{ "payload": { "tool": "protein_properties_calculator", "version": "1.0.0", "input": { "sequence_type": "fasta", "sequence_source": "inline", "format": "fasta" }, "parameters": { "calculate_mw": true, "calculate_pi": true, "calculate_composition": true, "calculate_gravy": true, "calculate_instability_index": true, "precision": { "molecular_weight": 2, "isoelectric_point": 2, "hydropathicity": 3, "instability_index": 2, "composition_percentage": 2 } }, "example_sequences": { "hemoglobin_alpha": ">sp|P69905|HBA_HUMAN Hemoglobin subunit alpha\nMKVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR", "lysozyme": ">sp|P00698|LYZ_CHICK Lysozyme C\nMVLLILVLVFLVGVGVNPTIQAELPALSTTDDLAAANGNLLDFVKSNLDRYRPGGNNRPGAIAVRDNSVNWGSSGGRIRLLSHRDDPAYAAPYLGRGYYFYSSYVNNDGRTLTLNDIALWMRDVNAGWLSATDYGILQINSRYWCNDGKGRDVQLAARNVKLFGNFGADKRAASRERNPLSIDKFIAIKDASGKFTCSWTAADNAYHAIDQYDSTDMKFSSFAKALGIKADKDLNYTLDVNAAHAAPLSKEAAAIAKLLKSIKDNKDLKEVFAEAKEKAFKDLKEVVFEAAFKVFSQYADLGCYCGVGSSKDVQLINLNNKPFVDLKNKYFNDICHVALGGLSQTPLFAILHR", "insulin": ">sp|P01308|INS_HUMAN Insulin\nMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "small_peptide": "MKFLLK" }, "output_options": { "format": "json", "include_metadata": true, "pretty_print": true } }, "api_spec": { "method": "POST", "endpoint": "/api/v1/protein/properties", "content_type": "application/json", "request_body": { "type": "object", "properties": { "sequence": { "type": "string", "description": "Protein sequence in FASTA format or plain format", "example": "MKVLSPADKTNVKAAWGKVGAHAGEY" }, "sequence_id": { "type": "string", "description": "Optional identifier for the sequence", "example": "P69905" }, "options": { "type": "object", "properties": { "all_properties": { "type": "boolean", "default": true }, "precision": { "type": "object" } } } }, "required": [ "sequence" ] }, "response": { "success": { "status_code": 200, "schema": "SKILL.md#Output" }, "error": { "status_codes": [ 400, 422 ], "schema": { "status": "error", "error": { "code": "string", "message": "string" } } } } }, "cli_usage": { "command": "python execute.py [OPTIONS]", "options": [ { "flag": "--input, -i", "type": "string", "description": "Input FASTA file path", "required": true }, { "flag": "--output, -o", "type": "string", "description": "Output JSON file path (default: stdout)", "required": false }, { "flag": "--sequence, -s", "type": "string", "description": "Direct sequence input (overrides --input)", "required": false }, { "flag": "--format, -f", "type": "string", "description": "Output format: json, yaml, table", "default": "json" } ], "examples": [ "python execute.py --input test_inputs/protein.fasta", "python execute.py --input test_inputs/protein.fasta --output result.json", "python execute.py --sequence MKVLSPADKTNVKAAWGKVGAHAGEY" ] } }