npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.4.2 → 0.5.0 - Mend

@cyanheads/pubchem-mcp-server 0.4.2 → 0.5.0

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.

Files changed (41) hide show

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.4.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.5.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
 </div>

package/dist/mcp-server/resources/definitions/assay.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"assay.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/assay.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIrD,eAAO,MAAM,aAAa;;wCAiBxB,CAAC"}

package/dist/mcp-server/resources/definitions/assay.resource.js CHANGED Viewed

@@ -7,7 +7,7 @@ import { notFound } from '@cyanheads/mcp-ts-core/errors';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 export const assayResource = resource('pubchem://assay/{aid}', {
     name: 'pubchem-assay',
-    description: 'Summary for a PubChem BioAssay by AID (mirrors pubchem_get_summary for assays).',
+    description: 'Summary for a PubChem BioAssay by AID — name, description, source, protocol, and substance counts.',
     mimeType: 'application/json',
     params: z.object({
         aid: z.coerce.number().int().positive().describe('PubChem Assay ID.'),

package/dist/mcp-server/resources/definitions/assay.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js CHANGED Viewed

@@ -8,7 +8,7 @@ import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 const MAX_RESULTS = 25;
 export const compoundBioactivityResource = resource('pubchem://compound/{cid}/bioactivity', {
     name: 'pubchem-compound-bioactivity',
-    description: 'Bioassay activity profile for a PubChem compound by CID (mirrors pubchem_get_bioactivity). Returns up to 25 assays; use the tool to filter and page.',
+    description: 'Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target, raise the cap, and page through the rest with offset.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound-image.resource.js CHANGED Viewed

@@ -6,7 +6,7 @@ import { resource, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 export const compoundImageResource = resource('pubchem://compound/{cid}/image', {
     name: 'pubchem-compound-image',
-    description: 'A 2D structure diagram (PNG) for a PubChem compound by CID (mirrors pubchem_get_compound_image).',
+    description: 'A 2D structure diagram (PNG, 300x300) for a PubChem compound by CID. Use pubchem_get_compound_image to choose the image size.',
     mimeType: 'image/png',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound-image.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound-safety.resource.js CHANGED Viewed

@@ -6,7 +6,7 @@ import { resource, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 export const compoundSafetyResource = resource('pubchem://compound/{cid}/safety', {
     name: 'pubchem-compound-safety',
-    description: 'GHS hazard classification for a PubChem compound by CID (mirrors pubchem_get_compound_safety).',
+    description: 'GHS hazard classification for a PubChem compound by CID — signal word, pictograms, hazard (H) and precautionary (P) statements. Not every compound carries a deposited classification.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js CHANGED Viewed

@@ -9,7 +9,7 @@ const RESOURCE_XREF_TYPES = ['RN', 'RegistryID', 'PubMedID'];
 const MAX_PER_TYPE = 25;
 export const compoundXrefsResource = resource('pubchem://compound/{cid}/xrefs', {
     name: 'pubchem-compound-xrefs',
-    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID (mirrors pubchem_get_compound_xrefs). Use the tool for the full set of xref types.',
+    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types and a higher per-type cap.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound.resource.js CHANGED Viewed

@@ -8,7 +8,7 @@ import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 import { DEFAULT_PROPERTIES } from '../../../services/pubchem/types.js';
 export const compoundResource = resource('pubchem://compound/{cid}', {
     name: 'pubchem-compound',
-    description: 'Core physicochemical properties for a PubChem compound by CID (mirrors pubchem_get_compound_details).',
+    description: 'Core physicochemical properties for a PubChem compound by CID. Use pubchem_get_compound_details to select properties or add descriptions, synonyms, drug-likeness, and classification.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts CHANGED Viewed

@@ -13,6 +13,7 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     }>>;
     targetGeneId: z.ZodOptional<z.ZodNumber>;
     targetAccession: z.ZodOptional<z.ZodString>;
+    offset: z.ZodDefault<z.ZodNumber>;
     maxResults: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     cid: z.ZodNumber;
@@ -36,6 +37,8 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly targetFilter: z.ZodOptional<z.ZodString>;
     readonly filteredCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;
+    readonly offset: z.ZodNumber;
+    readonly nextOffset: z.ZodOptional<z.ZodNumber>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;
     readonly shown: z.ZodOptional<z.ZodNumber>;
     readonly cap: z.ZodOptional<z.ZodNumber>;

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoPzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js CHANGED Viewed

@@ -34,12 +34,18 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .string()
             .optional()
             .describe('Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.'),
         maxResults: z
             .number()
             .min(1)
             .max(100)
             .default(20)
-            .describe('Max assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20.'),
+            .describe('Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.'),
     }),
     output: z.object({
         cid: z.number().describe('PubChem Compound ID.'),
@@ -78,9 +84,14 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .describe('Assay result entry.'))
             .describe('Assay results matching the filter.'),
     }),
-    // Agent-facing context — filter echo, the filtered/returned cap boundary, and a notice
-    // distinguishing "no data" from "filter excluded everything". Reaches structuredContent
-    // and content[]; keys disjoint from output (cid/totalAssays live there).
+    // Agent-facing context — filter echo, the page boundary, and a notice distinguishing
+    // "no data" from "filter excluded everything". Reaches structuredContent and content[];
+    // keys disjoint from output (cid/totalAssays live there).
+    //
+    // Bounded-total convention: a reported total states only what the server actually
+    // observed, and pairs with an `…AtLeast` floor when the exact figure is unknowable.
+    // Every count here is exact and needs no such twin — PubChem's assay summary has no
+    // pagination of its own, so the full table is in hand before any filter runs.
     enrichment: {
         outcomeFilter: z.string().describe('Outcome filter applied: active, inactive, or all.'),
         targetFilter: z
@@ -89,13 +100,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .describe('Target filter applied (gene ID and/or protein accession), when set.'),
         filteredCount: z
             .number()
-            .describe('Assays matching the outcome and target filters, before the maxResults cap.'),
-        returnedCount: z.number().describe('Assays returned after the maxResults cap.'),
-        truncated: z
-            .boolean()
+            .describe('Exact number of assays matching the outcome and target filters, across all pages.'),
+        returnedCount: z.number().describe('Assays returned on this page.'),
+        offset: z.number().describe('Zero-based index of the first assay returned.'),
+        nextOffset: z
+            .number()
             .optional()
-            .describe('True when results were capped at maxResults — more matching assays exist.'),
-        shown: z.number().optional().describe('Assays returned after the maxResults cap.'),
+            .describe('Offset to pass on the next call to continue past this page. Omitted when no further assays match.'),
+        truncated: z.boolean().optional().describe('True when matching assays remain past this page.'),
+        shown: z.number().optional().describe('Assays returned on this page.'),
         cap: z.number().optional().describe('The maxResults cap that was applied.'),
         notice: z
             .string()
@@ -128,21 +141,29 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
         if (input.targetAccession) {
             filtered = filtered.filter((r) => r.targetAccession === input.targetAccession);
         }
-        const results = filtered.slice(0, input.maxResults);
+        // Offset is applied client-side: PubChem's assay summary endpoint accepts no
+        // offset/start/limit/page parameter, so getAssaySummary already holds every row.
+        const results = filtered.slice(input.offset, input.offset + input.maxResults);
+        const nextOffset = input.offset + results.length;
+        const hasMore = nextOffset < filtered.length;
         ctx.log.info('Bioactivity fetched', {
             cid: input.cid,
             total: allRows.length,
             active: activeCount,
             filtered: filtered.length,
+            offset: input.offset,
             returned: results.length,
         });
         ctx.enrich({
             outcomeFilter: input.outcomeFilter,
             filteredCount: filtered.length,
             returnedCount: results.length,
+            offset: input.offset,
         });
         if (targetLabel)
             ctx.enrich({ targetFilter: targetLabel });
+        if (hasMore)
+            ctx.enrich({ nextOffset });
         if (allRows.length === 0) {
             ctx.enrich.notice(`No bioactivity data found for CID ${input.cid}. The compound may be uncharacterized, or verify the CID with pubchem_search_compounds.`);
         }
@@ -151,8 +172,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                 ? `CID ${input.cid} has ${allRows.length} assay(s) but none match the target filter (${targetLabel})${input.outcomeFilter !== 'all' ? ` with outcomeFilter="${input.outcomeFilter}"` : ''}. Verify the target identifier appears in this compound's assays, or widen the filter.`
                 : `CID ${input.cid} has ${allRows.length} assay(s) but none match outcomeFilter="${input.outcomeFilter}". Use outcomeFilter="all" to see them.`);
         }
-        else if (filtered.length > results.length) {
-            ctx.enrich.truncated({ shown: results.length, cap: input.maxResults });
+        else if (results.length === 0) {
+            ctx.enrich.notice(`offset ${input.offset} is past the ${filtered.length} assay(s) matching the filter. Pass an offset below ${filtered.length}.`);
+        }
+        else if (hasMore) {
+            ctx.enrich.truncated({
+                shown: results.length,
+                cap: input.maxResults,
+                guidance: `Showing assays ${input.offset + 1}-${nextOffset} of ${filtered.length}. Pass offset=${nextOffset} for the next page.`,
+            });
         }
         return {
             cid: input.cid,

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map CHANGED Viewed

	@@ -1 +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;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,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+KAA+K,CAChL;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,2JAA2J,CAC5J;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,qFAAqF;IACrF,wFAAwF;IACxF,0DAA0D;IAC1D,EAAE;IACF,kFAAkF;IAClF,oFAAoF;IACpF,oFAAoF;IACpF,8EAA8E;IAC9E,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,CACP,mFAAmF,CACpF;QACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACnE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QAC5E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QAC9F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACtE,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,6EAA6E;QAC7E,iFAAiF;QACjF,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC9E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;QACjD,MAAM,OAAO,GAAG,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QAE7C,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,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,OAAO,CAAC,MAAM;SACzB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAA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package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js CHANGED Viewed

@@ -17,7 +17,7 @@ const DEFAULT_BOND_CAP = 200;
 const DEFAULT_SDF_LINE_CAP = 500;
 export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure', {
     title: 'Get Compound 3D Structure',
-    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).',
+    description: 'Get a compound\'s default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; 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).',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -36,7 +36,7 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
         includeAlternateConformerIds: z
             .boolean()
             .default(false)
-            .describe('List the IDs of additional computed conformers beyond the default. Adds one extra API call. Default: false.'),
+            .describe('List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false.'),
         maxAtoms: z
             .number()
             .int()

package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map CHANGED Viewed

	@@ -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;AA4GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~wCA2Y7B~~,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAuZ7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-details.tool.js CHANGED Viewed

@@ -96,7 +96,7 @@ function computeDrugLikeness(properties) {
 // ── Tool definition ────────────────────────────────────────────────────
 export const getCompoundDetails = tool('pubchem_get_compound_details', {
     title: 'Get Compound Details',
-    description: 'Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.',
+    description: 'Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -107,7 +107,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .array(z.number().int().positive())
             .min(1)
             .max(100)
-            .describe('PubChem Compound IDs to fetch (1-100). Batched efficiently. Resolve from names/SMILES with pubchem_search_compounds.'),
+            .describe('PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds.'),
         properties: z
             .array(propertyEnum)
             .optional()
@@ -122,11 +122,11 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .min(1)
             .max(20)
             .default(3)
-            .describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; we dedup and cap to keep responses focused. Default: 3.'),
+            .describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.'),
         includeSynonyms: z
             .boolean()
             .default(false)
-            .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). One API call per CID — slower than the property batch for large CID lists.'),
+            .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). Slower for large CID lists.'),
         maxSynonyms: z
             .number()
             .int()
@@ -137,7 +137,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
         includeDrugLikeness: z
             .boolean()
             .default(false)
-            .describe('Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties.'),
+            .describe('Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency.'),
         includeClassification: z
             .boolean()
             .default(false)
@@ -371,11 +371,17 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                     lines.push(`  FDA: ${cls.fdaClasses.join(', ')}`);
                 if (cls.fdaMechanisms.length > 0)
                     lines.push(`  MoA: ${cls.fdaMechanisms.join(', ')}`);
+                /**
+                 * MeSH classes render in full — structuredContent carries the whole list uncapped.
+                 * Each value is a multi-sentence scope note that routinely contains both "; " and
+                 * ", ", so no inline separator can mark an entry boundary unambiguously. One entry
+                 * per line instead: inlineData collapses embedded newlines, so a value cannot forge
+                 * a bullet of its own and the line break is an unforgeable entry boundary.
+                 */
                 if (cls.meshClasses.length > 0) {
-                    const meshDisplay = cls.meshClasses.length > 3
-                        ? `${cls.meshClasses.slice(0, 3).join('; ')} (+${cls.meshClasses.length - 3} more)`
-                        : cls.meshClasses.join('; ');
-                    lines.push(`  MeSH: ${meshDisplay}`);
+                    lines.push('  MeSH:');
+                    for (const meshClass of cls.meshClasses)
+                        lines.push(`    - ${inlineData(meshClass)}`);
                 }
                 if (cls.atcCodes.length > 0) {
                     const atcDisplay = cls.atcCodes
@@ -412,7 +418,15 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 const total = c.synonymsTotal ?? c.synonyms.length;
                 const more = total - c.synonyms.length;
                 const suffix = more > 0 ? ` (+${more} more)` : '';
-                const syns = c.synonyms.map(inlineData).join(', ');
+                /**
+                 * Pipe-separated: CAS-style inverted names ("Benzoic acid, 2-(acetyloxy)-") carry
+                 * their own ", ", which would split one synonym into two. " | " is this formatter's
+                 * existing inline multi-value separator. A bare "|" does turn up in depositor
+                 * synonyms as mangled Greek letters ("17|A-Oestradiol"), so the delimiter is the
+                 * space-padded form; that exact sequence was absent from every synonym sampled,
+                 * but unlike the MeSH line break it is a rare-collision separator, not a proof.
+                 */
+                const syns = c.synonyms.map(inlineData).join(' | ');
                 blocks.push(`\n**Synonyms** (${total} total): ${syns}${suffix}`);
             }
             blocks.push('');

package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js CHANGED Viewed

@@ -99,9 +99,9 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
                 : `${xref.totalAvailable} total`;
             lines.push(`**${xref.type}** (${countInfo})`);
             if (xref.ids.length > 0) {
-                const display = xref.ids.slice(0, 20);
-                const more = xref.ids.length > 20 ? `, ... (+${xref.ids.length - 20} more)` : '';
-                lines.push(`  ${display.join(', ')}${more}`);
+                // Rendered in full: the handler already capped ids at maxPerType and the header
+                // discloses that cap, so a second slice here would hide IDs structuredContent returned.
+                lines.push(`  ${xref.ids.join(', ')}`);
             }
             else {
                 lines.push('  None found');

package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map CHANGED Viewed

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