@cyanheads/pubchem-mcp-server 0.1.21 → 0.1.22
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 +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts +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-image.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts +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-xrefs.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +17 -13
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +6 -4
- package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.js +19 -21
- package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +5 -3
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js +18 -9
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
- package/manifest.json +1 -1
- package/package.json +4 -3
- 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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@@ -29,5 +29,5 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
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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.$strip>, undefined>;
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}, z.core.$strip>, undefined, undefined>;
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//# sourceMappingURL=get-bioactivity.tool.d.ts.map
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;wCAuIzB,CAAC"}
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@@ -74,5 +74,5 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
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meshClasses: z.ZodArray<z.ZodString>;
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}, z.core.$strip>>;
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}, z.core.$strip>>;
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}, z.core.$strip>, undefined>;
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}, z.core.$strip>, undefined, undefined>;
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//# sourceMappingURL=get-compound-details.tool.d.ts.map
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{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAgX7B,CAAC"}
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@@ -15,5 +15,5 @@ export declare const getCompoundImage: import("@cyanheads/mcp-ts-core").ToolDefi
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mimeType: z.ZodString;
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}, z.core.$strip>, undefined>;
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}, z.core.$strip>, undefined, undefined>;
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//# sourceMappingURL=get-compound-image.tool.d.ts.map
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{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;
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{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;wCAoD3B,CAAC"}
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@@ -21,5 +21,5 @@ export declare const getCompoundSafety: import("@cyanheads/mcp-ts-core").ToolDef
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}, z.core.$strip>>;
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source: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>, undefined>;
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//# sourceMappingURL=get-compound-safety.tool.d.ts.map
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{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;wCAyG5B,CAAC"}
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totalAvailable: z.ZodNumber;
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truncated: z.ZodBoolean;
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}, z.core.$strip>>;
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}, z.core.$strip>, undefined>;
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}, z.core.$strip>, undefined, undefined>;
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//# sourceMappingURL=get-compound-xrefs.tool.d.ts.map
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{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;
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{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;wCAmH3B,CAAC"}
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@@ -35,5 +35,5 @@ export declare const getSummary: import("@cyanheads/mcp-ts-core").ToolDefinition
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lineage: z.ZodOptional<z.ZodArray<z.ZodString>>;
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}, z.core.$strip>>;
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//# sourceMappingURL=get-summary.tool.d.ts.map
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{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAsGrB,CAAC"}
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unit: import("zod").ZodOptional<import("zod").ZodString>;
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}, import("zod/v4/core").$strip>>;
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}, import("zod/v4/core").$strip>>;
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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cids: import("zod").ZodArray<import("zod").ZodNumber>;
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properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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entityType: import("zod").ZodEnum<{
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lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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}, import("zod/v4/core").$strip>>;
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}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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targetType: import("zod").ZodEnum<{
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}, import("zod/v4/core").$strip>, undefined
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}, import("zod/v4/core").$strip>, undefined, {
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}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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readonly when: "substructure/superstructure/similarity search missing query or queryType";
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}>)[];
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAS9B,CAAC"}
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}>;
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{"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY
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{"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;EAiFvB,CAAC"}
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@@ -28,13 +28,21 @@ export const searchAssays = tool('pubchem_search_assays', {
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.describe('Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.'),
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output: z.object({
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}),
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// Agent-facing context — target echo, total before cap, and an empty-result notice.
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enrichment: {
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.describe('Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession.'),
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totalFound: z.number().describe('Total AIDs found.'),
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totalFound: z.number().describe('Total AIDs found before the maxResults cap.'),
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.string()
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.optional()
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.describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
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},
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totalFound,
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};
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ctx.enrich.notice(`No assays found for "${input.targetQuery}" (${input.targetType}). Try a different targetType (e.g. switch from proteinname to genesymbol), verify the identifier spelling, or use pubchem_get_summary for gene/protein entity lookups.`);
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}
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const truncated = result.totalFound > result.aids.length
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? ` (showing ${result.aids.length} of ${result.totalFound})`
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: '';
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const lines = [
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`Found ${result.totalFound} assay${result.totalFound !== 1 ? 's' : ''} for "${result.targetQuery}" (${result.targetType})${truncated}`,
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'',
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];
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}
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else {
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lines.push('No assays found.');
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return [{ type: 'text', text: `AIDs: ${result.aids.join(', ')}` }];
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}
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return [{ type: 'text', text:
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return [{ type: 'text', text: 'No assays found.' }];
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{"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.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,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,qOAAqO;IACvO,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;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,wFAAwF,CACzF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,
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1
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+
{"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.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,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,qOAAqO;IACvO,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;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,wFAAwF,CACzF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACzD,CAAC;IACF,oFAAoF;IACpF,mFAAmF;IACnF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uIAAuI,CACxI;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC;QAEvF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEhD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,UAAU;YACV,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,qEAAqE;QACrE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,KAAK,CAAC,WAAW,EAAE,UAAU,EAAE,CAAC,CAAC;QACzF,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,KAAK,CAAC,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACzO,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,IAAI,EAAE,CAAC;IAClB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACrE,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC,CAAC;IACtD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -32,8 +32,6 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
|
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|
32
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|
[x: string]: string;
|
|
33
33
|
}>>>;
|
|
34
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|
}, z.core.$strip>, z.ZodObject<{
|
|
35
|
-
searchType: z.ZodString;
|
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-
totalFound: z.ZodNumber;
|
|
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|
results: z.ZodArray<z.ZodObject<{
|
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cid: z.ZodNumber;
|
|
39
37
|
identifier: z.ZodOptional<z.ZodString>;
|
|
@@ -54,5 +52,9 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
|
|
|
54
52
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
55
53
|
readonly when: "substructure/superstructure/similarity search missing query or queryType";
|
|
56
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|
readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
|
|
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|
-
}]
|
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55
|
+
}], {
|
|
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|
+
readonly searchType: z.ZodString;
|
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readonly totalFound: z.ZodNumber;
|
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+
readonly notice: z.ZodOptional<z.ZodString>;
|
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+
}>;
|
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//# sourceMappingURL=search-compounds.tool.d.ts.map
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@@ -1 +1 @@
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{"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe
|
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1
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+
{"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6Q1B,CAAC"}
|
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@@ -72,10 +72,6 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
72
72
|
.describe('Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].'),
|
|
73
73
|
}),
|
|
74
74
|
output: z.object({
|
|
75
|
-
searchType: z
|
|
76
|
-
.string()
|
|
77
|
-
.describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
|
|
78
|
-
totalFound: z.number().describe('Total CIDs found (before maxResults cap).'),
|
|
79
75
|
results: z
|
|
80
76
|
.array(z
|
|
81
77
|
.object({
|
|
@@ -92,6 +88,18 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
92
88
|
.describe('Matching compound entry.'))
|
|
93
89
|
.describe('Matching compounds.'),
|
|
94
90
|
}),
|
|
91
|
+
// Agent-facing context — search strategy echo, total before cap, and an empty-result
|
|
92
|
+
// notice. Reaches structuredContent and content[] automatically; not in the domain return.
|
|
93
|
+
enrichment: {
|
|
94
|
+
searchType: z
|
|
95
|
+
.string()
|
|
96
|
+
.describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
|
|
97
|
+
totalFound: z.number().describe('Total CIDs found before the maxResults cap.'),
|
|
98
|
+
notice: z
|
|
99
|
+
.string()
|
|
100
|
+
.optional()
|
|
101
|
+
.describe('Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.'),
|
|
102
|
+
},
|
|
95
103
|
errors: [
|
|
96
104
|
{
|
|
97
105
|
reason: 'missing_identifier_args',
|
|
@@ -175,6 +183,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
175
183
|
totalFound,
|
|
176
184
|
returned: cappedCids.length,
|
|
177
185
|
});
|
|
186
|
+
// Agent-facing context: search strategy echo, total, and empty-result notice.
|
|
187
|
+
ctx.enrich({ searchType: input.searchType, totalFound });
|
|
188
|
+
if (cappedCids.length === 0) {
|
|
189
|
+
ctx.enrich.notice(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
|
|
190
|
+
}
|
|
178
191
|
// Optionally hydrate with properties
|
|
179
192
|
let propsMap;
|
|
180
193
|
if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
|
|
@@ -193,14 +206,10 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
193
206
|
}
|
|
194
207
|
return result;
|
|
195
208
|
});
|
|
196
|
-
return {
|
|
209
|
+
return { results };
|
|
197
210
|
},
|
|
198
211
|
format(result) {
|
|
199
212
|
const lines = [];
|
|
200
|
-
const count = result.results.length;
|
|
201
|
-
const truncated = result.totalFound > count ? ` (showing ${count} of ${result.totalFound})` : '';
|
|
202
|
-
lines.push(`Found ${result.totalFound} compound${result.totalFound !== 1 ? 's' : ''}${truncated} — ${result.searchType} search`);
|
|
203
|
-
lines.push('');
|
|
204
213
|
if (result.results.length === 0) {
|
|
205
214
|
lines.push('No results.');
|
|
206
215
|
return [{ type: 'text', text: lines.join('\n') }];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/manifest.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"manifest_version": "0.3",
|
|
3
3
|
"name": "pubchem-mcp-server",
|
|
4
|
-
"version": "0.1.
|
|
4
|
+
"version": "0.1.22",
|
|
5
5
|
"description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
|
|
6
6
|
"author": {
|
|
7
7
|
"name": "cyanheads"
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubchem-mcp-server",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.22",
|
|
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",
|
|
@@ -18,7 +18,8 @@
|
|
|
18
18
|
"audit:refresh": "rm -f bun.lock && bun install && bun audit",
|
|
19
19
|
"tree": "bun scripts/tree.ts",
|
|
20
20
|
"list-skills": "bun scripts/list-skills.ts",
|
|
21
|
-
"format": "biome check --write
|
|
21
|
+
"format": "biome check --write .",
|
|
22
|
+
"format:unsafe": "biome check --write --unsafe .",
|
|
22
23
|
"lint:mcp": "bun scripts/lint-mcp.ts",
|
|
23
24
|
"lint:packaging": "bun scripts/lint-packaging.ts",
|
|
24
25
|
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubchem-mcp-server.mcpb",
|
|
@@ -71,7 +72,7 @@
|
|
|
71
72
|
"access": "public"
|
|
72
73
|
},
|
|
73
74
|
"dependencies": {
|
|
74
|
-
"@cyanheads/mcp-ts-core": "^0.9.
|
|
75
|
+
"@cyanheads/mcp-ts-core": "^0.9.16",
|
|
75
76
|
"pino-pretty": "^13.1.3",
|
|
76
77
|
"zod": "^4.4.3"
|
|
77
78
|
},
|
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.
|
|
9
|
+
"version": "0.1.22",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
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"registryBaseUrl": "https://registry.npmjs.org",
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20
20
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"identifier": "@cyanheads/pubchem-mcp-server",
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21
21
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"runtimeHint": "bun",
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22
|
-
"version": "0.1.
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22
|
+
"version": "0.1.22",
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23
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"packageArguments": [
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24
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|
{ "type": "positional", "value": "run" },
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25
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{ "type": "positional", "value": "start:stdio" }
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@@ -42,7 +42,7 @@
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42
42
|
"registryBaseUrl": "https://registry.npmjs.org",
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43
43
|
"identifier": "@cyanheads/pubchem-mcp-server",
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|
44
44
|
"runtimeHint": "bun",
|
|
45
|
-
"version": "0.1.
|
|
45
|
+
"version": "0.1.22",
|
|
46
46
|
"packageArguments": [
|
|
47
47
|
{ "type": "positional", "value": "run" },
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|
48
48
|
{ "type": "positional", "value": "start:http" }
|