AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:692-739 (handler)

  The handler function that implements the download_structure tool. It fetches the structure prediction for a UniProt ID from the AlphaFold API, selects the appropriate format URL (pdb, cif, or bcif), downloads the file content, and returns it embedded in a text response.

  private async handleDownloadStructure(args: any) {
    if (!isValidUniProtArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid download structure arguments');
    }
  
    try {
      const response = await this.apiClient.get(`/prediction/${args.uniprotId}`);
      const structures = response.data;
  
      if (!structures || structures.length === 0) {
        return {
          content: [
            {
              type: 'text',
              text: `No structure available for ${args.uniprotId}`,
            },
          ],
        };
      }
  
      const structure = structures[0];
      const format = args.format || 'pdb';
      const url = format === 'pdb' ? structure.pdbUrl :
                 format === 'cif' ? structure.cifUrl :
                 format === 'bcif' ? structure.bcifUrl : structure.pdbUrl;
  
      const fileResponse = await axios.get(url);
  
      return {
        content: [
          {
            type: 'text',
            text: `Structure file for ${args.uniprotId} (${format.toUpperCase()} format):\n\n${fileResponse.data}`,
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error downloading structure: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:360-370 (schema)

  The input schema definition for the download_structure tool as returned by ListToolsRequestSchema. Defines the expected parameters: uniprotId (string, required) and optional format (enum: pdb, cif, bcif).

    name: 'download_structure',
    description: 'Download AlphaFold structure file in specified format',
    inputSchema: {
      type: 'object',
      properties: {
        uniprotId: { type: 'string', description: 'UniProt accession' },
        format: { type: 'string', enum: ['pdb', 'cif', 'bcif'], description: 'File format (default: pdb)' },
      },
      required: ['uniprotId'],
    },
  },

• src/index.ts:582-582 (registration)

  The case statement in the CallToolRequestSchema handler's switch that dispatches calls to the download_structure tool to its handler function.

  return this.handleDownloadStructure(args);

• src/index.ts:58-67 (helper)

  Type guard and validation function for UniProt arguments (uniprotId and optional format), used by the download_structure handler to validate input parameters.

  const isValidUniProtArgs = (
    args: any
  ): args is { uniprotId: string; format?: 'pdb' | 'cif' | 'bcif' | 'json' } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.uniprotId === 'string' &&
      args.uniprotId.length > 0 &&
      (args.format === undefined || ['pdb', 'cif', 'bcif', 'json'].includes(args.format))
    );