get_structure_quality
Retrieve structure quality metrics and validation data for PDB entries to assess molecular model reliability.
Instructions
Get structure quality metrics and validation data
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | PDB ID (4-character code) |
Implementation Reference
- src/index.ts:568-613 (handler)The handler function that implements the core logic for the 'get_structure_quality' tool. It validates input, fetches PDB entry data via API, constructs quality metrics (some mocked), and returns formatted JSON response.
private async handleGetStructureQuality(args: any) { if (!isValidPDBIdArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid structure quality arguments'); } try { const pdbId = args.pdb_id.toLowerCase(); const entryResponse = await this.apiClient.get(`/core/entry/${pdbId}`); const qualityData = { pdb_id: pdbId, overall_quality: 'GOOD', resolution: entryResponse.data.resolution, r_work: entryResponse.data.r_work, r_free: entryResponse.data.r_free, validation_available: true, quality_indicators: { clash_score: Math.random() * 10, ramachandran_favored: 95 + Math.random() * 5, ramachandran_outliers: Math.random() * 2, rotamer_outliers: Math.random() * 3, c_beta_deviations: Math.random() * 5 } }; return { content: [ { type: 'text', text: JSON.stringify(qualityData, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error fetching structure quality: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:296-302 (schema)Input schema definition for the 'get_structure_quality' tool, specifying the required 'pdb_id' parameter.
inputSchema: { type: 'object', properties: { pdb_id: { type: 'string', description: 'PDB ID (4-character code)' }, }, required: ['pdb_id'], }, - src/index.ts:293-303 (registration)Tool registration object listing the name, description, and input schema, included in the tools array passed to server.setTools.
{ name: 'get_structure_quality', description: 'Get structure quality metrics and validation data', inputSchema: { type: 'object', properties: { pdb_id: { type: 'string', description: 'PDB ID (4-character code)' }, }, required: ['pdb_id'], }, },