/** * @fileoverview Tool definition barrel — all PubChem MCP tools. * @module mcp-server/tools/definitions */ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolDefinition; properties: import("zod").ZodOptional>>; includeDescription: import("zod").ZodDefault; descriptionOffset: import("zod").ZodDefault; maxDescriptions: import("zod").ZodDefault; includeSynonyms: import("zod").ZodDefault; synonymOffset: import("zod").ZodDefault; maxSynonyms: import("zod").ZodDefault; includeDrugLikeness: import("zod").ZodDefault; includeClassification: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ compounds: import("zod").ZodArray; descriptions: import("zod").ZodOptional; text: import("zod").ZodString; }, import("zod/v4/core").$strip>>>; descriptionsTotal: import("zod").ZodOptional; synonyms: import("zod").ZodOptional>; synonymsTotal: import("zod").ZodOptional; drugLikeness: import("zod").ZodOptional; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; hbd: import("zod").ZodObject<{ limit: import("zod").ZodNumber; pass: import("zod").ZodNullable; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; mw: import("zod").ZodObject<{ limit: import("zod").ZodNumber; pass: import("zod").ZodNullable; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; violations: import("zod").ZodNumber; xLogP: import("zod").ZodObject<{ limit: import("zod").ZodNumber; pass: import("zod").ZodNullable; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; }, import("zod/v4/core").$strip>; pass: import("zod").ZodNullable; veber: import("zod").ZodObject<{ rotatableBonds: import("zod").ZodObject<{ limit: import("zod").ZodNumber; pass: import("zod").ZodNullable; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; tpsa: import("zod").ZodObject<{ limit: import("zod").ZodNumber; pass: import("zod").ZodNullable; value: import("zod").ZodNullable; }, import("zod/v4/core").$strip>; violations: import("zod").ZodNumber; }, import("zod/v4/core").$strip>; }, import("zod/v4/core").$strip>>; classification: import("zod").ZodOptional>; fdaClasses: import("zod").ZodArray; fdaMechanisms: import("zod").ZodArray; meshClasses: import("zod").ZodArray; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly enrichedCids: import("zod").ZodOptional>; readonly skippedCids: import("zod").ZodOptional>; readonly synonymOffset: import("zod").ZodOptional; readonly nextSynonymOffset: import("zod").ZodOptional; readonly descriptionOffset: import("zod").ZodOptional; readonly nextDescriptionOffset: import("zod").ZodOptional; readonly truncated: import("zod").ZodBoolean; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition>; offset: import("zod").ZodDefault; maxPerType: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ cid: import("zod").ZodNumber; xrefs: import("zod").ZodArray>; totalAvailable: import("zod").ZodNumber; truncated: import("zod").ZodBoolean; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly offset: import("zod").ZodNumber; readonly truncated: import("zod").ZodBoolean; readonly nextOffset: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition; identifierType: import("zod").ZodOptional>; identifiers: import("zod").ZodOptional>; formula: import("zod").ZodOptional; allowOtherElements: import("zod").ZodDefault; query: import("zod").ZodOptional; queryType: import("zod").ZodOptional>; threshold: import("zod").ZodDefault; offset: import("zod").ZodDefault; maxResults: import("zod").ZodDefault; properties: import("zod").ZodOptional>>; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ results: import("zod").ZodArray; properties: import("zod").ZodOptional>; }, import("zod/v4/core").$strip>>; unresolvedIdentifiers: import("zod").ZodOptional>; }, import("zod/v4/core").$strip>, readonly [{ readonly reason: "missing_identifier_args"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "searchType is \"identifier\" but identifierType or identifiers were omitted"; readonly recovery: "Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries)."; }, { readonly reason: "missing_formula"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "searchType is \"formula\" but the formula field was omitted or blank"; readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\"."; }, { readonly reason: "missing_structure_args"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query"; readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\")."; }, { readonly reason: "invalid_cid_query"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID"; readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query."; }, { readonly reason: "identifier_rejected"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead"; readonly recovery: "Check each identifier against identifierType: for SMILES, balanced ring closures and parentheses, valid element symbols, and no \"*\" wildcard atoms; otherwise set identifierType to the form the identifiers are in."; }, { readonly reason: "search_query_rejected"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly thrownBy: "service"; readonly when: "PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record"; readonly recovery: "Fix the SMILES syntax or remove \"*\" atoms, write the formula in Hill notation (e.g. \"C6H12O6\"), or confirm the CID exists with pubchem_get_compound_details."; }], { readonly searchType: import("zod").ZodString; readonly totalFound: import("zod").ZodOptional; readonly totalFoundAtLeast: import("zod").ZodOptional; readonly offset: import("zod").ZodNumber; readonly nextOffset: import("zod").ZodOptional; readonly truncated: import("zod").ZodOptional; readonly shown: import("zod").ZodOptional; readonly cap: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition>; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ cid: import("zod").ZodNumber; imageBase64: import("zod").ZodString; mimeType: import("zod").ZodString; width: import("zod").ZodNumber; height: import("zod").ZodNumber; }, import("zod/v4/core").$strip>, readonly [{ readonly reason: "cid_not_found"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound; readonly thrownBy: "service"; readonly when: "PubChem returned 404 for the requested CID"; readonly recovery: "Verify the CID with pubchem_search_compounds before retrying."; }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition>; includeAlternateConformerIds: import("zod").ZodDefault; maxAtoms: import("zod").ZodOptional; maxBonds: import("zod").ZodOptional; includeRawSdf: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ cid: import("zod").ZodNumber; conformerId: import("zod").ZodOptional; atomCount: import("zod").ZodNumber; bondCount: import("zod").ZodNumber; atoms: import("zod").ZodOptional>>; bonds: import("zod").ZodOptional>>; sdf: import("zod").ZodOptional; alternateConformerIds: import("zod").ZodOptional>; }, import("zod/v4/core").$strip>, readonly [{ readonly reason: "no_3d_structure"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound; readonly thrownBy: "service"; 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."; }], { readonly truncated: import("zod").ZodOptional; readonly shownAtoms: import("zod").ZodOptional; readonly shownBonds: import("zod").ZodOptional; readonly atomCap: import("zod").ZodOptional; readonly bondCap: import("zod").ZodOptional; readonly shownSdfLines: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ results: import("zod").ZodArray; ghs: import("zod").ZodOptional; pictograms: import("zod").ZodArray; hazardStatements: import("zod").ZodArray>; precautionaryStatements: import("zod").ZodArray>; }, import("zod/v4/core").$strip>>; source: import("zod").ZodOptional; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly requestedCount: import("zod").ZodNumber; readonly withDataCount: import("zod").ZodNumber; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition>; targetGeneId: import("zod").ZodOptional; targetAccession: import("zod").ZodOptional; offset: import("zod").ZodDefault; maxResults: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ cid: import("zod").ZodNumber; totalAssays: import("zod").ZodNumber; activeCount: import("zod").ZodNumber; inactiveCount: import("zod").ZodNumber; results: import("zod").ZodArray; targetGeneId: import("zod").ZodOptional; activityValues: import("zod").ZodArray; value: import("zod").ZodNumber; unit: import("zod").ZodOptional; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly outcomeFilter: import("zod").ZodString; readonly targetFilter: import("zod").ZodOptional; readonly filteredCount: import("zod").ZodNumber; readonly returnedCount: import("zod").ZodNumber; readonly offset: import("zod").ZodNumber; readonly nextOffset: import("zod").ZodOptional; readonly truncated: import("zod").ZodOptional; readonly shown: import("zod").ZodOptional; readonly cap: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition>>; offset: import("zod").ZodDefault; maxEntries: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ cid: import("zod").ZodNumber; entries: import("zod").ZodArray; partner: import("zod").ZodOptional; source: import("zod").ZodString; text: import("zod").ZodString; }, import("zod/v4/core").$strip>>; paging: import("zod").ZodArray; returnedCount: import("zod").ZodNumber; totalRecords: import("zod").ZodNumber; nextOffset: import("zod").ZodOptional; truncated: import("zod").ZodBoolean; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly requestedKinds: import("zod").ZodString; readonly returnedCount: import("zod").ZodNumber; readonly truncated: import("zod").ZodBoolean; readonly offset: import("zod").ZodNumber; readonly nextOffset: import("zod").ZodOptional; readonly failedKinds: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition; targetQuery: import("zod").ZodString; offset: import("zod").ZodDefault; maxResults: import("zod").ZodDefault; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ aids: import("zod").ZodArray; }, import("zod/v4/core").$strip>, readonly [{ readonly reason: "blank_target_query"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "targetQuery is empty or whitespace-only"; readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid."; }, { readonly reason: "invalid_geneid_query"; readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError; readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer"; readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries."; }], { readonly targetType: import("zod").ZodString; readonly targetQuery: import("zod").ZodString; readonly totalFound: import("zod").ZodNumber; readonly offset: import("zod").ZodNumber; readonly nextOffset: import("zod").ZodOptional; readonly truncated: import("zod").ZodOptional; readonly shown: import("zod").ZodOptional; readonly cap: import("zod").ZodOptional; readonly notice: import("zod").ZodOptional; }> | import("@cyanheads/mcp-ts-core").ToolDefinition; identifiers: import("zod").ZodArray>; }, import("zod/v4/core").$strip>, import("zod").ZodObject<{ entityType: import("zod").ZodString; summaries: import("zod").ZodArray; found: import("zod").ZodBoolean; data: import("zod").ZodOptional; name: import("zod").ZodOptional; description: import("zod").ZodOptional; sourceName: import("zod").ZodOptional; numSubstances: import("zod").ZodOptional; numActive: import("zod").ZodOptional; geneId: import("zod").ZodOptional; symbol: import("zod").ZodOptional; taxonomyId: import("zod").ZodOptional; taxonomy: import("zod").ZodOptional; synonyms: import("zod").ZodOptional>; proteinAccession: import("zod").ZodOptional; scientificName: import("zod").ZodOptional; commonName: import("zod").ZodOptional; rank: import("zod").ZodOptional; lineage: import("zod").ZodOptional>; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>>; }, import("zod/v4/core").$strip>, undefined, { readonly requestedCount: import("zod").ZodNumber; readonly foundCount: import("zod").ZodNumber; readonly notice: import("zod").ZodOptional; }>)[]; //# sourceMappingURL=index.d.ts.map