PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1113-1115 (handler)

  The main handler function for the 'assess_drug_likeness' tool. Currently a placeholder that returns a 'not yet implemented' message with input arguments.

  private async handleAssessDrugLikeness(args: any) {
    return { content: [{ type: 'text', text: JSON.stringify({ message: 'Drug-likeness assessment not yet implemented', args }, null, 2) }] };
  }

• src/index.ts:539-550 (registration)

  Registration of the 'assess_drug_likeness' tool in the tools array, including its name, description, and input schema.

  {
    name: 'assess_drug_likeness',
    description: 'Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters',
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        smiles: { type: 'string', description: 'SMILES string (alternative to CID)' },
      },
      required: [],
    },
  },

• src/index.ts:772-773 (registration)

  Dispatch case in the tool request handler switch statement that routes 'assess_drug_likeness' calls to its handler function.

  case 'assess_drug_likeness':
    return await this.handleAssessDrugLikeness(args);

• src/index.ts:542-549 (schema)

  Input schema for the 'assess_drug_likeness' tool defining parameters cid or smiles.

  inputSchema: {
    type: 'object',
    properties: {
      cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      smiles: { type: 'string', description: 'SMILES string (alternative to CID)' },
    },
    required: [],
  },