{ "skill_name": "PDB Structure Analyzer", "version": "1.0.0", "description": "Analyzes PDB files to extract structural information, amino acid composition, active sites, and ligand interactions.", "input_schema": { "type": "object", "properties": { "pdb_input": { "type": "string", "description": "PDB file path (local) or PDB ID (e.g., '1ABC' or '/path/to/file.pdb')", "examples": [ "1ABC", "/data/structures/3hhp.pdb", "./test_inputs/test.pdb" ] }, "output_file": { "type": "string", "description": "Optional output file path for the markdown report", "default": null }, "include_hydrogens": { "type": "boolean", "description": "Include hydrogen atoms in analysis", "default": false }, "verbose": { "type": "boolean", "description": "Enable verbose output with detailed atom information", "default": false } }, "required": [ "pdb_input" ] }, "output_schema": { "type": "object", "properties": { "success": { "type": "boolean" }, "report": { "type": "string", "description": "Markdown formatted analysis report" }, "structure_summary": { "type": "object", "properties": { "pdb_id": { "type": "string" }, "title": { "type": "string" }, "method": { "type": "string" }, "resolution": { "type": "number" }, "r_factor": { "type": "number" }, "num_chains": { "type": "integer" }, "num_residues": { "type": "integer" }, "num_atoms": { "type": "integer" }, "molecular_weight": { "type": "number" } } }, "amino_acid_composition": { "type": "object", "description": "Count of each amino acid type" }, "ligands": { "type": "array", "items": { "type": "object", "properties": { "name": { "type": "string" }, "chain": { "type": "string" }, "resnum": { "type": "integer" }, "type": { "type": "string" } } } }, "metal_ions": { "type": "array", "items": { "type": "object", "properties": { "ion": { "type": "string" }, "chain": { "type": "string" }, "resnum": { "type": "integer" }, "count": { "type": "integer" } } } } } }, "execution": { "type": "local", "command": "python execute.py {pdb_input} {output_file}", "environment": { "python_version": ">=3.8", "dependencies": [ "biopython", "requests" ] } }, "test_case": { "input": "./test_inputs/test.pdb", "expected_output_file": "expected_output.txt" } }