@cyanheads/pubchem-mcp-server 0.3.1 → 0.4.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +2 -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 +2 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +12 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +106 -4
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.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 +12 -4
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +8 -3
- package/dist/mcp-server/tools/definitions/get-compound-interactions.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 +4 -3
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.js +17 -4
- package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +12 -1
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/untrusted-text.d.ts +35 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.js +65 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.js.map +1 -0
- package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
- package/dist/services/pubchem/pubchem-client.js +137 -10
- package/dist/services/pubchem/pubchem-client.js.map +1 -1
- package/manifest.json +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/README.md
CHANGED
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@@ -7,7 +7,7 @@
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<div align="center">
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-
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -104,6 +104,7 @@ Get a compound's interaction data by CID.
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Get a compound's default 3D conformer by CID.
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- `format="json"` returns parsed atoms (element + x/y/z) and bonds for direct reasoning; `format="sdf"` returns raw V2000 SDF for passthrough to docking or rendering
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+
- `maxAtoms`/`maxBonds` bound the atom/bond preview and `includeRawSdf` opts into a large raw SDF past the safe line cap; `atomCount`/`bondCount` always report the totals and any capping is disclosed
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- Optionally lists alternate conformer IDs
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- Returns a typed not-found when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)
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@@ -1 +1 @@
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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;
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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;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkNzB,CAAC"}
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@@ -5,6 +5,7 @@
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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import { inlineData } from './untrusted-text.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 (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".',
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@@ -175,7 +176,7 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
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const target = [r.targetGeneId ? `GeneID:${r.targetGeneId}` : undefined, r.targetAccession]
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.filter(Boolean)
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.join(' — ');
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lines.push(`**AID ${r.aid}** — ${r.assayName} (${r.outcome})`);
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lines.push(`**AID ${r.aid}** — ${inlineData(r.assayName)} (${r.outcome})`);
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if (target)
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lines.push(` Target: ${target}`);
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for (const av of r.activityValues) {
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@@ -1 +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;
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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;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,kYAAkY;IACpY,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,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,2OAA2O,CAC5O;QACH,eAAe,EAAE,CAAC;aACf,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,kMAAkM,CACnM;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;IACF,uFAAuF;IACvF,wFAAwF;IACxF,yEAAyE;IACzE,UAAU,EAAE;QACV,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACvF,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qEAAqE,CAAC;QAClF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CAAC,4EAA4E,CAAC;QACzF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAC/E,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,2EAA2E,CAAC;QACxF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAClF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;KACJ;IAED,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,2EAA2E;QAC3E,yFAAyF;QACzF,IAAI,QAAQ,GAAG,OAAO,CAAC;QACvB,IAAI,KAAK,CAAC,aAAa,KAAK,QAAQ,EAAE,CAAC;YACrC,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC;QAC5D,CAAC;aAAM,IAAI,KAAK,CAAC,aAAa,KAAK,UAAU,EAAE,CAAC;YAC9C,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC;QAC9D,CAAC;QAED,MAAM,WAAW,GAAG;YAClB,KAAK,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS;YACvE,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,aAAa,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,SAAS;SACzE;aACE,MAAM,CAAC,OAAO,CAAC;aACf,IAAI,CAAC,GAAG,CAAC,CAAC;QACb,IAAI,KAAK,CAAC,YAAY,IAAI,IAAI,EAAE,CAAC;YAC/B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,KAAK,CAAC,YAAY,CAAC,CAAC;QAC3E,CAAC;QACD,IAAI,KAAK,CAAC,eAAe,EAAE,CAAC;YAC1B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,KAAK,KAAK,CAAC,eAAe,CAAC,CAAC;QACjF,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,QAAQ,CAAC,MAAM;YACzB,QAAQ,EAAE,OAAO,CAAC,MAAM;SACzB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC;YACT,aAAa,EAAE,KAAK,CAAC,aAAa;YAClC,aAAa,EAAE,QAAQ,CAAC,MAAM;YAC9B,aAAa,EAAE,OAAO,CAAC,MAAM;SAC9B,CAAC,CAAC;QACH,IAAI,WAAW;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,WAAW,EAAE,CAAC,CAAC;QAC3D,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,yFAAyF,CACxI,CAAC;QACJ,CAAC;aAAM,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,WAAW;gBACT,CAAC,CAAC,OAAO,KAAK,CAAC,GAAG,QAAQ,OAAO,CAAC,MAAM,+CAA+C,WAAW,IAAI,KAAK,CAAC,aAAa,KAAK,KAAK,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,aAAa,GAAG,CAAC,CAAC,CAAC,EAAE,wFAAwF;gBACjR,CAAC,CAAC,OAAO,KAAK,CAAC,GAAG,QAAQ,OAAO,CAAC,MAAM,2CAA2C,KAAK,CAAC,aAAa,yCAAyC,CAClJ,CAAC;QACJ,CAAC;aAAM,IAAI,QAAQ,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;YAC5C,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;QACzE,CAAC;QAED,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,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC;YAC3E,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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json: "json";
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}>>;
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includeAlternateConformerIds: z.ZodDefault<z.ZodBoolean>;
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maxAtoms: z.ZodOptional<z.ZodNumber>;
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maxBonds: z.ZodOptional<z.ZodNumber>;
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includeRawSdf: z.ZodDefault<z.ZodBoolean>;
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}, z.core.$strip>, z.ZodObject<{
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cid: z.ZodNumber;
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conformerId: z.ZodOptional<z.ZodString>;
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@@ -34,5 +37,13 @@ export declare const getCompound3dStructure: import("@cyanheads/mcp-ts-core").To
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readonly code: JsonRpcErrorCode.NotFound;
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readonly when: "PubChem has no computed 3D conformer for the requested CID";
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readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
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}],
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}], {
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readonly truncated: z.ZodOptional<z.ZodBoolean>;
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readonly shownAtoms: z.ZodOptional<z.ZodNumber>;
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readonly shownBonds: z.ZodOptional<z.ZodNumber>;
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readonly atomCap: z.ZodOptional<z.ZodNumber>;
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readonly bondCap: z.ZodOptional<z.ZodNumber>;
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readonly shownSdfLines: z.ZodOptional<z.ZodNumber>;
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readonly notice: z.ZodOptional<z.ZodString>;
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}>;
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//# sourceMappingURL=get-compound-3d-structure.tool.d.ts.map
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{"version":3,"file":"get-compound-3d-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
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{"version":3,"file":"get-compound-3d-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAcjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiRjC,CAAC"}
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@@ -6,6 +6,15 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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import { parseSdfV2000 } from '../../../services/pubchem/sdf-parser.js';
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import { fencedData } from './untrusted-text.js';
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/**
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* Safe-default ceilings applied when the caller sets no explicit cap. Sized to
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* pass small drug-like conformers (aspirin: 21 atoms/bonds, ~60 SDF lines)
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* through unchanged while bounding pathologically large records.
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*/
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const DEFAULT_ATOM_CAP = 200;
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const DEFAULT_BOND_CAP = 200;
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const DEFAULT_SDF_LINE_CAP = 500;
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export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure', {
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title: 'Get Compound 3D Structure',
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description: 'Get a compound\'s default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns parsed atoms and bonds the model can reason over directly; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).',
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@@ -28,6 +37,22 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
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.boolean()
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.default(false)
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.describe('List the IDs of additional computed conformers beyond the default. Adds one extra API call. Default: false.'),
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maxAtoms: z
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.number()
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.int()
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.positive()
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.optional()
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.describe('Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.'),
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maxBonds: z
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.number()
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.int()
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.positive()
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.optional()
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.describe('Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.'),
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includeRawSdf: z
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.boolean()
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.default(false)
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.describe('For format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json".'),
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}),
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output: z.object({
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cid: z.number().describe('PubChem Compound ID.'),
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@@ -64,6 +89,41 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
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.optional()
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.describe('Conformer IDs beyond the default. Present when includeAlternateConformerIds is set and alternates exist.'),
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}),
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// Agent-facing context — truncation disclosure when a preview is capped below
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// the total. Reaches structuredContent and content[]; keys disjoint from output
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// (atomCount/bondCount always report the full totals). Follows the sibling
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// truncated/shown/cap convention, split per-list because atoms, bonds, and the
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// raw SDF cap independently.
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enrichment: {
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truncated: z
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.boolean()
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.optional()
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.describe('True when the atom list, bond list, or raw SDF was capped below its total. atomCount/bondCount always report the full totals.'),
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shownAtoms: z
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.number()
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.optional()
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.describe('Atoms returned after the cap, when fewer than atomCount. Raise maxAtoms for more.'),
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shownBonds: z
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.number()
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.optional()
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.describe('Bonds returned after the cap, when fewer than bondCount. Raise maxBonds for more.'),
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atomCap: z
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.number()
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.optional()
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.describe('The atom cap applied (explicit maxAtoms or the safe default), when the atom list was capped.'),
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bondCap: z
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.number()
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.optional()
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.describe('The bond cap applied (explicit maxBonds or the safe default), when the bond list was capped.'),
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shownSdfLines: z
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.number()
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.optional()
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.describe('SDF lines returned when format="sdf" and the raw text was line-capped. Set includeRawSdf for the full record.'),
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notice: z
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.string()
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.optional()
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.describe('Guidance naming which lists were capped and how to widen them.'),
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},
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errors: [
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{
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reason: 'no_3d_structure',
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@@ -78,12 +138,24 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
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const sdf = await client.getSdf3d(input.cid);
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const parsed = parseSdfV2000(sdf);
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const out = { cid: input.cid, atomCount: parsed.atomCount, bondCount: parsed.bondCount };
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const atomCap = input.maxAtoms ?? DEFAULT_ATOM_CAP;
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const bondCap = input.maxBonds ?? DEFAULT_BOND_CAP;
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let sdfTruncated = false;
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let shownSdfLines = 0;
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if (input.format === 'json') {
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out.atoms = parsed.atoms;
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out.bonds = parsed.bonds;
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out.atoms = parsed.atoms.slice(0, atomCap);
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out.bonds = parsed.bonds.slice(0, bondCap);
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}
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else {
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-
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const sdfLines = sdf.split(/\r\n?|\n/);
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if (input.includeRawSdf || sdfLines.length <= DEFAULT_SDF_LINE_CAP) {
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out.sdf = sdf;
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}
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else {
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out.sdf = sdfLines.slice(0, DEFAULT_SDF_LINE_CAP).join('\n');
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sdfTruncated = true;
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shownSdfLines = DEFAULT_SDF_LINE_CAP;
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}
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}
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if (input.includeAlternateConformerIds) {
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const ids = await client.getConformerIds(input.cid);
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@@ -100,6 +172,28 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
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atoms: parsed.atomCount,
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bonds: parsed.bondCount,
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});
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// Truncation disclosure — atoms, bonds, and SDF each cap independently.
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const atomsTruncated = out.atoms !== undefined && parsed.atomCount > out.atoms.length;
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const bondsTruncated = out.bonds !== undefined && parsed.bondCount > out.bonds.length;
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if (atomsTruncated || bondsTruncated || sdfTruncated) {
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ctx.enrich({
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truncated: true,
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...(atomsTruncated ? { shownAtoms: out.atoms?.length, atomCap } : {}),
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...(bondsTruncated ? { shownBonds: out.bonds?.length, bondCap } : {}),
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...(sdfTruncated ? { shownSdfLines } : {}),
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});
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const parts = [];
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if (atomsTruncated) {
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parts.push(`atoms (${out.atoms?.length} of ${parsed.atomCount}; raise maxAtoms)`);
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}
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if (bondsTruncated) {
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parts.push(`bonds (${out.bonds?.length} of ${parsed.bondCount}; raise maxBonds)`);
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}
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if (sdfTruncated) {
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parts.push(`SDF (first ${shownSdfLines} lines; set includeRawSdf for the full record)`);
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}
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ctx.enrich.notice(`Output capped — ${parts.join('; ')}.`);
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}
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return out;
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},
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format(result) {
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@@ -117,15 +211,23 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
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for (const a of result.atoms) {
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lines.push(` ${a.element}: ${a.x}, ${a.y}, ${a.z}`);
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}
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if (result.atomCount > result.atoms.length) {
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lines.push(` _Showing ${result.atoms.length} of ${result.atomCount} atoms — raise maxAtoms for the rest._`);
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}
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}
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if (result.bonds && result.bonds.length > 0) {
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lines.push('', '**Bonds** (a1–a2, order):');
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for (const b of result.bonds) {
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lines.push(` ${b.a1}–${b.a2}, order ${b.order}`);
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}
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if (result.bondCount > result.bonds.length) {
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lines.push(` _Showing ${result.bonds.length} of ${result.bondCount} bonds — raise maxBonds for the rest._`);
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}
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}
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if (result.sdf) {
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-
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// fencedData lengthens the fence past any backtick run in the payload so a
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// stray ``` in the SDF cannot break out of the code block.
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lines.push('', '**SDF (V2000):**', fencedData(result.sdf.trimEnd()));
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}
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return [{ type: 'text', text: lines.join('\n') }];
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},
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@@ -1 +1 @@
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1
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{"version":3,"file":"get-compound-3d-structure.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAC;
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1
|
+
{"version":3,"file":"get-compound-3d-structure.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAC;AACjE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,oBAAoB,GAAG,GAAG,CAAC;AAEjC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC9E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,qaAAqa;IACva,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,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;aACrB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,sIAAsI,CACvI;QACH,4BAA4B,EAAE,CAAC;aAC5B,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,6GAA6G,CAC9G;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,oMAAoM,CACrM;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,oMAAoM,CACrM;QACH,aAAa,EAAE,CAAC;aACb,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,uMAAuM,CACxM;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;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACnE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACnE,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;YACpE,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YACnD,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YACnD,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;SACpD,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YACtD,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;YACvD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;SACrF,CAAC;aACD,QAAQ,CAAC,yBAAyB,CAAC,CACvC;aACA,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QACvF,qBAAqB,EAAE,CAAC;aACrB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CACP,0GAA0G,CAC3G;KACJ,CAAC;IACF,8EAA8E;IAC9E,gFAAgF;IAChF,2EAA2E;IAC3E,+EAA+E;IAC/E,6BAA6B;IAC7B,UAAU,EAAE;QACV,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CACP,+HAA+H,CAChI;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+GAA+G,CAChH;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,gEAAgE,CAAC;KAC9E;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,4DAA4D;YAClE,QAAQ,EACN,uGAAuG;SAC1G;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,mFAAmF;QACnF,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAC7C,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,CAAC,CAAC;QAElC,MAAM,GAAG,GASL,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC;QAEjF,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,IAAI,gBAAgB,CAAC;QACnD,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,IAAI,gBAAgB,CAAC;QAEnD,IAAI,YAAY,GAAG,KAAK,CAAC;QACzB,IAAI,aAAa,GAAG,CAAC,CAAC;QAEtB,IAAI,KAAK,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC5B,GAAG,CAAC,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC;YAC3C,GAAG,CAAC,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YACvC,IAAI,KAAK,CAAC,aAAa,IAAI,QAAQ,CAAC,MAAM,IAAI,oBAAoB,EAAE,CAAC;gBACnE,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC;YAChB,CAAC;iBAAM,CAAC;gBACN,GAAG,CAAC,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,oBAAoB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC7D,YAAY,GAAG,IAAI,CAAC;gBACpB,aAAa,GAAG,oBAAoB,CAAC;YACvC,CAAC;QACH,CAAC;QAED,IAAI,KAAK,CAAC,4BAA4B,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;gBACX,GAAG,CAAC,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;gBACzB,MAAM,UAAU,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gBAChC,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;oBAAE,GAAG,CAAC,qBAAqB,GAAG,UAAU,CAAC;YACpE,CAAC;QACH,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,KAAK,EAAE,MAAM,CAAC,SAAS;YACvB,KAAK,EAAE,MAAM,CAAC,SAAS;SACxB,CAAC,CAAC;QAEH,wEAAwE;QACxE,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@@ -1 +1 @@
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1
|
-
{"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;
|
|
1
|
+
{"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;AA4GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCA2Y7B,CAAC"}
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@@ -6,6 +6,7 @@
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|
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6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
7
|
import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
|
|
8
8
|
import { COMPOUND_PROPERTIES, DEFAULT_PROPERTIES } from '../../../services/pubchem/types.js';
|
|
9
|
+
import { inlineData, quoteData } from './untrusted-text.js';
|
|
9
10
|
const propertyEnum = z.enum(COMPOUND_PROPERTIES);
|
|
10
11
|
const drugLikenessRuleSchema = z.object({
|
|
11
12
|
limit: z.number().describe('Rule threshold.'),
|
|
@@ -276,7 +277,9 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
276
277
|
}
|
|
277
278
|
const p = c.properties;
|
|
278
279
|
const name = p.IUPACName ?? p.Title ?? '';
|
|
279
|
-
const header = name
|
|
280
|
+
const header = name
|
|
281
|
+
? `## CID ${c.cid} — ${inlineData(name)} (found)`
|
|
282
|
+
: `## CID ${c.cid} (found)`;
|
|
280
283
|
blocks.push(header);
|
|
281
284
|
const lines = ['**Properties:**'];
|
|
282
285
|
// Key identifiers
|
|
@@ -391,8 +394,12 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
391
394
|
: `\n**Descriptions** (${total} total)`;
|
|
392
395
|
const descLines = [header];
|
|
393
396
|
for (const d of c.descriptions) {
|
|
394
|
-
|
|
395
|
-
|
|
397
|
+
// Upstream free text — render the statement as a blockquote data block
|
|
398
|
+
// so it reads as retrieved data, not server instructions.
|
|
399
|
+
const label = d.source
|
|
400
|
+
? `**Description (${inlineData(d.source)}):**`
|
|
401
|
+
: '**Description:**';
|
|
402
|
+
descLines.push(`${label}\n${quoteData(d.text)}`);
|
|
396
403
|
}
|
|
397
404
|
const more = total - shown;
|
|
398
405
|
if (more > 0) {
|
|
@@ -405,7 +412,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
|
|
|
405
412
|
const total = c.synonymsTotal ?? c.synonyms.length;
|
|
406
413
|
const more = total - c.synonyms.length;
|
|
407
414
|
const suffix = more > 0 ? ` (+${more} more)` : '';
|
|
408
|
-
|
|
415
|
+
const syns = c.synonyms.map(inlineData).join(', ');
|
|
416
|
+
blocks.push(`\n**Synonyms** (${total} total): ${syns}${suffix}`);
|
|
409
417
|
}
|
|
410
418
|
blocks.push('');
|
|
411
419
|
}
|
|
@@ -1 +1 @@
|
|
|
1
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-
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1
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+
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@@ -1 +1 @@
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1
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-
{"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;
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1
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+
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;EAsIlC,CAAC"}
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@@ -4,6 +4,7 @@
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4
4
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*/
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5
5
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
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6
6
|
import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
|
|
7
|
+
import { inlineData, quoteData } from './untrusted-text.js';
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|
7
8
|
export const getCompoundInteractions = tool('pubchem_get_compound_interactions', {
|
|
8
9
|
title: 'Get Compound Interactions',
|
|
9
10
|
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.",
|
|
@@ -100,9 +101,13 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
|
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|
100
101
|
return [{ type: 'text', text: lines.join('\n') }];
|
|
101
102
|
}
|
|
102
103
|
for (const e of result.entries) {
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|
103
|
-
const partner = e.partner ? ` **${e.partner}**` : '';
|
|
104
|
-
const severity = e.severity ? ` [severity: ${e.severity}]` : '';
|
|
105
|
-
lines.push(`- (${e.kind})${partner}${severity}
|
|
104
|
+
const partner = e.partner ? ` **${inlineData(e.partner)}**` : '';
|
|
105
|
+
const severity = e.severity ? ` [severity: ${inlineData(e.severity)}]` : '';
|
|
106
|
+
lines.push(`- (${e.kind})${partner}${severity} _(source: ${inlineData(e.source)})_`);
|
|
107
|
+
// The interaction statement is upstream free text — render it as an
|
|
108
|
+
// indented blockquote so the data/instruction boundary is explicit.
|
|
109
|
+
for (const q of quoteData(e.text).split('\n'))
|
|
110
|
+
lines.push(` ${q}`);
|
|
106
111
|
}
|
|
107
112
|
return [{ type: 'text', text: lines.join('\n') }];
|
|
108
113
|
},
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;
|
|
1
|
+
{"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.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,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAE5D,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC/E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,oTAAoT;IACtT,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,KAAK,EAAE,CAAC;aACL,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC;aACtB,QAAQ,CACP,6LAA6L,CAC9L;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,gGAAgG,CACjG;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACpF,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;YACjF,QAAQ,EAAE,CAAC;iBACR,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,kJAAkJ,CACnJ;YACH,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;SACxD,CAAC;aACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;aACA,QAAQ,CAAC,iDAAiD,CAAC;KAC/D,CAAC;IACF,8FAA8F;IAC9F,oFAAoF;IACpF,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;QAC1F,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4JAA4J,CAC7J;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,sEAAsE,CAAC;KACpF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAC3D,KAAK,CAAC,GAAG,EACT,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,UAAU,CACjB,CAAC;QAEF,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;YAC5B,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,yBAAyB,EAAE;gBACzC,GAAG,EAAE,KAAK,CAAC,GAAG;gBACd,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,OAAO;aACjB,CAAC,CAAC;QACL,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,QAAQ,EAAE,OAAO,CAAC,MAAM;YACxB,MAAM,EAAE,WAAW,CAAC,MAAM;SAC3B,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,aAAa,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;QAEtF,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACxD,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACtC,GAAG,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC,CAAC;YACnC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,sBAAsB,KAAK,eAAe,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,YAAY,KAAK,CAAC,GAAG,IAC9E,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,qCAAqC,CAAC,CAAC,CAAC,EAC/D,wBAAwB,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,GAAG,CAClD,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,mCAAmC,KAAK,CAAC,GAAG,4GAA4G,CACpL,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,CAAC;IACrC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,yBAAyB,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEpE,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,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,UAAU,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;YACjE,MAAM,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,eAAe,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5E,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,IAAI,OAAO,GAAG,QAAQ,cAAc,UAAU,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACrF,oEAAoE;YACpE,oEAAoE;YACpE,KAAK,MAAM,CAAC,IAAI,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACtE,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
|
-
{"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;
|
|
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;AAmCjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;EAmI5B,CAAC"}
|
|
@@ -4,6 +4,7 @@
|
|
|
4
4
|
*/
|
|
5
5
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
6
6
|
import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
|
|
7
|
+
import { inlineData } from './untrusted-text.js';
|
|
7
8
|
const ghsSchema = z
|
|
8
9
|
.object({
|
|
9
10
|
signalWord: z.string().optional().describe('GHS signal word: "Danger" or "Warning".'),
|
|
@@ -124,16 +125,16 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
|
|
|
124
125
|
if (g.hazardStatements.length > 0) {
|
|
125
126
|
lines.push('', '**Hazard Statements:**');
|
|
126
127
|
for (const h of g.hazardStatements)
|
|
127
|
-
lines.push(` ${h.code}: ${h.statement}`);
|
|
128
|
+
lines.push(` ${h.code}: ${inlineData(h.statement)}`);
|
|
128
129
|
}
|
|
129
130
|
if (g.precautionaryStatements.length > 0) {
|
|
130
131
|
lines.push('', '**Precautionary Statements:**');
|
|
131
132
|
for (const p of g.precautionaryStatements) {
|
|
132
|
-
lines.push(p.statement ? ` ${p.code}: ${p.statement}` : ` ${p.code}`);
|
|
133
|
+
lines.push(p.statement ? ` ${p.code}: ${inlineData(p.statement)}` : ` ${p.code}`);
|
|
133
134
|
}
|
|
134
135
|
}
|
|
135
136
|
if (r.source)
|
|
136
|
-
lines.push('', `*Source: ${r.source}*`);
|
|
137
|
+
lines.push('', `*Source: ${inlineData(r.source)}*`);
|
|
137
138
|
blocks.push(lines.join('\n'), '');
|
|
138
139
|
}
|
|
139
140
|
return [{ type: 'text', text: blocks.join('\n') }];
|
|
@@ -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;
|
|
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,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,SAAS,GAAG,CAAC;KAChB,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;IACrF,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAC7F,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;KACzD,CAAC;SACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;SACA,QAAQ,CAAC,wBAAwB,CAAC;IACrC,uBAAuB,EAAE,CAAC;SACvB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KAChE,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC;KACD,QAAQ,CAAC,0BAA0B,CAAC,CAAC;AAExC,sGAAsG;AACtG,MAAM,aAAa,GAAG,EAAE,CAAC;AAEzB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,qSAAqS;IACvS,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC;aACJ,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC;aAClC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,gHAAgH,CACjH;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YAChD,OAAO,EAAE,CAAC;iBACP,OAAO,EAAE;iBACT,QAAQ,CAAC,yDAAyD,CAAC;YACtE,GAAG,EAAE,SAAS,CAAC,QAAQ,EAAE;YACzB,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,wBAAwB,CAAC,CACtC;aACA,QAAQ,CAAC,gEAAgE,CAAC;KAC9E,CAAC;IACF,6FAA6F;IAC7F,0FAA0F;IAC1F,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACtD,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC1E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gGAAgG,CACjG;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,sDAAsD;QACtD,MAAM,SAAS,GAAG,IAAI,GAAG,EAAoC,CAAC;QAC9D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,aAAa,EAAE,CAAC;YAC1D,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,CAAC;YACrD,MAAM,SAAS,GAAG,MAAM,OAAO,CAAC,GAAG,CACjC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,MAAM,MAAM,CAAC,aAAa,CAAC,GAAG,CAAC,CAAU,CAAC,CAC1E,CAAC;YACF,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,SAAS;gBAAE,SAAS,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;QAChE,CAAC;QAED,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrC,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC;YACxC,IAAI,CAAC,IAAI;gBAAE,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,KAAc,EAAE,CAAC;YACnD,OAAO;gBACL,GAAG;gBACH,OAAO,EAAE,IAAa;gBACtB,GAAG,EAAE;oBACH,UAAU,EAAE,IAAI,CAAC,UAAU;oBAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;oBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,uBAAuB,EAAE,IAAI,CAAC,uBAAuB;iBACtD;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAE9D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,SAAS,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM;YAC5B,QAAQ,EAAE,aAAa;SACxB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC;QACjE,IAAI,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACtC,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACpE,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,OAAO,CAAC,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,YAAY,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,0IAA0I,CACpP,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,OAAO,EAAE,CAAC;IACrB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,yBAAyB,EAAE,CAAC,CAAC;QAC7D,CAAC;QAED,MAAM,MAAM,GAAa,EAAE,CAAC;QAC5B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,uBAAuB,EAAE,EAAE,CAAC,CAAC;gBACxD,SAAS;YACX,CAAC;YAED,MAAM,KAAK,GAAa,CAAC,4BAA4B,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC;YAEhB,IAAI,CAAC,CAAC,UAAU;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;YACjE,IAAI,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAEtF,IAAI,CAAC,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,wBAAwB,CAAC,CAAC;gBACzC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,gBAAgB;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;YAC5F,CAAC;YAED,IAAI,CAAC,CAAC,uBA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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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;AAmCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmIrB,CAAC"}
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@@ -4,6 +4,7 @@
|
|
|
4
4
|
*/
|
|
5
5
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
6
6
|
import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
|
|
7
|
+
import { inlineData, quoteData } from './untrusted-text.js';
|
|
7
8
|
const entityTypeEnum = z.enum(['assay', 'gene', 'protein', 'taxonomy']);
|
|
8
9
|
/**
|
|
9
10
|
* Union-of-shapes schema for entity summaries. All fields are optional because the
|
|
@@ -110,18 +111,30 @@ export const getSummary = tool('pubchem_get_summary', {
|
|
|
110
111
|
}
|
|
111
112
|
const d = s.data;
|
|
112
113
|
const displayName = d.name ?? d.symbol ?? String(s.identifier);
|
|
113
|
-
lines.push(`**${displayName}** (identifier: ${s.identifier}, found)`);
|
|
114
|
+
lines.push(`**${inlineData(displayName)}** (identifier: ${s.identifier}, found)`);
|
|
114
115
|
for (const [key, value] of Object.entries(d)) {
|
|
115
116
|
if (value == null || key === 'name')
|
|
116
117
|
continue;
|
|
118
|
+
// description is upstream prose — frame it as a blockquote data block.
|
|
119
|
+
if (key === 'description' && typeof value === 'string') {
|
|
120
|
+
lines.push(` ${formatKey(key)}:`);
|
|
121
|
+
for (const q of quoteData(value).split('\n'))
|
|
122
|
+
lines.push(` ${q}`);
|
|
123
|
+
continue;
|
|
124
|
+
}
|
|
117
125
|
if (Array.isArray(value)) {
|
|
118
126
|
if (value.length === 0)
|
|
119
127
|
continue;
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
|
|
128
|
+
// synonyms / lineage — upstream free text; escape each element inline.
|
|
129
|
+
const items = value.map((v) => inlineData(String(v)));
|
|
130
|
+
const display = items.length > 10
|
|
131
|
+
? `${items.slice(0, 10).join(', ')} (+${items.length - 10} more)`
|
|
132
|
+
: items.join(', ');
|
|
123
133
|
lines.push(` ${formatKey(key)}: ${display}`);
|
|
124
134
|
}
|
|
135
|
+
else if (typeof value === 'string') {
|
|
136
|
+
lines.push(` ${formatKey(key)}: ${inlineData(value)}`);
|
|
137
|
+
}
|
|
125
138
|
else {
|
|
126
139
|
lines.push(` ${formatKey(key)}: ${value}`);
|
|
127
140
|
}
|