sh/) or higher (or Node.js v24+)
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### Installation
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package/dist/index.js
CHANGED
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@@ -9,6 +9,7 @@ import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
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import { initPubChemClient } from './services/pubchem/pubchem-client.js';
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await createApp({
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tools: allToolDefinitions,
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instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, or bioactivity. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups.",
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landing: {
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tagline: 'Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.',
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repoRoot: 'https://github.com/cyanheads/pubchem-mcp-server',
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,YAAY,EACV,8gBAA8gB;IAChhB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;6BAuIzB,CAAC"}
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@@ -7,21 +7,22 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
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import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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export const getBioactivity = tool('pubchem_get_bioactivity', {
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title: 'Get Bioactivity',
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description: "Get a compound's bioactivity profile: which assays tested it, activity outcomes "
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'(Active/Inactive/Inconclusive), target information (gene symbols, protein names), ' +
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'and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome to focus on active results.',
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description: "Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome to focus on active results.",
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annotations: {
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readOnlyHint: true,
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idempotentHint: true,
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openWorldHint: true,
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},
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input: z.object({
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cid: z
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cid: z
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.number()
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.int()
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.positive()
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.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
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outcomeFilter: z
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.enum(['active', 'inactive', 'all'])
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.default('all')
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.describe('Filter by activity outcome. "active" shows only assays where the compound showed activity — '
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'most useful for understanding biological profile. Default: "all".'),
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.describe('Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".'),
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maxResults: z
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.number()
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.min(1)
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{"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,
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{"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,6QAA6Q;IAC/Q,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,aAAa,EAAE,CAAC;aACb,IAAI,CAAC,CAAC,QAAQ,EAAE,UAAU,EAAE,KAAK,CAAC,CAAC;aACnC,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+JAA+J,CAChK;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,qGAAqG,CACtG;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC1E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACjE,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QACrE,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC7C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACnD,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,CAAC,gEAAgE,CAAC;YAC7E,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YACpE,cAAc,EAAE,CAAC;iBACd,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CACP,oEAAoE,CACrE;gBACH,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC7C,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CAAC,+DAA+D,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,0CAA0C,CAAC,CACxD;iBACA,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC;aACD,QAAQ,CAAC,qBAAqB,CAAC,CACnC;aACA,QAAQ,CAAC,oCAAoC,CAAC;KAClD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExD,MAAM,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACzE,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAE7E,oBAAoB;QACpB,IAAI,QAAQ,GAAG,OAAO,CAAC;QACvB,IAAI,KAAK,CAAC,aAAa,KAAK,QAAQ,EAAE,CAAC;YACrC,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC;QAC3D,CAAC;aAAM,IAAI,KAAK,CAAC,aAAa,KAAK,UAAU,EAAE,CAAC;YAC9C,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC;QAC7D,CAAC;QAED,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEpD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,OAAO,CAAC,MAAM;YACrB,MAAM,EAAE,WAAW;YACnB,QAAQ,EAAE,OAAO,CAAC,MAAM;SACzB,CAAC,CAAC;QAEH,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,OAAO,CAAC,MAAM;YAC3B,WAAW;YACX,aAAa;YACb,OAAO;SACR,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa;YACtB,wBAAwB,MAAM,CAAC,GAAG,EAAE;YACpC,iBAAiB,MAAM,CAAC,WAAW,cAAc,MAAM,CAAC,WAAW,gBAAgB,MAAM,CAAC,aAAa,EAAE;YACzG,EAAE;SACH,CAAC;QAEF,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,eAAe,CAAC;iBACxF,MAAM,CAAC,OAAO,CAAC;iBACf,IAAI,CAAC,KAAK,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC;YAC/D,IAAI,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,EAAE,CAAC,CAAC;YAC9C,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,cAAc,EAAE,CAAC;gBAClC,MAAM,KAAK,GAAG,EAAE,CAAC,IAAI,IAAI,OAAO,CAAC;gBACjC,MAAM,IAAI,GAAG,EAAE,CAAC,IAAI,IAAI,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,KAAK,EAAE,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjE,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAgX7B,CAAC"}
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.object({
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hba: drugLikenessRuleSchema.describe('HBond acceptor count rule (≤10).'),
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hbd: drugLikenessRuleSchema.describe('HBond donor count rule (≤5).'),
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mw: drugLikenessRuleSchema.describe('Molecular weight rule (≤500).'),
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mw: drugLikenessRuleSchema.describe('Molecular weight rule (≤500 g/mol).'),
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violations: z.number().describe('Number of Lipinski violations (0-4).'),
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xLogP: drugLikenessRuleSchema.describe('XLogP rule (≤5).'),
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xLogP: drugLikenessRuleSchema.describe('XLogP rule (≤5; calculated logP).'),
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})
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.describe('Lipinski Rule of Five evaluation.'),
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pass: z
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@@ -29,7 +29,7 @@ const drugLikenessSchema = z.object({
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veber: z
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.object({
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rotatableBonds: drugLikenessRuleSchema.describe('Rotatable bond count rule (≤10).'),
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tpsa: drugLikenessRuleSchema.describe('
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tpsa: drugLikenessRuleSchema.describe('Topological polar surface area rule (≤140 Ų).'),
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violations: z.number().describe('Number of Veber violations (0-2).'),
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})
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.describe('Veber rules evaluation.'),
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@@ -95,11 +95,7 @@ function computeDrugLikeness(properties) {
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// ── Tool definition ────────────────────────────────────────────────────
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export const getCompoundDetails = tool('pubchem_get_compound_details', {
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title: 'Get Compound Details',
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-
description: 'Get detailed compound information by CID. Returns physicochemical properties '
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99
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'(molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual ' +
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100
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-
'description (pharmacology, mechanism, therapeutic use), all known synonyms, ' +
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101
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-
'drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification ' +
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'(FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.',
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98
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+
description: 'Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.',
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103
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annotations: {
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readOnlyHint: true,
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105
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idempotentHint: true,
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@@ -110,42 +106,34 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
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.array(z.number().int().positive())
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.min(1)
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.max(100)
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113
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.describe('PubChem Compound IDs to fetch (1-100). Batched efficiently.'),
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109
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+
.describe('PubChem Compound IDs to fetch (1-100). Batched efficiently. Resolve from names/SMILES with pubchem_search_compounds.'),
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114
110
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properties: z
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115
111
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.array(propertyEnum)
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112
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.optional()
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117
|
-
.describe('Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, '
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118
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-
'IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, ' +
|
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119
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-
'HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity.'),
|
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113
|
+
.describe('Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity.'),
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includeDescription: z
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.boolean()
|
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116
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.default(false)
|
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123
|
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.describe('Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. '
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124
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'Well-studied compounds have many overlapping summaries — capped via maxDescriptions. ' +
|
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125
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'Slower when enabled — prefer small CID batches.'),
|
|
117
|
+
.describe('Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — capped via maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions.'),
|
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maxDescriptions: z
|
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119
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.number()
|
|
128
120
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.int()
|
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121
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.min(1)
|
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130
122
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.max(20)
|
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131
123
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.default(3)
|
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132
|
-
.describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate '
|
|
133
|
-
'summaries from many depositors; we dedup and cap to keep responses focused. Default: 3.'),
|
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124
|
+
.describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; we dedup and cap to keep responses focused. Default: 3.'),
|
|
134
125
|
includeSynonyms: z
|
|
135
126
|
.boolean()
|
|
136
127
|
.default(false)
|
|
137
|
-
.describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers).'),
|
|
128
|
+
.describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). One API call per CID — slower than the property batch for large CID lists.'),
|
|
138
129
|
includeDrugLikeness: z
|
|
139
130
|
.boolean()
|
|
140
131
|
.default(false)
|
|
141
|
-
.describe('Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and '
|
|
142
|
-
'Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties.'),
|
|
132
|
+
.describe('Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties.'),
|
|
143
133
|
includeClassification: z
|
|
144
134
|
.boolean()
|
|
145
135
|
.default(false)
|
|
146
|
-
.describe('Include pharmacological classification: FDA Established Pharmacologic Classes, '
|
|
147
|
-
'mechanisms of action, MeSH classes, and ATC codes. ' +
|
|
148
|
-
'Slower when enabled — prefer small CID batches.'),
|
|
136
|
+
.describe('Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification.'),
|
|
149
137
|
}),
|
|
150
138
|
output: z.object({
|
|
151
139
|
compounds: z
|
|
@@ -157,7 +145,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
157
145
|
.describe('False when the CID does not exist in PubChem (properties, description, etc. are empty).'),
|
|
158
146
|
properties: z
|
|
159
147
|
.record(z.string(), z.unknown())
|
|
160
|
-
.describe('
|
|
148
|
+
.describe('Physicochemical properties keyed by name (echoes input.properties or the default core set; drug-likeness inputs are appended automatically when includeDrugLikeness is true).'),
|
|
161
149
|
descriptions: z
|
|
162
150
|
.array(z
|
|
163
151
|
.object({
|
|
@@ -169,13 +157,11 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
169
157
|
})
|
|
170
158
|
.describe('Description entry with optional source attribution.'))
|
|
171
159
|
.optional()
|
|
172
|
-
.describe('Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries '
|
|
173
|
-
'optional source attribution.'),
|
|
160
|
+
.describe('Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries optional source attribution.'),
|
|
174
161
|
descriptionsTotal: z
|
|
175
162
|
.number()
|
|
176
163
|
.optional()
|
|
177
|
-
.describe('Total distinct descriptions available before truncation. Larger than descriptions.length '
|
|
178
|
-
'when more sources exist — increase maxDescriptions to see them.'),
|
|
164
|
+
.describe('Total distinct descriptions available before truncation. Larger than descriptions.length when more sources exist — increase maxDescriptions to see them.'),
|
|
179
165
|
synonyms: z.array(z.string()).optional().describe('Known names and synonyms.'),
|
|
180
166
|
drugLikeness: drugLikenessSchema
|
|
181
167
|
.optional()
|
|
@@ -246,9 +232,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
246
232
|
});
|
|
247
233
|
const compounds = input.cids.map((cid) => {
|
|
248
234
|
const found = isFound(cid);
|
|
249
|
-
const
|
|
250
|
-
const properties = { ...rawProps };
|
|
251
|
-
delete properties.CID;
|
|
235
|
+
const { CID: _CID, ...properties } = propsMap.get(cid) ?? { CID: cid };
|
|
252
236
|
const compound = { cid, found, properties };
|
|
253
237
|
// Skip enrichment for CIDs not in PubChem — properties is already empty.
|
|
254
238
|
if (!found)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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-
{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;
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1
|
+
{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;6BAoD3B,CAAC"}
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@@ -13,7 +13,11 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
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13
13
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openWorldHint: true,
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14
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},
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15
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input: z.object({
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-
cid: z
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+
cid: z
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+
.number()
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.int()
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19
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+
.positive()
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20
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+
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
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21
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size: z
|
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18
22
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.enum(['small', 'large'])
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19
23
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.default('large')
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@@ -22,7 +26,7 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
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26
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output: z.object({
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27
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cid: z.number().describe('PubChem Compound ID.'),
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28
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imageBase64: z.string().describe('Base64-encoded PNG image data.'),
|
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25
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-
mimeType: z.string().describe('
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29
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+
mimeType: z.string().describe('MIME type — always "image/png".'),
|
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26
30
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width: z.number().describe('Image width in pixels.'),
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31
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height: z.number().describe('Image height in pixels.'),
|
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28
32
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}),
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC,
|
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1
|
+
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;aACxB,OAAO,CAAC,OAAO,CAAC;aAChB,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KACvD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5D,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAE/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAE9F,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;YACnD,QAAQ,EAAE,WAAW;YACrB,KAAK,EAAE,GAAG;YACV,MAAM,EAAE,GAAG;SACZ,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,OAAO;YACL,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE;YACtE;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,wBAAwB,MAAM,CAAC,GAAG,KAAK,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG;aAC9E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;
|
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1
|
+
{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;6BAyG5B,CAAC"}
|
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@@ -6,16 +6,18 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
|
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6
6
|
import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
|
|
7
7
|
export const getCompoundSafety = tool('pubchem_get_compound_safety', {
|
|
8
8
|
title: 'Get Compound Safety',
|
|
9
|
-
description: 'Get GHS (Globally Harmonized System) hazard classification and safety data for a compound. '
|
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10
|
-
'Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes). ' +
|
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11
|
-
'Data sourced from PubChem depositors — source attribution included.',
|
|
9
|
+
description: 'Get GHS (Globally Harmonized System) hazard classification and safety data for a compound. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes). Data sourced from PubChem depositors — source attribution included.',
|
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12
10
|
annotations: {
|
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13
11
|
readOnlyHint: true,
|
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14
12
|
idempotentHint: true,
|
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15
13
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openWorldHint: true,
|
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16
14
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},
|
|
17
15
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input: z.object({
|
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18
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-
cid: z
|
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16
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+
cid: z
|
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17
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+
.number()
|
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18
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+
.int()
|
|
19
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+
.positive()
|
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20
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+
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
|
19
21
|
}),
|
|
20
22
|
output: z.object({
|
|
21
23
|
cid: z.number().describe('PubChem Compound ID.'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,
|
|
1
|
+
{"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,sQAAsQ;IACxQ,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;KAC5F,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;QACxF,GAAG,EAAE,CAAC;aACH,MAAM,CAAC;YACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;YACrF,UAAU,EAAE,CAAC;iBACV,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;iBACjB,QAAQ,CAAC,mDAAmD,CAAC;YAChE,gBAAgB,EAAE,CAAC;iBAChB,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;gBAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;aACzD,CAAC;iBACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;iBACA,QAAQ,CAAC,wBAAwB,CAAC;YACrC,uBAAuB,EAAE,CAAC;iBACvB,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;gBAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;aAChE,CAAC;iBACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;iBACA,QAAQ,CAAC,+BAA+B,CAAC;SAC7C,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CAAC,0BAA0B,CAAC;QACvC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KACnE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAEnD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,IAAI,KAAK,IAAI,EAAE,CAAC,CAAC;QAEhF,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC;QAC5C,CAAC;QAED,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,OAAO,EAAE,IAAI;YACb,GAAG,EAAE;gBACH,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,uBAAuB,EAAE,IAAI,CAAC,uBAAuB;aACtD;YACD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,CAAC,MAAM,CAAC,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC;YACnC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,wCAAwC,MAAM,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC;QACzF,CAAC;QAED,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QACvE,MAAM,CAAC,GAAG,MAAM,CAAC,GAAG,CAAC;QAErB,IAAI,CAAC,CAAC,UAAU;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;QACjE,IAAI,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC;YAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAEtF,IAAI,CAAC,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAClC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,wBAAwB,CAAC,CAAC;YACzC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,gBAAgB,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC;QAED,IAAI,CAAC,CAAC,uBAAuB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACzC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,+BAA+B,CAAC,CAAC;YAChD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,uBAAuB,EAAE,CAAC;gBAC1C,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC;QAED,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,YAAY,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC;QAC/C,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
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-
{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;
|
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1
|
+
{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;6BAmH3B,CAAC"}
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@@ -8,35 +8,37 @@ import { XREF_TYPES } from '../../../services/pubchem/types.js';
|
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8
8
|
const xrefTypeEnum = z.enum(XREF_TYPES);
|
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9
9
|
export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
|
|
10
10
|
title: 'Get Compound Cross-References',
|
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11
|
-
description: 'Get external database cross-references for a compound: PubMed citations, patent IDs, '
|
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12
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-
'gene/protein associations, registry numbers, and taxonomy IDs. Results are capped per ' +
|
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13
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-
'type with total counts reported.',
|
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11
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+
description: 'Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are capped per type with total counts reported.',
|
|
14
12
|
annotations: {
|
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15
13
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readOnlyHint: true,
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16
14
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idempotentHint: true,
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17
15
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openWorldHint: true,
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18
16
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},
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17
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input: z.object({
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-
cid: z
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18
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+
cid: z
|
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19
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+
.number()
|
|
20
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+
.int()
|
|
21
|
+
.positive()
|
|
22
|
+
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
|
21
23
|
xrefTypes: z
|
|
22
24
|
.array(xrefTypeEnum)
|
|
23
25
|
.min(1)
|
|
24
|
-
.describe('Cross-reference types to retrieve.
|
|
25
|
-
'PubMedID, PatentID, GeneID, ProteinGI, TaxonomyID.'),
|
|
26
|
+
.describe('Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID.'),
|
|
26
27
|
maxPerType: z
|
|
27
28
|
.number()
|
|
28
29
|
.min(1)
|
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29
30
|
.max(500)
|
|
30
31
|
.default(50)
|
|
31
|
-
.describe('Max IDs to return per xref type (1-500). A compound may have thousands of PubMed '
|
|
32
|
-
'references — this cap prevents bloat. Total count always reported. Default: 50.'),
|
|
32
|
+
.describe('Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references. Total count always reported. Default: 50.'),
|
|
33
33
|
}),
|
|
34
34
|
output: z.object({
|
|
35
35
|
cid: z.number().describe('PubChem Compound ID.'),
|
|
36
36
|
xrefs: z
|
|
37
37
|
.array(z
|
|
38
38
|
.object({
|
|
39
|
-
type: z
|
|
39
|
+
type: z
|
|
40
|
+
.string()
|
|
41
|
+
.describe('Cross-reference type: RegistryID, RN, PubMedID, PatentID, GeneID, ProteinGI, or TaxonomyID.'),
|
|
40
42
|
ids: z
|
|
41
43
|
.array(z
|
|
42
44
|
.union([
|
|
@@ -1 +1 @@
|
|
|
1
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-
{"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,
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+
{"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6MAA6M;IAC/M,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wIAAwI,CACzI;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,GAAG,EAAE,CAAC;iBACH,KAAK,CACJ,CAAC;iBACE,KAAK,CAAC;gBACL,CAAC;qBACE,MAAM,EAAE;qBACR,QAAQ,CAAC,2DAA2D,CAAC;gBACxE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,kEAAkE,CAAC,CAChF;iBACA,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;YAC7E,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,iDAAiD;QACjD,MAAM,KAAK,GAKN,EAAE,CAAC;QAER,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YACvC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;YAC1D,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;YAE9C,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,cAAc,GAAG,KAAK,CAAC,UAAU;aAC7C,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,SAAS;YACtB,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;SAC1D,CAAC,CAAC;QAEH,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACnC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEvE,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAChC,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS;gBAC9B,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,oBAAoB;gBAClE,CAAC,CAAC,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,OAAO,SAAS,GAAG,CAAC,CAAC;YAE9C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxB,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjF,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAC/C,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YAC7B,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -1,6 +1,5 @@
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1
1
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/**
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-
* @fileoverview Get descriptive summaries for PubChem entities: assays, genes,
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* proteins, pathways, taxonomy, cell lines, or substances.
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* @fileoverview Get descriptive summaries for PubChem entities: assays, genes, proteins, or taxonomy.
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4
3
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* @module mcp-server/tools/definitions/get-summary
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5
4
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*/
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6
5
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import { z } from '@cyanheads/mcp-ts-core';
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA
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1
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+
{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsGrB,CAAC"}
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@@ -1,6 +1,5 @@
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1
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/**
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2
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-
* @fileoverview Get descriptive summaries for PubChem entities: assays, genes,
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3
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* proteins, pathways, taxonomy, cell lines, or substances.
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2
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+
* @fileoverview Get descriptive summaries for PubChem entities: assays, genes, proteins, or taxonomy.
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4
3
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* @module mcp-server/tools/definitions/get-summary
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5
4
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*/
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6
5
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import { tool, z } from '@cyanheads/mcp-ts-core';
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@@ -32,8 +31,7 @@ const entitySummaryDataSchema = z.object({
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32
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});
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33
32
|
export const getSummary = tool('pubchem_get_summary', {
|
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34
33
|
title: 'Get Entity Summary',
|
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35
|
-
description: 'Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), '
|
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36
|
-
'proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.',
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34
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+
description: 'Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.',
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37
35
|
annotations: {
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38
36
|
readOnlyHint: true,
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39
37
|
idempotentHint: true,
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@@ -50,11 +48,7 @@ export const getSummary = tool('pubchem_get_summary', {
|
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|
50
48
|
.describe('Entity identifier — string or number depending on entityType.'))
|
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51
49
|
.min(1)
|
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52
50
|
.max(10)
|
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53
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-
.describe('Entity identifiers (1-10). Type depends on entityType:\n'
|
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54
|
-
'- assay: AID (number), e.g. [1000]\n' +
|
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55
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-
'- gene: Gene ID (number), e.g. [1956]\n' +
|
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56
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-
'- protein: UniProt accession (string), e.g. ["P00533"]\n' +
|
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57
|
-
'- taxonomy: Tax ID (number), e.g. [9606]'),
|
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51
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+
.describe('Entity identifiers (1-10). Type depends on entityType:\n- assay: AID (number), e.g. [1000]\n- gene: Gene ID (number), e.g. [1956]\n- protein: UniProt accession (string), e.g. ["P00533"]\n- taxonomy: Tax ID (number), e.g. [9606]'),
|
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58
52
|
}),
|
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59
53
|
output: z.object({
|
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60
54
|
entityType: z.string().describe('Entity type queried.'),
|
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-summary.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA
|
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1
|
+
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