prodigy/params.json

{
    "params": {
        "pdb": {
            "type": "file",
            "description": "Path to input PDB or mmCIF structure file(s) for binding affinity prediction",
            "default": "s3://omic/eureka/prodigy/*.pdb",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.pdb",
            "examples": [
                "s3://omic/eureka/prodigy/3bzd.pdb",
                "s3://omic/eureka/prodigy/*.pdb"
            ],
            "pattern": ".*\\.(pdb|cif)$",
            "enum": [],
            "validation": {},
            "notes": "Input protein-protein complex structure in PDB or mmCIF format. Can be a single file or glob pattern for batch processing."
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for PRODIGY prediction results",
            "default": "s3://omic/eureka/prodigy/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/prodigy/output",
                "s3://omic/eureka/prodigy/custom_output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where prediction results will be stored. Created if it does not exist."
        },
        "distance_cutoff": {
            "type": "float",
            "description": "Distance cutoff (Angstrom) for calculating intermolecular contacts",
            "default": 5.5,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.distance_cutoff",
            "examples": [
                5.5,
                4.0,
                6.0
            ],
            "pattern": null,
            "enum": [],
            "validation": {
                "min": 1.0,
                "max": 20.0
            },
            "notes": "Default value of 5.5 Angstrom was optimized in Vangone & Bonvin (2015) eLife. This threshold includes different non-bonded interactions including salt bridges."
        },
        "acc_threshold": {
            "type": "float",
            "description": "Accessibility threshold for buried surface area (BSA) analysis",
            "default": 0.05,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.acc_threshold",
            "examples": [
                0.05,
                0.1
            ],
            "pattern": null,
            "enum": [],
            "validation": {
                "min": 0.0,
                "max": 1.0
            },
            "notes": "Relative accessibility threshold used to identify surface residues for non-interacting surface (NIS) calculations."
        },
        "temperature": {
            "type": "float",
            "description": "Temperature (Celsius) for dissociation constant (Kd) prediction",
            "default": 25.0,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.temperature",
            "examples": [
                25.0,
                37.0,
                4.0
            ],
            "pattern": null,
            "enum": [],
            "validation": {
                "min": -273.15,
                "max": 100.0
            },
            "notes": "Temperature used to convert predicted binding free energy (deltaG) to dissociation constant (Kd)."
        },
        "selection": {
            "type": "string",
            "description": "Chain selection for interface calculation",
            "default": "",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.selection",
            "examples": [
                "A B",
                "A,B C",
                "H,L A"
            ],
            "pattern": null,
            "enum": [],
            "validation": {},
            "notes": "Specify chains to consider for binding affinity calculation. Format: 'A B' calculates contacts between chains A and B. 'A,B C' treats chains A and B as one molecule interacting with chain C. Useful for antibody-antigen complexes where heavy and light chains should be grouped."
        },
        "contact_list": {
            "type": "boolean",
            "description": "Output list of intermolecular contacts",
            "default": false,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.contact_list",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "When enabled, outputs a detailed list of all residue-residue contacts at the interface."
        },
        "pymol_selection": {
            "type": "boolean",
            "description": "Output PyMOL script to visualize interface",
            "default": false,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.pymol_selection",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "When enabled, generates a PyMOL script (.pml) to highlight interface residues for visualization."
        },
        "quiet": {
            "type": "boolean",
            "description": "Output only predicted affinity values",
            "default": false,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.quiet",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "When enabled, outputs only the predicted binding affinity value without detailed analysis. Useful for batch processing and downstream parsing."
        }
    }
}