@cyanheads/pubchem-mcp-server 0.1.1

package/dist/mcp-server/tools/definitions/search-compounds.tool.js

@@ -0,0 +1,204 @@
+/**
+ * @fileoverview Search PubChem for chemical compounds by name, SMILES, InChIKey,
+ * formula, substructure, superstructure, or 2D similarity.
+ * @module mcp-server/tools/definitions/search-compounds
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+import { COMPOUND_PROPERTIES } from '../../../services/pubchem/types.js';
+const searchTypeEnum = z.enum([
+    'identifier',
+    'formula',
+    'substructure',
+    'superstructure',
+    'similarity',
+]);
+const identifierTypeEnum = z.enum(['name', 'smiles', 'inchikey']);
+const queryTypeEnum = z.enum(['smiles', 'cid']);
+const propertyEnum = z.enum(COMPOUND_PROPERTIES);
+export const searchCompounds = tool('pubchem_search_compounds', {
+    title: 'Search Compounds',
+    description: `Search PubChem for chemical compounds. Five search modes:\n` +
+        `- identifier: Resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)\n` +
+        `- formula: Find compounds by molecular formula (Hill notation, e.g. "C6H12O6")\n` +
+        `- substructure: Find compounds containing a substructure (SMILES or CID)\n` +
+        `- superstructure: Find compounds that are substructures of the query\n` +
+        `- similarity: Find structurally similar compounds by 2D Tanimoto similarity\n\n` +
+        `Optionally hydrate results with properties to avoid a follow-up details call.`,
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: true,
+    },
+    input: z.object({
+        searchType: searchTypeEnum.describe('Search strategy: "identifier" (name/SMILES/InChIKey lookup), "formula", "substructure", "superstructure", or "similarity".'),
+        identifierType: identifierTypeEnum
+            .optional()
+            .describe('Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey".'),
+        identifiers: z
+            .array(z.string())
+            .min(1)
+            .max(25)
+            .optional()
+            .describe('Required for identifier search. Array of identifiers to resolve (1-25). ' +
+            'Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES.'),
+        formula: z
+            .string()
+            .optional()
+            .describe('Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2").'),
+        allowOtherElements: z
+            .boolean()
+            .default(false)
+            .describe('Formula search only. When true, includes compounds with additional elements beyond the formula.'),
+        query: z
+            .string()
+            .optional()
+            .describe('Required for substructure/superstructure/similarity searches. ' +
+            'A SMILES string or PubChem CID (as string) for the query structure.'),
+        queryType: queryTypeEnum
+            .optional()
+            .describe('Required for structure/similarity searches. Format of the query: "smiles" or "cid".'),
+        threshold: z
+            .number()
+            .min(70)
+            .max(100)
+            .default(90)
+            .describe('Similarity search only. Minimum Tanimoto similarity (70-100). ' +
+            '90+ for close analogs, 70-80 for scaffold hops. Default: 90.'),
+        maxResults: z
+            .number()
+            .min(1)
+            .max(200)
+            .default(20)
+            .describe('Maximum CIDs to return (1-200). Default: 20.'),
+        properties: z
+            .array(propertyEnum)
+            .optional()
+            .describe('Optional: fetch these properties for each result, avoiding a follow-up details call. ' +
+            'E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].'),
+    }),
+    output: z.object({
+        searchType: z.string().describe('The search strategy used.'),
+        totalFound: z.number().describe('Total CIDs found (before maxResults cap).'),
+        results: z
+            .array(z.object({
+            cid: z.number().describe('PubChem Compound ID.'),
+            identifier: z
+                .string()
+                .optional()
+                .describe('Echoed input identifier (identifier mode only).'),
+            properties: z
+                .record(z.string(), z.unknown())
+                .optional()
+                .describe('Compound properties when requested.'),
+        }))
+            .describe('Matching compounds.'),
+    }),
+    async handler(input, ctx) {
+        const client = getPubChemClient();
+        let allCids = [];
+        const identifierMap = new Map();
+        switch (input.searchType) {
+            case 'identifier': {
+                const { identifierType, identifiers } = input;
+                if (!identifierType || !identifiers) {
+                    throw new Error('identifierType and identifiers are required for identifier search');
+                }
+                const lookups = identifiers.map(async (id) => {
+                    let cids;
+                    switch (identifierType) {
+                        case 'name':
+                            cids = await client.searchByName(id);
+                            break;
+                        case 'smiles':
+                            cids = await client.searchBySmiles(id);
+                            break;
+                        case 'inchikey':
+                            cids = await client.searchByInchiKey(id);
+                            break;
+                    }
+                    for (const cid of cids)
+                        identifierMap.set(cid, id);
+                    return cids;
+                });
+                const results = await Promise.all(lookups);
+                allCids = results.flat();
+                break;
+            }
+            case 'formula': {
+                if (!input.formula)
+                    throw new Error('formula is required for formula search');
+                allCids = await client.searchByFormula(input.formula, input.allowOtherElements);
+                break;
+            }
+            case 'substructure':
+            case 'superstructure':
+            case 'similarity': {
+                if (!input.query || !input.queryType) {
+                    throw new Error('query and queryType are required for structure/similarity searches');
+                }
+                allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
+                break;
+            }
+        }
+        // Deduplicate and cap
+        const uniqueCids = [...new Set(allCids)];
+        const totalFound = uniqueCids.length;
+        const cappedCids = uniqueCids.slice(0, input.maxResults);
+        ctx.log.info('Search completed', {
+            searchType: input.searchType,
+            totalFound,
+            returned: cappedCids.length,
+        });
+        // Optionally hydrate with properties
+        let propsMap;
+        if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
+            const rows = await client.getProperties(cappedCids, input.properties);
+            propsMap = new Map(rows.map((r) => [r.CID, r]));
+        }
+        const results = cappedCids.map((cid) => {
+            const result = { cid };
+            const identifier = identifierMap.get(cid);
+            if (identifier)
+                result.identifier = identifier;
+            const rawProps = propsMap?.get(cid);
+            if (rawProps) {
+                const props = { ...rawProps };
+                delete props.CID;
+                result.properties = props;
+            }
+            return result;
+        });
+        return { searchType: input.searchType, totalFound, results };
+    },
+    format(result) {
+        const lines = [];
+        const count = result.results.length;
+        const truncated = result.totalFound > count ? ` (showing ${count} of ${result.totalFound})` : '';
+        lines.push(`Found ${result.totalFound} compound${result.totalFound !== 1 ? 's' : ''}${truncated} — ${result.searchType} search`);
+        lines.push('');
+        if (result.results.length === 0) {
+            lines.push('No results.');
+            return [{ type: 'text', text: lines.join('\n') }];
+        }
+        const hasProps = result.results.some((r) => r.properties);
+        if (hasProps) {
+            for (const r of result.results) {
+                const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
+                lines.push(`**${label}**`);
+                if (r.properties) {
+                    const entries = Object.entries(r.properties);
+                    lines.push(entries.map(([k, v]) => `  ${k}: ${v}`).join('\n'));
+                }
+                lines.push('');
+            }
+        }
+        else {
+            const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
+            lines.push(`CIDs: ${items.join(', ')}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=search-compounds.tool.js.map

package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"search-compounds.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.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,mBAAmB,EAAE,MAAM,6BAA6B,CAAC;AAElE,MAAM,cAAc,GAAG,CAAC,CAAC,IAAI,CAAC;IAC5B,YAAY;IACZ,SAAS;IACT,cAAc;IACd,gBAAgB;IAChB,YAAY;CACb,CAAC,CAAC;AAEH,MAAM,kBAAkB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,QAAQ,EAAE,UAAU,CAAC,CAAC,CAAC;AAClE,MAAM,aAAa,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;AAChD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,mBAAuD,CAAC,CAAC;AAErF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,0BAA0B,EAAE;IAC9D,KAAK,EAAE,kBAAkB;IACzB,WAAW,EACT,6DAA6D;QAC7D,uFAAuF;QACvF,kFAAkF;QAClF,4EAA4E;QAC5E,wEAAwE;QACxE,iFAAiF;QACjF,+EAA+E;IACjF,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,eAAe,EAAE,KAAK;QACtB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,cAAc,CAAC,QAAQ,CACjC,4HAA4H,CAC7H;QACD,cAAc,EAAE,kBAAkB;aAC/B,QAAQ,EAAE;aACV,QAAQ,CACP,+FAA+F,CAChG;QACH,WAAW,EAAE,CAAC;aACX,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,0EAA0E;YACxE,uFAAuF,CAC1F;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6FAA6F,CAC9F;QACH,kBAAkB,EAAE,CAAC;aAClB,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,iGAAiG,CAClG;QACH,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gEAAgE;YAC9D,qEAAqE,CACxE;QACH,SAAS,EAAE,aAAa;aACrB,QAAQ,EAAE;aACV,QAAQ,CACP,qFAAqF,CACtF;QACH,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,GAAG,CAAC,EAAE,CAAC;aACP,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,gEAAgE;YAC9D,8DAA8D,CACjE;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,8CAA8C,CAAC;QAC3D,UAAU,EAAE,CAAC;aACV,KAAK,CAAC,YAAY,CAAC;aACnB,QAAQ,EAAE;aACV,QAAQ,CACP,uFAAuF;YACrF,kEAAkE,CACrE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC5D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAC5E,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YAChD,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,iDAAiD,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;iBAC/B,QAAQ,EAAE;iBACV,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC,CACH;aACA,QAAQ,CAAC,qBAAqB,CAAC;KACnC,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,IAAI,OAAO,GAAa,EAAE,CAAC;QAC3B,MAAM,aAAa,GAAG,IAAI,GAAG,EAAkB,CAAC;QAEhD,QAAQ,KAAK,CAAC,UAAU,EAAE,CAAC;YACzB,KAAK,YAAY,CAAC,CAAC,CAAC;gBAClB,MAAM,EAAE,cAAc,EAAE,WAAW,EAAE,GAAG,KAAK,CAAC;gBAC9C,IAAI,CAAC,cAAc,IAAI,CAAC,WAAW,EAAE,CAAC;oBACpC,MAAM,IAAI,KAAK,CAAC,mEAAmE,CAAC,CAAC;gBACvF,CAAC;gBACD,MAAM,OAAO,GAAG,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,EAAE,EAAE,EAAE;oBAC3C,IAAI,IAAc,CAAC;oBACnB,QAAQ,cAAc,EAAE,CAAC;wBACvB,KAAK,MAAM;4BACT,IAAI,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,EAAE,CAAC,CAAC;4BACrC,MAAM;wBACR,KAAK,QAAQ;4BACX,IAAI,GAAG,MAAM,MAAM,CAAC,cAAc,CAAC,EAAE,CAAC,CAAC;4BACvC,MAAM;wBACR,KAAK,UAAU;4BACb,IAAI,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC;4BACzC,MAAM;oBACV,CAAC;oBACD,KAAK,MAAM,GAAG,IAAI,IAAI;wBAAE,aAAa,CAAC,GAAG,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;oBACnD,OAAO,IAAI,CAAC;gBACd,CAAC,CAAC,CAAC;gBACH,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;gBAC3C,OAAO,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC;gBACzB,MAAM;YACR,CAAC;YACD,KAAK,SAAS,CAAC,CAAC,CAAC;gBACf,IAAI,CAAC,KAAK,CAAC,OAAO;oBAAE,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAC;gBAC9E,OAAO,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,kBAAkB,CAAC,CAAC;gBAChF,MAAM;YACR,CAAC;YACD,KAAK,cAAc,CAAC;YACpB,KAAK,gBAAgB,CAAC;YACtB,KAAK,YAAY,CAAC,CAAC,CAAC;gBAClB,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,SAAS,EAAE,CAAC;oBACrC,MAAM,IAAI,KAAK,CAAC,oEAAoE,CAAC,CAAC;gBACxF,CAAC;gBACD,OAAO,GAAG,MAAM,MAAM,CAAC,iBAAiB,CACtC,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,SAAS,EACf,KAAK,CAAC,SAAS,CAChB,CAAC;gBACF,MAAM;YACR,CAAC;QACH,CAAC;QAED,sBAAsB;QACtB,MAAM,UAAU,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC;QACzC,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,MAAM,UAAU,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEzD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE;YAC/B,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,UAAU;YACV,QAAQ,EAAE,UAAU,CAAC,MAAM;SAC5B,CAAC,CAAC;QAEH,qCAAqC;QACrC,IAAI,QAA0D,CAAC;QAC/D,IAAI,KAAK,CAAC,UAAU,IAAI,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC7E,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,UAAU,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;YACtE,QAAQ,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAClD,CAAC;QAED,MAAM,OAAO,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrC,MAAM,MAAM,GAIR,EAAE,GAAG,EAAE,CAAC;YAEZ,MAAM,UAAU,GAAG,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YAC1C,IAAI,UAAU;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC/C,MAAM,QAAQ,GAAG,QAAQ,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC;YACpC,IAAI,QAAQ,EAAE,CAAC;gBACb,MAAM,KAAK,GAAG,EAAE,GAAG,QAAQ,EAAE,CAAC;gBAC9B,OAAQ,KAAiC,CAAC,GAAG,CAAC;gBAC9C,MAAM,CAAC,UAAU,GAAG,KAAK,CAAC;YAC5B,CAAC;YACD,OAAO,MAAM,CAAC;QAChB,CAAC,CAAC,CAAC;QAEH,OAAO,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,UAAU,EAAE,OAAO,EAAE,CAAC;IAC/D,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC;QACpC,MAAM,SAAS,GACb,MAAM,CAAC,UAAU,GAAG,KAAK,CAAC,CAAC,CAAC,aAAa,KAAK,OAAO,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;QACjF,KAAK,CAAC,IAAI,CACR,SAAS,MAAM,CAAC,UAAU,YAAY,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,SAAS,MAAM,MAAM,CAAC,UAAU,SAAS,CACrH,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAEf,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;YAC1B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QAE1D,IAAI,QAAQ,EAAE,CAAC;YACb,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBAC/B,MAAM,KAAK,GAAG,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,CAAC;gBAC/E,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,IAAI,CAAC,CAAC;gBAC3B,IAAI,CAAC,CAAC,UAAU,EAAE,CAAC;oBACjB,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;oBAC7C,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;gBACjE,CAAC;gBACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACjB,CAAC;QACH,CAAC;aAAM,CAAC;YACN,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CACrC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAC5D,CAAC;YACF,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC1C,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

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

@@ -0,0 +1,37 @@
+/**
+ * @fileoverview PubChem API client with rate limiting, retry, and response parsing.
+ * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
+ * @module services/pubchem/pubchem-client
+ */
+import type { BioactivityRow, GHSClassification } from './types.js';
+export declare class PubChemClient {
+    private readonly pugBase;
+    private readonly viewBase;
+    private readonly rateLimiter;
+    private fetchJson;
+    private fetchBinary;
+    /** Fetch CID list, with automatic ListKey polling for async searches */
+    private fetchCids;
+    /** Poll a PubChem ListKey until results are ready */
+    private pollListKey;
+    searchByName(name: string): Promise<number[]>;
+    searchBySmiles(smiles: string): Promise<number[]>;
+    searchByInchiKey(inchikey: string): Promise<number[]>;
+    searchByFormula(formula: string, allowOther?: boolean): Promise<number[]>;
+    searchByStructure(mode: 'substructure' | 'superstructure' | 'similarity', query: string, queryType: 'smiles' | 'cid', threshold?: number): Promise<number[]>;
+    getProperties(cids: number[], properties: string[]): Promise<Array<Record<string, unknown> & {
+        CID: number;
+    }>>;
+    getSynonyms(cid: number): Promise<string[]>;
+    getImage(cid: number, size?: 'small' | 'large'): Promise<ArrayBuffer>;
+    getXrefs(cid: number, xrefType: string): Promise<(string | number)[]>;
+    getDescription(cid: number): Promise<string | null>;
+    getSafetyData(cid: number): Promise<GHSClassification | null>;
+    getAssaySummary(cid: number): Promise<BioactivityRow[]>;
+    private parseAssayTable;
+    searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;
+    getEntitySummary(entityType: string, identifier: string | number): Promise<Record<string, unknown> | null>;
+}
+export declare function initPubChemClient(): void;
+export declare function getPubChemClient(): PubChemClient;
+//# sourceMappingURL=pubchem-client.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AAuJpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAoBnD,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA4E7D,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA+DjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA6B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}