PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1121-1123 (handler)

  The main handler function that executes the tool logic for 'get_pharmacophore_features'. It is a placeholder returning a 'not yet implemented' message.

  private async handleGetPharmacophoreFeatures(args: any) {
    return { content: [{ type: 'text', text: JSON.stringify({ message: 'Pharmacophore features not yet implemented', args }, null, 2) }] };
  }

• src/index.ts:565-571 (schema)

  Input schema definition for the tool, specifying the required 'cid' parameter.

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

• src/index.ts:562-572 (registration)

  Tool registration in the tools array passed to server.setTools(), including name, description, and schema.

  {
    name: 'get_pharmacophore_features',
    description: 'Get pharmacophore features and binding site information',
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
  },

• src/index.ts:776-777 (registration)

  Dispatch case in the switch statement within the request handler that routes to the tool handler.

  case 'get_pharmacophore_features':
    return await this.handleGetPharmacophoreFeatures(args);