AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:823-855 (handler)

  The handler function that implements the core logic for the 'list_by_organism' tool. Validates input, makes API call to AlphaFold /prediction endpoint with organism filter, returns JSON structures list or error.

  private async handleListByOrganism(args: any) {
    if (!isValidOrganismArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid organism arguments');
    }
  
    try {
      const response = await this.apiClient.get('/prediction', {
        params: {
          organism: args.organism,
          size: args.size || 50,
        },
      });
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error listing structures by organism: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:397-407 (registration)

  Registration of the 'list_by_organism' tool in the tools list returned by ListToolsRequestHandler, defining name, description, and input schema.

    name: 'list_by_organism',
    description: 'List all available structures for a specific organism',
    inputSchema: {
      type: 'object',
      properties: {
        organism: { type: 'string', description: 'Organism name (e.g., "Homo sapiens", "Escherichia coli")' },
        size: { type: 'number', description: 'Number of results (1-100, default: 50)', minimum: 1, maximum: 100 },
      },
      required: ['organism'],
    },
  },

• src/index.ts:588-589 (registration)

  Dispatch in the CallToolRequestHandler switch statement that routes calls to the list_by_organism handler function.

  case 'list_by_organism':
    return this.handleListByOrganism(args);

• src/index.ts:97-107 (helper)

  Helper validation function (type guard) used in the handler to validate input parameters for the list_by_organism tool.

  const isValidOrganismArgs = (
    args: any
  ): args is { organism: string; size?: number } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.organism === 'string' &&
      args.organism.length > 0 &&
      (args.size === undefined || (typeof args.size === 'number' && args.size > 0 && args.size <= 100))
    );
  };