SureChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:845-894 (handler)

  The handler function that validates input, fetches chemical data from SureChEMBL API using the chemical_id, extracts and formats various molecular properties (e.g., SMILES, molecular weight, InChI, frequency), and returns a JSON response.

  private async handleGetChemicalProperties(args: any) {
    if (!args || typeof args.chemical_id !== 'string') {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid chemical ID');
    }
  
    try {
      const response = await this.apiClient.get(`/chemical/id/${args.chemical_id}`);
  
      // Extract and format properties
      const chemical = response.data.data?.[0];
      if (!chemical) {
        throw new Error('Chemical not found');
      }
  
      const properties = {
        chemical_id: chemical.chemical_id,
        name: chemical.name,
        molecular_weight: chemical.mol_weight,
        smiles: chemical.smiles,
        inchi: chemical.inchi,
        inchi_key: chemical.inchi_key,
        is_element: chemical.is_element === '1',
        global_frequency: chemical.global_frequency,
        structural_alerts: chemical.mchem_struct_alert === '1',
        // Additional computed properties if available
        log_p: chemical.log_p,
        donor_count: chemical.donor_count,
        acceptor_count: chemical.accept_count,
        ring_count: chemical.ring_count,
        rotatable_bonds: chemical.rotatable_bond_count
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({
              chemical_id: args.chemical_id,
              properties: properties
            }, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to get chemical properties: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:451-457 (schema)

  Input schema definition specifying that 'chemical_id' (string, SureChEMBL chemical ID) is required.

  inputSchema: {
    type: 'object',
    properties: {
      chemical_id: { type: 'string', description: 'SureChEMBL chemical ID' },
    },
    required: ['chemical_id'],
  },

• src/index.ts:448-458 (registration)

  Tool registration in the MCP server's tools list, including name, description, and input schema.

  {
    name: 'get_chemical_properties',
    description: 'Get molecular properties and descriptors for a chemical by ID',
    inputSchema: {
      type: 'object',
      properties: {
        chemical_id: { type: 'string', description: 'SureChEMBL chemical ID' },
      },
      required: ['chemical_id'],
    },
  },

• src/index.ts:564-565 (registration)

  Dispatch case in the MCP request handler switch statement that routes 'get_chemical_properties' calls to the handler method.

  case 'get_chemical_properties':
    return await this.handleGetChemicalProperties(args);