get_coverage_info

Retrieve sequence coverage details for AlphaFold protein structure predictions using a UniProt accession ID.

Instructions

Get information about sequence coverage in the AlphaFold prediction

Input Schema

TableJSON Schema

Name	Required	Description	Default
`uniprotId`	Yes	UniProt accession

Implementation Reference

src/index.ts:1437-1495 (handler)

The handler function that executes the get_coverage_info tool. It validates input, fetches AlphaFold prediction data via API, computes coverage metrics (percentage, completeness, gaps), and returns formatted JSON response.

private async handleGetCoverageInfo(args: any) {
  if (!isValidUniProtArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid coverage info 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 coverageInfo = {
      uniprotId: args.uniprotId,
      fullSequenceLength: structure.uniprotSequence.length,
      predictedRegion: {
        start: structure.uniprotStart,
        end: structure.uniprotEnd,
        length: structure.uniprotEnd - structure.uniprotStart + 1,
      },
      coverage: {
        percentage: ((structure.uniprotEnd - structure.uniprotStart + 1) / structure.uniprotSequence.length) * 100,
        isComplete: structure.uniprotStart === 1 && structure.uniprotEnd === structure.uniprotSequence.length,
      },
      gaps: {
        nTerminal: structure.uniprotStart > 1 ? structure.uniprotStart - 1 : 0,
        cTerminal: structure.uniprotEnd < structure.uniprotSequence.length ? structure.uniprotSequence.length - structure.uniprotEnd : 0,
      },
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(coverageInfo, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error getting coverage info: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:613-614 (registration)
Tool handler registration in the CallToolRequestSchema switch statement.
```
  return this.handleGetCoverageInfo(args);
case 'validate_structure_quality':
```

src/index.ts:515-525 (registration)

Tool registration entry in ListToolsRequestSchema, including name, description, and input schema.

{
  name: 'get_coverage_info',
  description: 'Get information about sequence coverage in the AlphaFold prediction',
  inputSchema: {
    type: 'object',
    properties: {
      uniprotId: { type: 'string', description: 'UniProt accession' },
    },
    required: ['uniprotId'],
  },
},

src/index.ts:518-524 (schema)

Input schema definition for the get_coverage_info tool.

inputSchema: {
  type: 'object',
  properties: {
    uniprotId: { type: 'string', description: 'UniProt accession' },
  },
  required: ['uniprotId'],
},

src/index.ts:58-68 (helper)

Validation helper function used to check UniProt ID arguments in the handler.

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))
  );
};

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