search_by_smiles
Find chemical compounds in the SureChEMBL patent database using SMILES structure notation to identify related patents and substances.
Instructions
Search for chemicals by SMILES structure notation
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| smiles | Yes | SMILES string of the chemical structure | |
| limit | No | Number of results to return (1-1000, default: 25) |
Implementation Reference
- src/index.ts:748-773 (handler)The handler function that implements the core logic for the 'search_by_smiles' tool. It validates the SMILES input and returns a structured response indicating that direct SMILES search is not supported by the SureChEMBL API, providing alternatives.
private async handleSearchBySmiles(args: any) { if (!args || typeof args.smiles !== 'string') { throw new McpError(ErrorCode.InvalidParams, 'Invalid SMILES string'); } try { // SureChEMBL doesn't have direct SMILES search, so we'll return a helpful message return { content: [ { type: 'text', text: JSON.stringify({ message: 'SMILES search not directly supported by SureChEMBL API', smiles: args.smiles, suggestion: 'Try converting SMILES to chemical name or use structure-based search tools' }, null, 2), }, ], }; } catch (error) { throw new McpError( ErrorCode.InternalError, `Failed to search by SMILES: ${error instanceof Error ? error.message : 'Unknown error'}` ); } } - src/index.ts:410-421 (registration)Registration of the 'search_by_smiles' tool in the ListToolsRequestSchema response, including name, description, and input schema definition.
{ name: 'search_by_smiles', description: 'Search for chemicals by SMILES structure notation', inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the chemical structure' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['smiles'], }, }, - src/index.ts:557-558 (registration)Dispatch case in the CallToolRequestSchema handler that routes calls to the search_by_smiles handler function.
case 'search_by_smiles': return await this.handleSearchBySmiles(args); - src/index.ts:413-420 (schema)Input schema defining the parameters for the search_by_smiles tool: required SMILES string and optional limit.
inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the chemical structure' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['smiles'], },