PubChem MCP Server

Instructions

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))
    );
  };