@cyanheads/pubchem-mcp-server 0.1.10 → 0.1.12

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Files changed (26) hide show
  1. package/README.md +1 -1
  2. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +2 -2
  3. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +12 -5
  5. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts +1 -1
  7. package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +30 -11
  9. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts +18 -1
  11. package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/get-summary.tool.js +88 -38
  13. package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/index.d.ts +21 -4
  15. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +3 -0
  18. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  19. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  20. package/dist/services/pubchem/pubchem-client.js +11 -6
  21. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  22. package/dist/services/pubchem/types.d.ts +4 -3
  23. package/dist/services/pubchem/types.d.ts.map +1 -1
  24. package/dist/services/pubchem/types.js.map +1 -1
  25. package/package.json +7 -7
  26. package/server.json +3 -3
package/README.md CHANGED
@@ -6,7 +6,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.1.10-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.1.12-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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  </div>
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package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts CHANGED
@@ -24,9 +24,9 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
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  targetAccession: z.ZodOptional<z.ZodString>;
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  targetGeneId: z.ZodOptional<z.ZodNumber>;
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  activityValues: z.ZodArray<z.ZodObject<{
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- name: z.ZodString;
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+ name: z.ZodOptional<z.ZodString>;
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  value: z.ZodNumber;
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- unit: z.ZodString;
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+ unit: z.ZodOptional<z.ZodString>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map CHANGED
@@ -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;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;kBAgIzB,CAAC"}
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js CHANGED
@@ -48,9 +48,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
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  targetGeneId: z.number().optional().describe('Target NCBI Gene ID.'),
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  activityValues: z
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  .array(z.object({
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- name: z.string().describe('Measurement name (e.g. IC50, EC50, Ki).'),
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+ name: z
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+ .string()
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+ .optional()
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+ .describe('Measurement name (e.g. IC50, EC50, Ki). Omitted when not reported.'),
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  value: z.number().describe('Measured value.'),
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- unit: z.string().describe('Unit of measurement (e.g. uM, nM).'),
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+ unit: z
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+ .string()
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+ .optional()
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+ .describe('Unit of measurement (e.g. uM, nM). Omitted when not reported.'),
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  }))
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  .describe('Quantitative activity measurements.'),
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  }))
@@ -101,9 +107,10 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
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  lines.push(`**AID ${r.aid}** — ${r.assayName} (${r.outcome})`);
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  if (target)
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  lines.push(` Target: ${target}`);
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- const meaningful = r.activityValues.filter((av) => av.name);
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- for (const av of meaningful) {
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- lines.push(` ${av.name}: ${av.value} ${av.unit}`);
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+ for (const av of r.activityValues) {
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+ const label = av.name ?? 'Value';
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+ const unit = av.unit ?? '';
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+ lines.push(` ${label}: ${av.value}${unit ? ` ${unit}` : ''}`);
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  }
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  lines.push('');
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  }
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map CHANGED
@@ -1 +1 @@
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1
+ {"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,kFAAkF;QAClF,oFAAoF;QACpF,+FAA+F;IACjG,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,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACjE,aAAa,EAAE,CAAC;aACb,IAAI,CAAC,CAAC,QAAQ,EAAE,UAAU,EAAE,KAAK,CAAC,CAAC;aACnC,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,8FAA8F;YAC5F,mEAAmE,CACtE;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,CAAC,MAAM,CAAC;YACP,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,CAAC,MAAM,CAAC;gBACP,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CAAC,oEAAoE,CAAC;gBACjF,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,CACH;iBACA,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC,CACH;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"}
package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts CHANGED
@@ -43,7 +43,7 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
43
43
  value: z.ZodNullable<z.ZodNumber>;
44
44
  }, z.core.$strip>;
45
45
  }, z.core.$strip>;
46
- pass: z.ZodBoolean;
46
+ pass: z.ZodNullable<z.ZodBoolean>;
47
47
  veber: z.ZodObject<{
48
48
  rotatableBonds: z.ZodObject<{
49
49
  limit: z.ZodNumber;
package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map CHANGED
@@ -1 +1 @@
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;AA0FjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2S7B,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;AAyGjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8S7B,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-details.tool.js CHANGED
@@ -22,7 +22,10 @@ const drugLikenessSchema = z.object({
22
22
  xLogP: drugLikenessRuleSchema.describe('XLogP rule (≤5).'),
23
23
  })
24
24
  .describe('Lipinski Rule of Five evaluation.'),
25
- pass: z.boolean().describe('Overall drug-likeness pass.'),
25
+ pass: z
26
+ .boolean()
27
+ .nullable()
28
+ .describe('Overall drug-likeness pass. Null when insufficient properties were available.'),
26
29
  veber: z
27
30
  .object({
28
31
  rotatableBonds: drugLikenessRuleSchema.describe('Rotatable bond count rule (≤10).'),
@@ -53,9 +56,19 @@ const DRUG_LIKENESS_PROPS = [
53
56
  'RotatableBondCount',
54
57
  ];
55
58
  function evaluateRule(value, limit) {
56
- if (value == null || typeof value !== 'number')
59
+ let num = null;
60
+ if (typeof value === 'number' && Number.isFinite(value)) {
61
+ num = value;
62
+ }
63
+ else if (typeof value === 'string') {
64
+ // PubChem returns some numeric properties (MolecularWeight, ExactMass, ...) as strings.
65
+ const parsed = Number(value);
66
+ if (Number.isFinite(parsed))
67
+ num = parsed;
68
+ }
69
+ if (num === null)
57
70
  return { limit, pass: null, value: null };
58
- return { limit, pass: value <= limit, value };
71
+ return { limit, pass: num <= limit, value: num };
59
72
  }
60
73
  function computeDrugLikeness(properties) {
61
74
  const mw = evaluateRule(properties.MolecularWeight, 500);
@@ -68,9 +81,12 @@ function computeDrugLikeness(properties) {
68
81
  const veberRules = [tpsa, rotatableBonds];
69
82
  const lipinskiViolations = lipinskiRules.filter((r) => r.pass === false).length;
70
83
  const veberViolations = veberRules.filter((r) => r.pass === false).length;
84
+ // Any null rule means the underlying property was unavailable — refuse to invent a pass/fail.
85
+ const hasGap = [...lipinskiRules, ...veberRules].some((r) => r.pass === null);
86
+ const pass = hasGap ? null : lipinskiViolations <= 1 && veberViolations === 0;
71
87
  return {
72
88
  lipinski: { hba, hbd, mw, violations: lipinskiViolations, xLogP },
73
- pass: lipinskiViolations <= 1 && veberViolations === 0,
89
+ pass,
74
90
  veber: { rotatableBonds, tpsa, violations: veberViolations },
75
91
  };
76
92
  }
@@ -102,8 +118,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
102
118
  includeDescription: z
103
119
  .boolean()
104
120
  .default(false)
105
- .describe('Fetch textual description from PUG View (pharmacology, mechanism, therapeutic use). ' +
106
- 'Adds one API call per CID — consider limiting CID count when enabled.'),
121
+ .describe('Include textual description (pharmacology, mechanism, therapeutic use). ' +
122
+ 'Slower when enabled — prefer small CID batches.'),
107
123
  includeSynonyms: z
108
124
  .boolean()
109
125
  .default(false)
@@ -116,9 +132,9 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
116
132
  includeClassification: z
117
133
  .boolean()
118
134
  .default(false)
119
- .describe('Fetch pharmacological classification from PUG View: FDA Established Pharmacologic ' +
120
- 'Classes, mechanisms of action, MeSH classes, and ATC codes. ' +
121
- 'Adds one API call per CID — consider limiting CID count when enabled.'),
135
+ .describe('Include pharmacological classification: FDA Established Pharmacologic Classes, ' +
136
+ 'mechanisms of action, MeSH classes, and ATC codes. ' +
137
+ 'Slower when enabled — prefer small CID batches.'),
122
138
  }),
123
139
  output: z.object({
124
140
  compounds: z
@@ -127,7 +143,10 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
127
143
  properties: z
128
144
  .record(z.string(), z.unknown())
129
145
  .describe('Requested physicochemical properties.'),
130
- description: z.string().optional().describe('Textual description from PUG View.'),
146
+ description: z
147
+ .string()
148
+ .optional()
149
+ .describe('Textual description of the compound when available.'),
131
150
  synonyms: z.array(z.string()).optional().describe('Known names and synonyms.'),
132
151
  drugLikeness: drugLikenessSchema
133
152
  .optional()
@@ -277,7 +296,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
277
296
  // Drug-likeness assessment
278
297
  if (c.drugLikeness) {
279
298
  const dl = c.drugLikeness;
280
- const status = dl.pass ? 'PASS' : 'FAIL';
299
+ const status = dl.pass === null ? 'N/A (insufficient data)' : dl.pass ? 'PASS' : 'FAIL';
281
300
  lines.length = 0;
282
301
  lines.push(`\n**Drug-likeness:** ${status}`);
283
302
  lines.push(` Lipinski (${dl.lipinski.violations}/4 violations): ` +
package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts CHANGED
@@ -17,7 +17,24 @@ export declare const getSummary: import("@cyanheads/mcp-ts-core").ToolDefinition
17
17
  summaries: z.ZodArray<z.ZodObject<{
18
18
  identifier: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
19
19
  found: z.ZodBoolean;
20
- data: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
20
+ data: z.ZodOptional<z.ZodObject<{
21
+ aid: z.ZodOptional<z.ZodNumber>;
22
+ name: z.ZodOptional<z.ZodString>;
23
+ description: z.ZodOptional<z.ZodString>;
24
+ sourceName: z.ZodOptional<z.ZodString>;
25
+ numSubstances: z.ZodOptional<z.ZodNumber>;
26
+ numActive: z.ZodOptional<z.ZodNumber>;
27
+ geneId: z.ZodOptional<z.ZodNumber>;
28
+ symbol: z.ZodOptional<z.ZodString>;
29
+ taxonomyId: z.ZodOptional<z.ZodNumber>;
30
+ taxonomy: z.ZodOptional<z.ZodString>;
31
+ synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
32
+ proteinAccession: z.ZodOptional<z.ZodString>;
33
+ scientificName: z.ZodOptional<z.ZodString>;
34
+ commonName: z.ZodOptional<z.ZodString>;
35
+ rank: z.ZodOptional<z.ZodString>;
36
+ lineage: z.ZodOptional<z.ZodArray<z.ZodString>>;
37
+ }, z.core.$strip>>;
21
38
  }, z.core.$strip>>;
22
39
  }, z.core.$strip>>;
23
40
  //# sourceMappingURL=get-summary.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map CHANGED
@@ -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;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAOjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;kBA6FrB,CAAC"}
1
+ {"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4FrB,CAAC"}
package/dist/mcp-server/tools/definitions/get-summary.tool.js CHANGED
@@ -6,6 +6,30 @@
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
7
7
  import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
8
8
  const entityTypeEnum = z.enum(['assay', 'gene', 'protein', 'taxonomy']);
9
+ /**
10
+ * Union-of-shapes schema for entity summaries. All fields are optional because the
11
+ * set of populated fields depends on entityType (assay/gene/protein/taxonomy).
12
+ * Fields absent from the upstream response are omitted entirely rather than filled
13
+ * with empty strings or zeros.
14
+ */
15
+ const entitySummaryDataSchema = z.object({
16
+ aid: z.number().optional().describe('Assay ID — present on assay summaries.'),
17
+ name: z.string().optional().describe('Primary display name.'),
18
+ description: z.string().optional().describe('Descriptive text when available.'),
19
+ sourceName: z.string().optional().describe('Data source attribution (assay summaries).'),
20
+ numSubstances: z.number().optional().describe('Substances tested (assay summaries).'),
21
+ numActive: z.number().optional().describe('Substances marked active (assay summaries).'),
22
+ geneId: z.number().optional().describe('NCBI Gene ID (gene summaries).'),
23
+ symbol: z.string().optional().describe('Gene symbol (gene summaries).'),
24
+ taxonomyId: z.number().optional().describe('NCBI Taxonomy ID (gene/protein/taxonomy summaries).'),
25
+ taxonomy: z.string().optional().describe('Taxonomy scientific name (gene/protein summaries).'),
26
+ synonyms: z.array(z.string()).optional().describe('Known synonyms / other names.'),
27
+ proteinAccession: z.string().optional().describe('Protein accession (protein summaries).'),
28
+ scientificName: z.string().optional().describe('Scientific name (taxonomy summaries).'),
29
+ commonName: z.string().optional().describe('Common name (taxonomy summaries).'),
30
+ rank: z.string().optional().describe('Taxonomic rank (taxonomy summaries).'),
31
+ lineage: z.array(z.string()).optional().describe('Parent taxonomy lineage (taxonomy summaries).'),
32
+ });
9
33
  export const getSummary = tool('pubchem_get_summary', {
10
34
  title: 'Get Entity Summary',
11
35
  description: 'Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), ' +
@@ -33,10 +57,9 @@ export const getSummary = tool('pubchem_get_summary', {
33
57
  .array(z.object({
34
58
  identifier: z.union([z.string(), z.number()]).describe('Queried identifier.'),
35
59
  found: z.boolean().describe('Whether the entity was found.'),
36
- data: z
37
- .record(z.string(), z.unknown())
60
+ data: entitySummaryDataSchema
38
61
  .optional()
39
- .describe('Entity summary data (shape varies by type).'),
62
+ .describe('Entity summary data. Populated fields depend on entityType.'),
40
63
  }))
41
64
  .describe('Summary results.'),
42
65
  }),
@@ -87,47 +110,74 @@ export const getSummary = tool('pubchem_get_summary', {
87
110
  },
88
111
  });
89
112
  // ── Summary extraction per entity type ──────────────────────────────
113
+ function toNum(v) {
114
+ if (typeof v === 'number' && Number.isFinite(v))
115
+ return v;
116
+ if (typeof v === 'string') {
117
+ const n = Number(v);
118
+ return Number.isFinite(n) ? n : undefined;
119
+ }
120
+ return;
121
+ }
122
+ function toStr(v) {
123
+ if (typeof v === 'string' && v.length > 0)
124
+ return v;
125
+ if (typeof v === 'number')
126
+ return String(v);
127
+ if (Array.isArray(v)) {
128
+ const joined = v.filter((x) => typeof x === 'string').join('\n');
129
+ return joined.length > 0 ? joined : undefined;
130
+ }
131
+ return;
132
+ }
133
+ function toStrArr(v) {
134
+ if (Array.isArray(v)) {
135
+ const arr = v.map((x) => (typeof x === 'string' ? x : String(x))).filter((s) => s.length > 0);
136
+ return arr.length > 0 ? arr : undefined;
137
+ }
138
+ if (typeof v === 'string' && v.length > 0)
139
+ return [v];
140
+ return;
141
+ }
142
+ /** Assign `value` to `target[key]` only when defined — keeps unknowns off the output. */
143
+ function put(target, key, value) {
144
+ if (value !== undefined)
145
+ target[key] = value;
146
+ }
90
147
  function extractSummary(entityType, raw) {
148
+ const data = {};
91
149
  switch (entityType) {
92
150
  case 'assay':
93
- return {
94
- aid: raw.AID,
95
- name: raw.Name ?? raw.AssayName,
96
- description: Array.isArray(raw.Description)
97
- ? raw.Description.join('\n')
98
- : raw.Description,
99
- sourceName: raw.SourceName,
100
- numSubstances: raw.NumberOfSubstances ?? raw.TotalSIDCount,
101
- numActive: raw.ActiveSidCount ?? raw.ActiveCount,
102
- };
151
+ put(data, 'aid', toNum(raw.AID));
152
+ put(data, 'name', toStr(raw.Name ?? raw.AssayName));
153
+ put(data, 'description', toStr(raw.Description));
154
+ put(data, 'sourceName', toStr(raw.SourceName));
155
+ put(data, 'numSubstances', toNum(raw.NumberOfSubstances ?? raw.TotalSIDCount));
156
+ put(data, 'numActive', toNum(raw.ActiveSidCount ?? raw.ActiveCount));
157
+ return data;
103
158
  case 'gene':
104
- return {
105
- geneId: raw.GeneID,
106
- symbol: raw.Symbol,
107
- name: raw.Name,
108
- taxonomyId: raw.TaxID ?? raw.TaxonomyID,
109
- taxonomy: raw.Taxonomy ?? raw.ScientificName,
110
- description: raw.Description ?? raw.Summary,
111
- synonyms: raw.Synonym ?? raw.OtherNames,
112
- };
159
+ put(data, 'geneId', toNum(raw.GeneID));
160
+ put(data, 'symbol', toStr(raw.Symbol));
161
+ put(data, 'name', toStr(raw.Name));
162
+ put(data, 'taxonomyId', toNum(raw.TaxID ?? raw.TaxonomyID));
163
+ put(data, 'taxonomy', toStr(raw.Taxonomy ?? raw.ScientificName));
164
+ put(data, 'description', toStr(raw.Description ?? raw.Summary));
165
+ put(data, 'synonyms', toStrArr(raw.Synonym ?? raw.OtherNames));
166
+ return data;
113
167
  case 'protein':
114
- return {
115
- proteinAccession: raw.ProteinAccession ?? raw.Accession,
116
- name: raw.Name ?? raw.Title,
117
- taxonomyId: raw.TaxID ?? raw.TaxonomyID,
118
- taxonomy: raw.Taxonomy ?? raw.ScientificName,
119
- synonyms: raw.Synonym ?? raw.OtherNames,
120
- };
168
+ put(data, 'proteinAccession', toStr(raw.ProteinAccession ?? raw.Accession));
169
+ put(data, 'name', toStr(raw.Name ?? raw.Title));
170
+ put(data, 'taxonomyId', toNum(raw.TaxID ?? raw.TaxonomyID));
171
+ put(data, 'taxonomy', toStr(raw.Taxonomy ?? raw.ScientificName));
172
+ put(data, 'synonyms', toStrArr(raw.Synonym ?? raw.OtherNames));
173
+ return data;
121
174
  case 'taxonomy':
122
- return {
123
- taxonomyId: raw.TaxonomyID ?? raw.TaxID,
124
- scientificName: raw.ScientificName,
125
- commonName: raw.CommonName,
126
- rank: raw.Rank,
127
- lineage: raw.Lineage ?? raw.ParentTaxList,
128
- };
129
- default:
130
- return raw;
175
+ put(data, 'taxonomyId', toNum(raw.TaxonomyID ?? raw.TaxID));
176
+ put(data, 'scientificName', toStr(raw.ScientificName));
177
+ put(data, 'commonName', toStr(raw.CommonName));
178
+ put(data, 'rank', toStr(raw.Rank));
179
+ put(data, 'lineage', toStrArr(raw.Lineage ?? raw.ParentTaxList));
180
+ return data;
131
181
  }
132
182
  }
133
183
  function capitalize(s) {
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@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -22,9 +22,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
22
22
  targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
23
23
  targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
24
24
  activityValues: import("zod").ZodArray<import("zod").ZodObject<{
25
- name: import("zod").ZodString;
25
+ name: import("zod").ZodOptional<import("zod").ZodString>;
26
26
  value: import("zod").ZodNumber;
27
- unit: import("zod").ZodString;
27
+ unit: import("zod").ZodOptional<import("zod").ZodString>;
28
28
  }, import("zod/v4/core").$strip>>;
29
29
  }, import("zod/v4/core").$strip>>;
30
30
  }, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
@@ -66,7 +66,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
66
66
  value: import("zod").ZodNullable<import("zod").ZodNumber>;
67
67
  }, import("zod/v4/core").$strip>;
68
68
  }, import("zod/v4/core").$strip>;
69
- pass: import("zod").ZodBoolean;
69
+ pass: import("zod").ZodNullable<import("zod").ZodBoolean>;
70
70
  veber: import("zod").ZodObject<{
71
71
  rotatableBonds: import("zod").ZodObject<{
72
72
  limit: import("zod").ZodNumber;
@@ -148,7 +148,24 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
148
148
  summaries: import("zod").ZodArray<import("zod").ZodObject<{
149
149
  identifier: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>;
150
150
  found: import("zod").ZodBoolean;
151
- data: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
151
+ data: import("zod").ZodOptional<import("zod").ZodObject<{
152
+ aid: import("zod").ZodOptional<import("zod").ZodNumber>;
153
+ name: import("zod").ZodOptional<import("zod").ZodString>;
154
+ description: import("zod").ZodOptional<import("zod").ZodString>;
155
+ sourceName: import("zod").ZodOptional<import("zod").ZodString>;
156
+ numSubstances: import("zod").ZodOptional<import("zod").ZodNumber>;
157
+ numActive: import("zod").ZodOptional<import("zod").ZodNumber>;
158
+ geneId: import("zod").ZodOptional<import("zod").ZodNumber>;
159
+ symbol: import("zod").ZodOptional<import("zod").ZodString>;
160
+ taxonomyId: import("zod").ZodOptional<import("zod").ZodNumber>;
161
+ taxonomy: import("zod").ZodOptional<import("zod").ZodString>;
162
+ synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
163
+ proteinAccession: import("zod").ZodOptional<import("zod").ZodString>;
164
+ scientificName: import("zod").ZodOptional<import("zod").ZodString>;
165
+ commonName: import("zod").ZodOptional<import("zod").ZodString>;
166
+ rank: import("zod").ZodOptional<import("zod").ZodString>;
167
+ lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
168
+ }, import("zod/v4/core").$strip>>;
152
169
  }, import("zod/v4/core").$strip>>;
153
170
  }, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
154
171
  targetType: import("zod").ZodEnum<{
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;oCAS9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;oCAS9B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgBjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAmO1B,CAAC"}
1
+ {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgBjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsO1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -39,6 +39,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
39
39
  .array(z.string())
40
40
  .min(1)
41
41
  .max(25)
42
+ .refine((arr) => arr.every((s) => s.trim().length > 0), {
43
+ message: 'identifiers must all be non-empty strings',
44
+ })
42
45
  .optional()
43
46
  .describe('Required for identifier search. Array of identifiers to resolve (1-25). ' +
44
47
  'Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES.'),
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AAgKpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAoBnD,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA0E7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IA8EtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA+DjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA+B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}
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package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -557,15 +557,20 @@ export class PubChemClient {
557
557
  }
558
558
  byAid.set(aid, entry);
559
559
  }
560
- // Collect activity value if present
560
+ // Collect activity value if present — omit name/unit when genuinely unknown
561
561
  if (actValueIdx >= 0 && cell[actValueIdx] != null) {
562
562
  const value = Number(cell[actValueIdx]);
563
563
  if (!Number.isNaN(value)) {
564
- byAid.get(aid)?.activityValues.push({
565
- name: actNameIdx >= 0 ? String(cell[actNameIdx] ?? '') : '',
566
- value,
567
- unit: actValueUnit,
568
- });
564
+ const entry = { value };
565
+ if (actNameIdx >= 0) {
566
+ const rawName = cell[actNameIdx];
567
+ if (rawName != null && String(rawName).trim().length > 0) {
568
+ entry.name = String(rawName);
569
+ }
570
+ }
571
+ if (actValueUnit)
572
+ entry.unit = actValueUnit;
573
+ byAid.get(aid)?.activityValues.push(entry);
569
574
  }
570
575
  }
571
576
  }
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/pubchem/types.d.ts CHANGED
@@ -110,9 +110,9 @@ export interface GHSClassification {
110
110
  /** Parsed bioactivity row from assay summary table */
111
111
  export interface BioactivityRow {
112
112
  activityValues: Array<{
113
- name: string;
113
+ name?: string;
114
114
  value: number;
115
- unit: string;
115
+ unit?: string;
116
116
  }>;
117
117
  aid: number;
118
118
  assayName: string;
@@ -149,7 +149,8 @@ export interface DrugLikenessAssessment {
149
149
  violations: number;
150
150
  xLogP: DrugLikenessRule;
151
151
  };
152
- pass: boolean;
152
+ /** Overall pass, or null when insufficient properties were available to assess. */
153
+ pass: boolean | null;
153
154
  veber: {
154
155
  rotatableBonds: DrugLikenessRule;
155
156
  tpsa: DrugLikenessRule;
package/dist/services/pubchem/types.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/pubchem/types.js.map CHANGED
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubchem-mcp-server",
3
- "version": "0.1.10",
3
+ "version": "0.1.12",
4
4
  "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
5
5
  "mcpName": "io.github.cyanheads/pubchem-mcp-server",
6
6
  "type": "module",
@@ -32,7 +32,7 @@
32
32
  "bugs": {
33
33
  "url": "https://github.com/cyanheads/pubchem-mcp-server/issues"
34
34
  },
35
- "author": "Casey Hand <casey@caseyjhand.com> (https://github.com/cyanheads)",
35
+ "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubchem-mcp-server#readme)",
36
36
  "keywords": [
37
37
  "mcp",
38
38
  "mcp-server",
@@ -62,7 +62,7 @@
62
62
  "access": "public"
63
63
  },
64
64
  "dependencies": {
65
- "@cyanheads/mcp-ts-core": "^0.2.8",
65
+ "@cyanheads/mcp-ts-core": "^0.3.5",
66
66
  "pino-pretty": "^13.1.3"
67
67
  },
68
68
  "overrides": {
@@ -71,12 +71,12 @@
71
71
  "picomatch": ">=4.0.4"
72
72
  },
73
73
  "devDependencies": {
74
- "@biomejs/biome": "^2.4.9",
75
- "@types/node": "^25.5.0",
74
+ "@biomejs/biome": "^2.4.12",
75
+ "@types/node": "^25.6.0",
76
76
  "depcheck": "^1.4.7",
77
77
  "ignore": "^7.0.5",
78
78
  "tsc-alias": "^1.8.16",
79
- "typescript": "^6.0.2",
80
- "vitest": "^4.1.2"
79
+ "typescript": "^6.0.3",
80
+ "vitest": "^4.1.4"
81
81
  }
82
82
  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubchem-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.1.10",
9
+ "version": "0.1.12",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubchem-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "0.1.10",
22
+ "version": "0.1.12",
23
23
  "packageArguments": [
24
24
  { "type": "positional", "value": "run" },
25
25
  { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
42
42
  "registryBaseUrl": "https://registry.npmjs.org",
43
43
  "identifier": "@cyanheads/pubchem-mcp-server",
44
44
  "runtimeHint": "bun",
45
- "version": "0.1.10",
45
+ "version": "0.1.12",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }