search_by_smiles
Find chemical compounds in PubChem using their SMILES string representation for exact molecular structure matching.
Instructions
Search for compounds by SMILES string (exact match)
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| smiles | Yes | SMILES string of the query molecule |
Implementation Reference
- src/index.ts:907-947 (handler)The main handler function for the 'search_by_smiles' tool. It validates input using isValidSmilesArgs, queries PubChem API for exact SMILES match to get CID, then fetches compound details (formula, weight, SMILES, IUPAC name), and returns formatted JSON response or error if no match.
private async handleSearchBySmiles(args: any) { if (!isValidSmilesArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid SMILES arguments'); } try { const response = await this.apiClient.get(`/compound/smiles/${encodeURIComponent(args.smiles)}/cids/JSON`); if (response.data?.IdentifierList?.CID?.length > 0) { const cid = response.data.IdentifierList.CID[0]; const detailsResponse = await this.apiClient.get(`/compound/cid/${cid}/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IUPACName/JSON`); return { content: [ { type: 'text', text: JSON.stringify({ query_smiles: args.smiles, found_cid: cid, details: detailsResponse.data, }, null, 2), }, ], }; } return { content: [ { type: 'text', text: JSON.stringify({ message: 'No exact match found', query_smiles: args.smiles }, null, 2), }, ], }; } catch (error) { throw new McpError( ErrorCode.InternalError, `Failed to search by SMILES: ${error instanceof Error ? error.message : 'Unknown error'}` ); } } - src/index.ts:395-405 (schema)The input schema definition for the 'search_by_smiles' tool, specifying that it requires a 'smiles' string parameter.
{ name: 'search_by_smiles', description: 'Search for compounds by SMILES string (exact match)', inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the query molecule' }, }, required: ['smiles'], }, }, - src/index.ts:744-745 (registration)The switch case in the CallToolRequestSchema handler that registers and dispatches calls to the search_by_smiles handler function.
case 'search_by_smiles': return await this.handleSearchBySmiles(args); - src/index.ts:76-87 (helper)Input validation helper function isValidSmilesArgs used by the handler to validate arguments before API call.
const isValidSmilesArgs = ( args: any ): args is { smiles: string; threshold?: number; max_records?: number } => { return ( typeof args === 'object' && args !== null && typeof args.smiles === 'string' && args.smiles.length > 0 && (args.threshold === undefined || (typeof args.threshold === 'number' && args.threshold >= 0 && args.threshold <= 100)) && (args.max_records === undefined || (typeof args.max_records === 'number' && args.max_records > 0 && args.max_records <= 10000)) ); };