@cyanheads/pubchem-mcp-server 0.1.23 → 0.2.1

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

@@ -1,108 +1,141 @@
 /**
- * @fileoverview Get GHS hazard classification and safety data for a PubChem compound.
+ * @fileoverview Get GHS hazard classification and safety data for PubChem compounds (batched).
  * @module mcp-server/tools/definitions/get-compound-safety
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+const ghsSchema = z
+    .object({
+    signalWord: z.string().optional().describe('GHS signal word: "Danger" or "Warning".'),
+    pictograms: z.array(z.string()).describe('GHS pictogram labels (e.g. "Flammable", "Toxic").'),
+    hazardStatements: z
+        .array(z
+        .object({
+        code: z.string().describe('H-code (e.g. "H225").'),
+        statement: z.string().describe('Hazard statement text.'),
+    })
+        .describe('GHS hazard statement entry.'))
+        .describe('GHS hazard statements.'),
+    precautionaryStatements: z
+        .array(z
+        .object({
+        code: z.string().describe('P-code (e.g. "P210").'),
+        statement: z.string().describe('Precautionary statement text.'),
+    })
+        .describe('GHS precautionary statement entry.'))
+        .describe('GHS precautionary statements.'),
+})
+    .describe('GHS classification data.');
+/** Fan-out cap: at most this many PUG View calls in flight at once (mirrors get_compound_details). */
+const MAX_IN_FLIGHT = 10;
 export const getCompoundSafety = tool('pubchem_get_compound_safety', {
     title: 'Get Compound Safety',
-    description: 'Get GHS (Globally Harmonized System) hazard classification and safety data for a compound. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes). Data sourced from PubChem depositors — source attribution included.',
+    description: 'Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
         openWorldHint: true,
     },
     input: z.object({
-        cid: z
-            .number()
-            .int()
-            .positive()
-            .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
+        cids: z
+            .array(z.number().int().positive())
+            .min(1)
+            .max(25)
+            .describe('PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.'),
     }),
     output: z.object({
-        cid: z.number().describe('PubChem Compound ID.'),
-        hasData: z.boolean().describe('Whether GHS safety data is available for this compound.'),
-        ghs: z
+        results: z
+            .array(z
             .object({
-            signalWord: z.string().optional().describe('GHS signal word: "Danger" or "Warning".'),
-            pictograms: z
-                .array(z.string())
-                .describe('GHS pictogram labels (e.g. "Flammable", "Toxic").'),
-            hazardStatements: z
-                .array(z
-                .object({
-                code: z.string().describe('H-code (e.g. "H225").'),
-                statement: z.string().describe('Hazard statement text.'),
-            })
-                .describe('GHS hazard statement entry.'))
-                .describe('GHS hazard statements.'),
-            precautionaryStatements: z
-                .array(z
-                .object({
-                code: z.string().describe('P-code (e.g. "P210").'),
-                statement: z.string().describe('Precautionary statement text.'),
-            })
-                .describe('GHS precautionary statement entry.'))
-                .describe('GHS precautionary statements.'),
+            cid: z.number().describe('PubChem Compound ID.'),
+            hasData: z
+                .boolean()
+                .describe('Whether GHS safety data is available for this compound.'),
+            ghs: ghsSchema.optional(),
+            source: z.string().optional().describe('Data source attribution.'),
         })
-            .optional()
-            .describe('GHS classification data.'),
-        source: z.string().optional().describe('Data source attribution.'),
+            .describe('Per-CID safety result.'))
+            .describe('Safety results, one per requested CID (input order preserved).'),
     }),
-    // Agent-facing context — a cross-tool notice when no GHS data exists, pointing to an
-    // alternative source. Reaches structuredContent and content[]; disjoint from output.
+    // Agent-facing context — requested/with-data counts and a cross-tool notice listing the CIDs
+    // that lack GHS data. Reaches structuredContent and content[]; keys disjoint from output.
     enrichment: {
+        requestedCount: z.number().describe('CIDs requested.'),
+        withDataCount: z.number().describe('CIDs with GHS safety data available.'),
         notice: z
             .string()
             .optional()
-            .describe('Cross-tool guidance when no GHS data is available, pointing to an alternative source.'),
+            .describe('Cross-tool guidance when one or more CIDs have no GHS data, pointing to an alternative source.'),
     },
     async handler(input, ctx) {
         const client = getPubChemClient();
-        const data = await client.getSafetyData(input.cid);
-        ctx.log.info('Safety data fetched', { cid: input.cid, hasData: data !== null });
-        if (!data) {
-            ctx.enrich.notice(`No GHS classification on file for CID ${input.cid}. Try pubchem_get_compound_details with includeDescription for hazard context, or the compound may simply lack deposited safety data.`);
-            return { cid: input.cid, hasData: false };
+        // Fan out per CID, capped at MAX_IN_FLIGHT in flight.
+        const dataByCid = new Map();
+        for (let i = 0; i < input.cids.length; i += MAX_IN_FLIGHT) {
+            const chunk = input.cids.slice(i, i + MAX_IN_FLIGHT);
+            const chunkData = await Promise.all(chunk.map(async (cid) => [cid, await client.getSafetyData(cid)]));
+            for (const [cid, data] of chunkData)
+                dataByCid.set(cid, data);
+        }
+        const results = input.cids.map((cid) => {
+            const data = dataByCid.get(cid) ?? null;
+            if (!data)
+                return { cid, hasData: false };
+            return {
+                cid,
+                hasData: true,
+                ghs: {
+                    signalWord: data.signalWord,
+                    pictograms: data.pictograms,
+                    hazardStatements: data.hazardStatements,
+                    precautionaryStatements: data.precautionaryStatements,
+                },
+                source: data.source,
+            };
+        });
+        const withDataCount = results.filter((r) => r.hasData).length;
+        ctx.log.info('Safety data fetched', {
+            requested: input.cids.length,
+            withData: withDataCount,
+        });
+        ctx.enrich({ requestedCount: input.cids.length, withDataCount });
+        if (withDataCount < input.cids.length) {
+            const missing = results.filter((r) => !r.hasData).map((r) => r.cid);
+            ctx.enrich.notice(`No GHS classification on file for ${missing.length} of ${input.cids.length} CID(s): ${missing.join(', ')}. Try pubchem_get_compound_details with includeDescription for hazard context, or those compounds may simply lack deposited safety data.`);
         }
-        return {
-            cid: input.cid,
-            hasData: true,
-            ghs: {
-                signalWord: data.signalWord,
-                pictograms: data.pictograms,
-                hazardStatements: data.hazardStatements,
-                precautionaryStatements: data.precautionaryStatements,
-            },
-            source: data.source,
-        };
+        return { results };
     },
     format(result) {
-        if (!result.hasData || !result.ghs) {
-            return [{ type: 'text', text: `No GHS safety data available for CID ${result.cid}.` }];
+        if (result.results.length === 0) {
+            return [{ type: 'text', text: 'No compounds requested.' }];
         }
-        const lines = [`## GHS Safety Data — CID ${result.cid}`, ''];
-        const g = result.ghs;
-        if (g.signalWord)
-            lines.push(`**Signal Word:** ${g.signalWord}`);
-        if (g.pictograms.length > 0)
-            lines.push(`**Pictograms:** ${g.pictograms.join(', ')}`);
-        if (g.hazardStatements.length > 0) {
-            lines.push('', '**Hazard Statements:**');
-            for (const h of g.hazardStatements) {
-                lines.push(`  ${h.code}: ${h.statement}`);
+        const blocks = [];
+        for (const r of result.results) {
+            if (!r.hasData || !r.ghs) {
+                blocks.push(`## CID ${r.cid} — no GHS safety data`, '');
+                continue;
             }
-        }
-        if (g.precautionaryStatements.length > 0) {
-            lines.push('', '**Precautionary Statements:**');
-            for (const p of g.precautionaryStatements) {
-                lines.push(`  ${p.code}: ${p.statement}`);
+            const lines = [`## GHS Safety Data — CID ${r.cid}`];
+            const g = r.ghs;
+            if (g.signalWord)
+                lines.push(`**Signal Word:** ${g.signalWord}`);
+            if (g.pictograms.length > 0)
+                lines.push(`**Pictograms:** ${g.pictograms.join(', ')}`);
+            if (g.hazardStatements.length > 0) {
+                lines.push('', '**Hazard Statements:**');
+                for (const h of g.hazardStatements)
+                    lines.push(`  ${h.code}: ${h.statement}`);
             }
+            if (g.precautionaryStatements.length > 0) {
+                lines.push('', '**Precautionary Statements:**');
+                for (const p of g.precautionaryStatements)
+                    lines.push(`  ${p.code}: ${p.statement}`);
+            }
+            if (r.source)
+                lines.push('', `*Source: ${r.source}*`);
+            blocks.push(lines.join('\n'), '');
         }
-        if (result.source) {
-            lines.push('', `*Source: ${result.source}*`);
-        }
-        return [{ type: 'text', text: lines.join('\n') }];
+        return [{ type: 'text', text: blocks.join('\n') }];
     },
 });
 //# sourceMappingURL=get-compound-safety.tool.js.map

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

@@ -1 +1 @@
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+{"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,C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package/dist/mcp-server/tools/definitions/index.d.ts

@@ -9,6 +9,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         inactive: "inactive";
         all: "all";
     }>>;
+    targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
+    targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
     maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
@@ -29,10 +31,41 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     }, import("zod/v4/core").$strip>>;
 }, import("zod/v4/core").$strip>, undefined, {
     readonly outcomeFilter: import("zod").ZodString;
+    readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
     readonly filteredCount: import("zod").ZodNumber;
     readonly returnedCount: import("zod").ZodNumber;
     readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
 }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    format: import("zod").ZodDefault<import("zod").ZodEnum<{
+        sdf: "sdf";
+        json: "json";
+    }>>;
+    includeAlternateConformerIds: import("zod").ZodDefault<import("zod").ZodBoolean>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    conformerId: import("zod").ZodOptional<import("zod").ZodString>;
+    atomCount: import("zod").ZodNumber;
+    bondCount: import("zod").ZodNumber;
+    atoms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
+        element: import("zod").ZodString;
+        x: import("zod").ZodNumber;
+        y: import("zod").ZodNumber;
+        z: import("zod").ZodNumber;
+    }, import("zod/v4/core").$strip>>>;
+    bonds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
+        a1: import("zod").ZodNumber;
+        a2: import("zod").ZodNumber;
+        order: import("zod").ZodNumber;
+    }, import("zod/v4/core").$strip>>>;
+    sdf: import("zod").ZodOptional<import("zod").ZodString>;
+    alternateConformerIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "no_3d_structure";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    readonly when: "PubChem has no computed 3D conformer for the requested CID";
+    readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
+}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cids: import("zod").ZodArray<import("zod").ZodNumber>;
     properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
         [x: string]: string;
@@ -121,23 +154,53 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     readonly recovery: "Verify the CID with pubchem_search_compounds before retrying.";
 }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
+    kinds: import("zod").ZodDefault<import("zod").ZodArray<import("zod").ZodEnum<{
+        "drug-drug": "drug-drug";
+        "drug-food": "drug-food";
+        target: "target";
+    }>>>;
+    maxEntries: import("zod").ZodDefault<import("zod").ZodNumber>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
-    hasData: import("zod").ZodBoolean;
-    ghs: import("zod").ZodOptional<import("zod").ZodObject<{
-        signalWord: import("zod").ZodOptional<import("zod").ZodString>;
-        pictograms: import("zod").ZodArray<import("zod").ZodString>;
-        hazardStatements: import("zod").ZodArray<import("zod").ZodObject<{
-            code: import("zod").ZodString;
-            statement: import("zod").ZodString;
-        }, import("zod/v4/core").$strip>>;
-        precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
-            code: import("zod").ZodString;
-            statement: import("zod").ZodString;
+    entries: import("zod").ZodArray<import("zod").ZodObject<{
+        kind: import("zod").ZodEnum<{
+            "drug-drug": "drug-drug";
+            "drug-food": "drug-food";
+            target: "target";
+        }>;
+        partner: import("zod").ZodOptional<import("zod").ZodString>;
+        source: import("zod").ZodString;
+        severity: import("zod").ZodOptional<import("zod").ZodString>;
+        text: import("zod").ZodString;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>, undefined, {
+    readonly requestedKinds: import("zod").ZodString;
+    readonly returnedCount: import("zod").ZodNumber;
+    readonly failedKinds: import("zod").ZodOptional<import("zod").ZodString>;
+    readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
+}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cids: import("zod").ZodArray<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    results: import("zod").ZodArray<import("zod").ZodObject<{
+        cid: import("zod").ZodNumber;
+        hasData: import("zod").ZodBoolean;
+        ghs: import("zod").ZodOptional<import("zod").ZodObject<{
+            signalWord: import("zod").ZodOptional<import("zod").ZodString>;
+            pictograms: import("zod").ZodArray<import("zod").ZodString>;
+            hazardStatements: import("zod").ZodArray<import("zod").ZodObject<{
+                code: import("zod").ZodString;
+                statement: import("zod").ZodString;
+            }, import("zod/v4/core").$strip>>;
+            precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
+                code: import("zod").ZodString;
+                statement: import("zod").ZodString;
+            }, import("zod/v4/core").$strip>>;
         }, import("zod/v4/core").$strip>>;
+        source: import("zod").ZodOptional<import("zod").ZodString>;
     }, import("zod/v4/core").$strip>>;
-    source: import("zod").ZodOptional<import("zod").ZodString>;
 }, import("zod/v4/core").$strip>, undefined, {
+    readonly requestedCount: import("zod").ZodNumber;
+    readonly withDataCount: import("zod").ZodNumber;
     readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
 }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;

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

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAS9B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}

package/dist/mcp-server/tools/definitions/index.js

@@ -3,8 +3,10 @@
  * @module mcp-server/tools/definitions
  */
 import { getBioactivity } from './get-bioactivity.tool.js';
+import { getCompound3dStructure } from './get-compound-3d-structure.tool.js';
 import { getCompoundDetails } from './get-compound-details.tool.js';
 import { getCompoundImage } from './get-compound-image.tool.js';
+import { getCompoundInteractions } from './get-compound-interactions.tool.js';
 import { getCompoundSafety } from './get-compound-safety.tool.js';
 import { getCompoundXrefs } from './get-compound-xrefs.tool.js';
 import { getSummary } from './get-summary.tool.js';
@@ -14,9 +16,11 @@ export const allToolDefinitions = [
     searchCompounds,
     getCompoundDetails,
     getCompoundImage,
+    getCompound3dStructure,
     getCompoundXrefs,
     getCompoundSafety,
     getBioactivity,
+    getCompoundInteractions,
     searchAssays,
     getSummary,
 ];

package/dist/mcp-server/tools/definitions/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EAAE,sBAAsB,EAAE,MAAM,qCAAqC,CAAC;AAC7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,gCAAgC,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,uBAAuB,EAAE,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAE7D,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,eAAe;IACf,kBAAkB;IAClB,gBAAgB;IAChB,sBAAsB;IACtB,gBAAgB;IAChB,iBAAiB;IACjB,cAAc;IACd,uBAAuB;IACvB,YAAY;IACZ,UAAU;CACX,CAAC"}

package/dist/services/pubchem/pubchem-client.d.ts

@@ -3,13 +3,22 @@
  * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
  * @module services/pubchem/pubchem-client
  */
-import type { BioactivityRow, CompoundClassification, GHSClassification } from './types.js';
+import type { BioactivityRow, CompoundClassification, GHSClassification, InteractionsResult } from './types.js';
 export declare class PubChemClient {
     private readonly pugBase;
     private readonly viewBase;
+    private readonly sdqBase;
     private readonly rateLimiter;
+    /** Shared HTTP core: rate-limit, 30s timeout, retry once on 5xx and once on a transient
+     * network error, and surface a clean timeout message. Returns the ok Response; callers
+     * extract the body (JSON, bytes, or text). Centralizing this keeps every fetch variant on
+     * one resilience contract — the divergence that left fetchBinary without retry or a clean
+     * timeout message (#16) cannot recur. */
+    private fetchResponse;
     private fetchJson;
     private fetchBinary;
+    /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
+    private fetchText;
     /** Fetch CID list, with automatic ListKey polling for async searches */
     private fetchCids;
     /** Poll a PubChem ListKey until results are ready */
@@ -35,6 +44,32 @@ export declare class PubChemClient {
     private parseAssayTable;
     searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;
     getEntitySummary(entityType: string, identifier: string | number): Promise<Record<string, unknown> | null>;
+    /** Fetch drug-drug, drug-food, and/or chemical-target interactions for a compound.
+     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
+     * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
+     * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
+    getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionsResult>;
+    private getInteractionsForKind;
+    private getDrugDrugInteractions;
+    /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
+     * ChEMBL, and others). That collection is cid-keyed and scopes correctly to the requested
+     * compound; the `consolidatedcompoundtarget` collection used previously is gene-indexed, so
+     * its `cid` filter was silently ignored — every CID returned the same default compound (#20).
+     * Only rows naming a molecular target are returned; untargeted assay outcomes are the domain
+     * of pubchem_get_bioactivity. */
+    private getTargetInteractions;
+    private getDrugFoodInteractions;
+    /** Query a PubChem SDQ external table for a single CID, projecting only the columns the
+     * caller maps. Projection keeps payloads small and excludes the free-text `citations` column
+     * whose unescaped quotes make PubChem emit invalid JSON (#20). Returns [] on not-found; on an
+     * unparseable body throws a contextful error rather than the bare `Failed to parse JSON`, so
+     * the caller and per-kind isolation can report it cleanly. */
+    private fetchSdq;
+    /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
+     * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
+    getSdf3d(cid: number): Promise<string>;
+    /** List the conformer IDs PubChem has computed for a compound. Returns [] on not-found. */
+    getConformerIds(cid: number): Promise<string[]>;
 }
 export declare function initPubChemClient(): void;
 export declare function getPubChemClient(): PubChemClient;

package/dist/services/pubchem/pubchem-client.d.ts.map

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