AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:1556-1619 (handler)

  The handler function that executes the tool logic: fetches AlphaFold structure data and generates a PyMOL script for visualization, optionally including confidence-based coloring instructions.

    private async handleExportForPymol(args: any) {
      if (!isValidExportArgs(args)) {
        throw new McpError(ErrorCode.InvalidParams, 'Invalid PyMOL export 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 includeConfidence = args.includeConfidence !== false;
  
        const pymolScript = `
  # PyMOL script for AlphaFold structure ${args.uniprotId}
  fetch ${structure.pdbUrl}
  as cartoon
  color spectrum
  ${includeConfidence ? `
  # Color by confidence
  # Very high confidence (pLDDT > 90): blue
  # Confident (pLDDT 70-90): cyan
  # Low confidence (pLDDT 50-70): yellow
  # Very low confidence (pLDDT < 50): orange
  ` : ''}
  center
  zoom
  `;
  
        return {
          content: [
            {
              type: 'text',
              text: JSON.stringify({
                uniprotId: args.uniprotId,
                pymolScript,
                structureUrl: structure.pdbUrl,
                instructions: 'Copy the PyMOL script above and paste it into PyMOL command line',
              }, null, 2),
            },
          ],
        };
      } catch (error) {
        return {
          content: [
            {
              type: 'text',
              text: `Error exporting for PyMOL: ${error instanceof Error ? error.message : 'Unknown error'}`,
            },
          ],
          isError: true,
        };
      }
    }

• src/index.ts:539-549 (registration)

  Registration of the 'export_for_pymol' tool in the ListToolsRequestSchema handler, including name, description, and input schema.

    name: 'export_for_pymol',
    description: 'Export structure data formatted for PyMOL visualization',
    inputSchema: {
      type: 'object',
      properties: {
        uniprotId: { type: 'string', description: 'UniProt accession' },
        includeConfidence: { type: 'boolean', description: 'Include confidence score coloring (default: true)' },
      },
      required: ['uniprotId'],
    },
  },

• src/index.ts:617-618 (registration)

  Switch case in CallToolRequestSchema handler that routes 'export_for_pymol' calls to the handler function.

  case 'export_for_pymol':
    return this.handleExportForPymol(args);

• src/index.ts:134-144 (schema)

  Type guard function validating input arguments for export tools (used by export_for_pymol handler).

  const isValidExportArgs = (
    args: any
  ): args is { uniprotId: string; includeConfidence?: boolean } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.uniprotId === 'string' &&
      args.uniprotId.length > 0 &&
      (args.includeConfidence === undefined || typeof args.includeConfidence === 'boolean')
    );
  };

• src/index.ts:541-548 (schema)

  Input schema definition for the 'export_for_pymol' tool.

  inputSchema: {
    type: 'object',
    properties: {
      uniprotId: { type: 'string', description: 'UniProt accession' },
      includeConfidence: { type: 'boolean', description: 'Include confidence score coloring (default: true)' },
    },
    required: ['uniprotId'],
  },