{
    "params": {
        "pdb": {
            "type": "file",
            "description": "Path to input PDB file for protein sequence design",
            "default": "/mnt/OmicNAS/private/old/olamide/ligandmpnn/input/1BC8.pdb",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.pdb",
            "examples": [
                "/mnt/workflow/input/protein.pdb",
                "/mnt/workflow/input/*.pdb"
            ],
            "pattern": ".*\\.pdb$",
            "enum": [],
            "validation": {},
            "notes": "Input PDB file containing the protein structure for sequence design."
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for LigandMPNN output results",
            "default": "/mnt/OmicNAS/private/old/olamide/ligandmpnn/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "/mnt/workflow/output",
                "/path/to/results"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where designed sequences and backbone PDBs will be saved."
        },
        "model_type": {
            "type": "string",
            "description": "Type of MPNN model to use for sequence design",
            "default": "ligand_mpnn",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.model_type",
            "examples": [
                "protein_mpnn",
                "ligand_mpnn",
                "soluble_mpnn"
            ],
            "pattern": "^(protein_mpnn|ligand_mpnn|soluble_mpnn|global_label_membrane_mpnn|per_residue_label_membrane_mpnn)$",
            "enum": ["protein_mpnn", "ligand_mpnn", "soluble_mpnn", "global_label_membrane_mpnn", "per_residue_label_membrane_mpnn"],
            "validation": {},
            "notes": "protein_mpnn: Original ProteinMPNN. ligand_mpnn: Context-aware with ligands. soluble_mpnn: Trained on soluble proteins."
        },
        "temperature": {
            "type": "number",
            "description": "Sampling temperature for sequence generation",
            "default": 0.1,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.temperature",
            "examples": [0.05, 0.1, 0.2],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Higher temperature gives more sequence diversity. Recommended range: 0.05-0.5"
        },
        "seed": {
            "type": "integer",
            "description": "Random seed for reproducibility",
            "default": 111,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.seed",
            "examples": [111, 42, 12345],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Set for reproducible results."
        },
        "batch_size": {
            "type": "integer",
            "description": "Number of sequences to generate per batch",
            "default": 1,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.batch_size",
            "examples": [1, 3, 5],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Higher batch sizes require more GPU memory."
        },
        "number_of_batches": {
            "type": "integer",
            "description": "Number of batches to run",
            "default": 1,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.number_of_batches",
            "examples": [1, 5, 10],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Total sequences = batch_size × number_of_batches"
        },
        "chains_to_design": {
            "type": "string",
            "description": "Comma-separated chain IDs to redesign",
            "default": "",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.chains_to_design",
            "examples": ["A", "A,B", "A,B,C"],
            "pattern": "^([A-Z],?)*$",
            "enum": [],
            "validation": {},
            "notes": "Leave empty to design all chains."
        },
        "fixed_residues": {
            "type": "string",
            "description": "Space-separated list of residues to keep fixed",
            "default": "",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.fixed_residues",
            "examples": ["A1 A2 A3", "A12 B25 B26"],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Format: ChainResidue (e.g., A12). Leave empty to design all residues."
        }
    }
}