search_similar_compounds
Find chemically similar compounds in PubChem using Tanimoto similarity. Input a SMILES string, set a similarity threshold, and retrieve relevant results for chemical analysis.
Instructions
Find chemically similar compounds using Tanimoto similarity
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| max_records | No | Maximum number of results (1-10000, default: 100) | |
| smiles | Yes | SMILES string of the query molecule | |
| threshold | No | Similarity threshold (0-100, default: 90) |
Implementation Reference
- src/index.ts:981-1010 (handler)The main handler function that validates input using isValidSmilesArgs, performs POST request to PubChem similarity endpoint with SMILES, threshold, and maxRecords, and returns the JSON response.
private async handleSearchSimilarCompounds(args: any) { if (!isValidSmilesArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid similarity search arguments'); } try { const threshold = args.threshold || 90; const maxRecords = args.max_records || 100; const response = await this.apiClient.post('/compound/similarity/smiles/JSON', { smiles: args.smiles, Threshold: threshold, MaxRecords: maxRecords, }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error) { throw new McpError( ErrorCode.InternalError, `Failed to search similar compounds: ${error instanceof Error ? error.message : 'Unknown error'}` ); } } - src/index.ts:444-452 (schema)Input schema definition for the search_similar_compounds tool, specifying required SMILES and optional threshold/max_records parameters.
inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the query molecule' }, threshold: { type: 'number', description: 'Similarity threshold (0-100, default: 90)', minimum: 0, maximum: 100 }, max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 }, }, required: ['smiles'], }, - src/index.ts:754-755 (registration)Switch case in the main CallToolRequestSchema handler that routes calls to search_similar_compounds to the specific handler function.
case 'search_similar_compounds': return await this.handleSearchSimilarCompounds(args); - src/index.ts:441-453 (registration)Tool registration in the ListToolsRequestSchema response, including name, description, and input schema.
{ name: 'search_similar_compounds', description: 'Find chemically similar compounds using Tanimoto similarity', inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the query molecule' }, threshold: { type: 'number', description: 'Similarity threshold (0-100, default: 90)', minimum: 0, maximum: 100 }, max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 }, }, required: ['smiles'], }, }, - src/index.ts:76-87 (helper)Type guard function used to validate inputs for SMILES-based searches, including similarity search.
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)) ); };