search_by_smiles
Find exact chemical compound matches using SMILES strings from PubChem's extensive database. Ideal for structure-based searches in chemical research and analysis.
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. Performs an exact match search using PubChem's SMILES endpoint, retrieves the first matching CID, fetches compound details (formula, weight, SMILES, IUPAC name), and returns formatted JSON response. Includes input validation using isValidSmilesArgs.
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:398-404 (schema)Input schema definition for the 'search_by_smiles' tool, specifying a required 'smiles' string parameter.
inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the query molecule' }, }, required: ['smiles'], }, - src/index.ts:395-405 (registration)Tool registration in the ListToolsRequestSchema response, defining name, description, and input schema.
{ 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)Dispatch case in the main CallToolRequestSchema switch statement that routes 'search_by_smiles' calls to the handler.
case 'search_by_smiles': return await this.handleSearchBySmiles(args); - src/index.ts:76-87 (helper)Validation helper function used in handleSearchBySmiles (and similar tools) to check input arguments for SMILES string and optional threshold/max_records.
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)) ); };