npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.2.3 → 0.3.0 - Mend

@cyanheads/pubchem-mcp-server 0.2.3 → 0.3.0

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 (18) hide show

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.2.3-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-^6.0.3-3178C6.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-0.3.0-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-^6.0.3-3178C6.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/index.js CHANGED Viewed

@@ -13,7 +13,7 @@ await createApp({
     title: 'pubchem-mcp-server',
     tools: allToolDefinitions,
     resources: allResourceDefinitions,
-    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
+    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. To find assays for a biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_summary` (`entityType: assay`) per AID; to check whether a compound is active against a target, call `pubchem_get_bioactivity` with a `cid` plus `targetGeneId`/`targetAccession`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
     landing: {
         tagline: 'Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.',
         repoRoot: 'https://github.com/cyanheads/pubchem-mcp-server',

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6CAA6C,CAAC;AACrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE,kBAAkB;IACzB,SAAS,EAAE,sBAAsB;IACjC,YAAY,EACV,q3BAAq3B;IACv3B,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}

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

@@ -12,6 +12,7 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
     includeDescription: z.ZodDefault<z.ZodBoolean>;
     maxDescriptions: z.ZodDefault<z.ZodNumber>;
     includeSynonyms: z.ZodDefault<z.ZodBoolean>;
+    maxSynonyms: z.ZodDefault<z.ZodNumber>;
     includeDrugLikeness: z.ZodDefault<z.ZodBoolean>;
     includeClassification: z.ZodDefault<z.ZodBoolean>;
 }, z.core.$strip>, z.ZodObject<{
@@ -25,6 +26,7 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
         }, z.core.$strip>>>;
         descriptionsTotal: z.ZodOptional<z.ZodNumber>;
         synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        synonymsTotal: z.ZodOptional<z.ZodNumber>;
         drugLikeness: z.ZodOptional<z.ZodObject<{
             lipinski: z.ZodObject<{
                 hba: z.ZodObject<{

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAoY7B,CAAC"}

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

@@ -126,6 +126,13 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .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.'),
+        maxSynonyms: z
+            .number()
+            .int()
+            .min(1)
+            .max(100)
+            .default(20)
+            .describe('Max synonyms returned per compound (1-100). PubChem lists hundreds for common drugs; capped to keep the response focused. Default: 20.'),
         includeDrugLikeness: z
             .boolean()
             .default(false)
@@ -163,6 +170,10 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 .optional()
                 .describe('Total distinct descriptions available before truncation. Larger than descriptions.length when more sources exist — increase maxDescriptions to see them.'),
             synonyms: z.array(z.string()).optional().describe('Known names and synonyms.'),
+            synonymsTotal: z
+                .number()
+                .optional()
+                .describe('Total synonyms available before truncation. Larger than synonyms.length when more exist — increase maxSynonyms to see them.'),
             drugLikeness: drugLikenessSchema
                 .optional()
                 .describe('Drug-likeness assessment. lipinski.violations ≤ 1 and veber.violations = 0 → pass.'),
@@ -243,8 +254,10 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 compound.descriptionsTotal = allDescs.length;
             }
             const syns = synMap?.get(cid);
-            if (syns)
-                compound.synonyms = syns;
+            if (syns) {
+                compound.synonyms = syns.slice(0, input.maxSynonyms);
+                compound.synonymsTotal = syns.length;
+            }
             if (input.includeDrugLikeness)
                 compound.drugLikeness = computeDrugLikeness(properties);
             const cls = classMap?.get(cid);
@@ -387,11 +400,12 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 }
                 blocks.push(descLines.join('\n\n'));
             }
-            // Synonyms
+            // Synonyms (capped at maxSynonyms in the handler; total reported)
             if (c.synonyms && c.synonyms.length > 0) {
-                const synShown = c.synonyms.slice(0, 20);
-                const more = c.synonyms.length > 20 ? ` (+${c.synonyms.length - 20} more)` : '';
-                blocks.push(`\n**Synonyms:** ${synShown.join(', ')}${more}`);
+                const total = c.synonymsTotal ?? c.synonyms.length;
+                const more = total - c.synonyms.length;
+                const suffix = more > 0 ? ` (+${more} more)` : '';
+                blocks.push(`\n**Synonyms** (${total} total): ${c.synonyms.join(', ')}${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-safety.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;~~EAiI5B~~,CAAC"}
1	+ {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;EAmI5B,CAAC"}

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

@@ -128,8 +128,9 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
             }
             if (g.precautionaryStatements.length > 0) {
                 lines.push('', '**Precautionary Statements:**');
-                for (const p of g.precautionaryStatements)
-                    lines.push(`  ${p.code}: ${p.statement}`);
+                for (const p of g.precautionaryStatements) {
+                    lines.push(p.statement ? `  ${p.code}: ${p.statement}` : `  ${p.code}`);
+                }
             }
             if (r.source)
                 lines.push('', `*Source: ${r.source}*`);

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

	@@ -1 +1 @@
1	- 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AC,EAAE,EAAE,+BAA+B,CAAC,CAAC;gBAChD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,uBAAuB;~~oBAAE~~,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;~~YACvF~~,CAAC;YAED,IAAI,CAAC,CAAC,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,YAAY,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;YAEtD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACpC,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACrD,CAAC;CACF,CAAC,CAAC"}
1	+ {"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAGxE,MAAM,SAAS,GAAG,CAAC;KAChB,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;IACrF,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAC7F,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;KACzD,CAAC;SACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;SACA,QAAQ,CAAC,wBAAwB,CAAC;IACrC,uBAAuB,EAAE,CAAC;SACvB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KAChE,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC;KACD,QAAQ,CAAC,0BAA0B,CAAC,CAAC;AAExC,sGAAsG;AACtG,MAAM,aAAa,GAAG,EAAE,CAAC;AAEzB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,qSAAqS;IACvS,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC;aACJ,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC;aAClC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,gHAAgH,CACjH;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YAChD,OAAO,EAAE,CAAC;iBACP,OAAO,EAAE;iBACT,QAAQ,CAAC,yDAAyD,CAAC;YACtE,GAAG,EAAE,SAAS,CAAC,QAAQ,EAAE;YACzB,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,wBAAwB,CAAC,CACtC;aACA,QAAQ,CAAC,gEAAgE,CAAC;KAC9E,CAAC;IACF,6FAA6F;IAC7F,0FAA0F;IAC1F,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACtD,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC1E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gGAAgG,CACjG;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,sDAAsD;QACtD,MAAM,SAAS,GAAG,IAAI,GAAG,EAAoC,CAAC;QAC9D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,aAAa,EAAE,CAAC;YAC1D,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,CAAC;YACrD,MAAM,SAAS,GAAG,MAAM,OAAO,CAAC,GAAG,CACjC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,MAAM,MAAM,CAAC,aAAa,CAAC,GAAG,CAAC,CAAU,CAAC,CAC1E,CAAC;YACF,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,SAAS;gBAAE,SAAS,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;QAChE,CAAC;QAED,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrC,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC;YACxC,IAAI,CAAC,IAAI;gBAAE,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,KAAc,EAAE,CAAC;YACnD,OAAO;gBACL,GAAG;gBACH,OAAO,EAAE,IAAa;gBACtB,GAAG,EAAE;oBACH,UAAU,EAAE,IAAI,CAAC,UAAU;oBAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;oBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,uBAAuB,EAAE,IAAI,CAAC,uBAAuB;iBACtD;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAE9D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,SAAS,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM;YAC5B,QAAQ,EAAE,aAAa;SACxB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC;QACjE,IAAI,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACtC,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACpE,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,OAAO,CAAC,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,YAAY,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,0IAA0I,CACpP,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,OAAO,EAAE,CAAC;IACrB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,yBAAyB,EAAE,CAAC,CAAC;QAC7D,CAAC;QAED,MAAM,MAAM,GAAa,EAAE,CAAC;QAC5B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,uBAAuB,EAAE,EAAE,CAAC,CAAC;gBACxD,SAAS;YACX,CAAC;YAED,MAAM,KAAK,GAAa,CAAC,4BAA4B,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC;YAEhB,IAAI,CAAC,CAAC,UAAU;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;YACjE,IAAI,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAEtF,IAAI,CAAC,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,wBAAwB,CAAC,CAAC;gBACzC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,gBAAgB;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAChF,CAAC;YAED,IAAI,CAAC,CAAC,uBAAuB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzC,KAAK,CAAC,IAAI,CA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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED Viewed

@@ -76,6 +76,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     includeDescription: import("zod").ZodDefault<import("zod").ZodBoolean>;
     maxDescriptions: import("zod").ZodDefault<import("zod").ZodNumber>;
     includeSynonyms: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    maxSynonyms: import("zod").ZodDefault<import("zod").ZodNumber>;
     includeDrugLikeness: import("zod").ZodDefault<import("zod").ZodBoolean>;
     includeClassification: import("zod").ZodDefault<import("zod").ZodBoolean>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
@@ -89,6 +90,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         }, import("zod/v4/core").$strip>>>;
         descriptionsTotal: import("zod").ZodOptional<import("zod").ZodNumber>;
         synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+        synonymsTotal: import("zod").ZodOptional<import("zod").ZodNumber>;
         drugLikeness: import("zod").ZodOptional<import("zod").ZodObject<{
             lipinski: import("zod").ZodObject<{
                 hba: import("zod").ZodObject<{

package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/pubchem/pubchem-client.js CHANGED Viewed

@@ -169,6 +169,21 @@ function parseCodedStatement(text) {
         return { code: codeOnly[1], statement: '' };
     return;
 }
+/** Parse PubChem's comma-separated precautionary code list — e.g.
+ * "P261, P264+P265, P305+P351+P338, P405, and P501" — into code-only entries.
+ * PubChem deposits precautionary statements as codes without descriptive text, so
+ * `statement` is always empty; we don't fabricate the standard P-statement text.
+ * Handles the terminal Oxford "and", combined (`Pxxx+Pyyy`) and triple codes, and
+ * skips any token that isn't a P-code. */
+function parsePrecautionaryCodes(text) {
+    const entries = [];
+    for (const token of text.split(',')) {
+        const code = token.trim().replace(/^and\s+/i, '');
+        if (/^P\d{3}(?:\+P\d{3})*$/.test(code))
+            entries.push({ code, statement: '' });
+    }
+    return entries;
+}
 /** Map PubChem pictogram markup strings to human labels */
 const PICTOGRAM_LABELS = {
     GHS01: 'Explosive',
@@ -448,10 +463,11 @@ export class PubChemClient {
                     }
                 }
                 else if (name.includes('precautionary') && name.includes('statement')) {
+                    // PubChem deposits precautionary statements as a single comma-separated code
+                    // list (codes only, no text) — not the "Pxxx: text" shape parseCodedStatement
+                    // expects. Split each list into individual code entries.
                     for (const s of strings) {
-                        const parsed = parseCodedStatement(s);
-                        if (parsed)
-                            result.precautionaryStatements.push(parsed);
+                        result.precautionaryStatements.push(...parsePrecautionaryCodes(s));
                     }
                 }
             }
@@ -486,26 +502,28 @@ export class PubChemClient {
                 fdaMechanisms: [],
                 meshClasses: [],
             };
-            // FDA Pharmacological Classification
+            // FDA Pharmacological Classification — PubChem emits two redundant shapes
+            // (either alone covers all classes):
+            //   individual: "<Type> [TAG] - <Name>"        (name after the dash)
+            //   combined:   "<Name> [TAG]; <Name> [TAG]; …" (name before the tag)
+            // Bucket EPC → fdaClasses, MoA → fdaMechanisms; CS/PE have no output field.
             const fdaSection = findSection(sections, 'FDA Pharmacological Classification');
             if (fdaSection) {
-                const strings = extractStrings(fdaSection);
-                for (const s of strings) {
-                    if (!s.startsWith('Pharmacological Classes:'))
-                        continue;
-                    const classes = s.slice('Pharmacological Classes:'.length).trim();
-                    for (const entry of classes.split(';')) {
+                for (const s of extractStrings(fdaSection)) {
+                    for (const entry of s.split(';')) {
                         const trimmed = entry.trim();
-                        const tagMatch = trimmed.match(/^(.+?)\s*\[(\w+)\]$/);
-                        if (!tagMatch)
+                        if (!trimmed)
                             continue;
-                        const [, name, tag] = tagMatch;
-                        if (!name)
+                        const individual = trimmed.match(/^.+\[(\w+)\]\s*-\s*(.+)$/);
+                        const tagAtEnd = individual ? null : trimmed.match(/^(.+?)\s*\[(\w+)\]$/);
+                        const tag = individual?.[1] ?? tagAtEnd?.[2];
+                        const name = (individual?.[2] ?? tagAtEnd?.[1])?.trim();
+                        if (!tag || !name)
                             continue;
-                        if (tag === 'EPC' || tag === 'CS')
-                            result.fdaClasses.push(name.trim());
+                        if (tag === 'EPC')
+                            result.fdaClasses.push(name);
                         else if (tag === 'MoA')
-                            result.fdaMechanisms.push(name.trim());
+                            result.fdaMechanisms.push(name);
                     }
                 }
                 result.fdaClasses = [...new Set(result.fdaClasses)];

package/dist/services/pubchem/pubchem-client.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.2.3",
+  "version": "0.3.0",
   "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
   "author": {
     "name": "cyanheads"

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.2.3",
+  "version": "0.3.0",
   "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",
@@ -73,17 +73,17 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.6",
+    "@cyanheads/mcp-ts-core": "^0.10.10",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.0",
-    "@types/node": "^25.9.3",
+    "@biomejs/biome": "^2.5.1",
+    "@types/node": "^26.0.1",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.8"
+    "vitest": "^4.1.9"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.2.3",
+  "version": "0.3.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.2.3",
+      "version": "0.3.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.2.3",
+      "version": "0.3.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }